Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 48 of 163
Found at i:11853470 original size:30 final size:30
Alignment explanation
Indices: 11853436--11853672 Score: 243
Period size: 30 Copynumber: 7.9 Consensus size: 30
11853426 GAGATCCCCG
* * *
11853436 AACTTCCCAAAAATCT-CATTTTAACCCTTA
1 AACTTTCCAAAAAT-TACATTTTGACCCCTA
*
11853466 AACTTTCCAAAAATCACA-TTTGACCCCTA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* * **
11853495 AACTTTTCAAAAATCACA-TTAAACCCCTA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* *
11853524 AACTTTCTAAAAATTACATTTTGACCCATA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
*
11853554 AACTTTCCAAAAATTACATTTTAACCCCTA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
*
11853584 AAC-TTCTCAAAAATTACATTTTGACCTCTA
1 AACTTTC-CAAAAATTACATTTTGACCCCTA
* *
11853614 AACTTCTCAAAAAAATACATTTTGA-CCCTCA
1 AACTT-TCCAAAAATTACATTTTGACCCCT-A
* *
11853645 AACTTTTCAAAACTT-CATTTTCGACCCC
1 AACTTTCCAAAAATTACATTTT-GACCCC
11853673 GTATTTTCCT
Statistics
Matches: 174, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
29 59 0.34
30 88 0.51
31 25 0.14
32 2 0.01
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.32
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTGACCCCTA
Found at i:11861919 original size:96 final size:97
Alignment explanation
Indices: 11861734--11861926 Score: 234
Period size: 96 Copynumber: 2.0 Consensus size: 97
11861724 AACTTTGGAA
* *
11861734 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGGACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
11861799 GAATCAGAGACAAAGAAACATTGCCTCGATTT
66 GAATCAGAAAAAAAGAAACATTGCCTCGATTT
* * * *
11861831 AAGGGTATTCAATTATTTCGATTTGAGGAAACA-TTGCACC-AGTAAGTTAAGGCACAAATATTT
1 AAGGATATTCAATTATCTCGATTTGAAGAAA-AGTCGCACCTAGTAAGTTAAGGCACAAAT-TTT
*
11861894 -AGAACTC-GAAATAAAAG-AATATTGCCTCGATTT
64 CAGAA-TCAGAAA-AAAAGAAACATTGCCTCGATTT
11861927 TAAAGTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
96 41 0.49
97 41 0.49
98 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (97 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
GAATCAGAAAAAAAGAAACATTGCCTCGATTT
Found at i:11862174 original size:29 final size:29
Alignment explanation
Indices: 11862140--11862352 Score: 193
Period size: 29 Copynumber: 7.3 Consensus size: 29
11862130 TGGAAATGTG
*
11862140 ATTTTTGGATACTCGGGGGGTAAAATGGTA
1 ATTTTTGGACACTC-GGGGGTAAAATGGTA
* *
11862170 A-TTTTGGTCACTCAGGGGTAAAATGGTA
1 ATTTTTGGACACTCGGGGGTAAAATGGTA
*** *
11862198 ATTTTCAAACACTTGGGGAAG-AAAATGGTA
1 ATTTTTGGACACTCGGGG--GTAAAATGGTA
* *
11862228 ATTTTTAGACACTCGAGGGTGAAAAT-GTA
1 ATTTTTGGACACTCGGGGGT-AAAATGGTA
* * *
11862257 ATTTTTGGACACCCGAGGGAAAAATGGTA
1 ATTTTTGGACACTCGGGGGTAAAATGGTA
* *
11862286 ATTTTTAGACACTCGAGGGTGAAAAT-GTA
1 ATTTTTGGACACTCGGGGGT-AAAATGGTA
*
11862315 ATTTTTGGACA-TCCGGAGGTAAAATGGTA
1 ATTTTTGGACACT-CGGGGGTAAAATGGTA
*
11862344 TTTTTTGGA
1 ATTTTTGGA
11862353 AAAATCAAGG
Statistics
Matches: 151, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
28 27 0.18
29 89 0.59
30 34 0.23
31 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (29 bp):
ATTTTTGGACACTCGGGGGTAAAATGGTA
Found at i:11862281 original size:58 final size:58
Alignment explanation
Indices: 11862219--11862349 Score: 219
Period size: 58 Copynumber: 2.3 Consensus size: 58
11862209 CTTGGGGAAG
11862219 AAAATGGTAATTTTTAGACACTCGAGGGTGAAAATGTAATTTTTGGACACCC-GAGGGA
1 AAAATGGTAATTTTTAGACACTCGAGGGTGAAAATGTAATTTTTGGACACCCGGA-GGA
* *
11862277 AAAATGGTAATTTTTAGACACTCGAGGGTGAAAATGTAATTTTTGGACATCCGGAGGT
1 AAAATGGTAATTTTTAGACACTCGAGGGTGAAAATGTAATTTTTGGACACCCGGAGGA
*
11862335 AAAATGGTATTTTTT
1 AAAATGGTAATTTTT
11862350 GGAAAAATCA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
58 67 0.97
59 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTAGACACTCGAGGGTGAAAATGTAATTTTTGGACACCCGGAGGA
Found at i:11862405 original size:29 final size:29
Alignment explanation
Indices: 11862240--11862466 Score: 148
Period size: 29 Copynumber: 7.8 Consensus size: 29
11862230 TTTTAGACAC
* *
11862240 TCGAGGGTGAAAATGTAATTTTTGGACA-C
1 TCGAGGGTAAAAATGTAATTTTTGGA-AGT
* * *
11862269 CCGAGGG-AAAAATGGTAATTTTTAGACA-C
1 TCGAGGGTAAAAAT-GTAATTTTTGGA-AGT
*
11862298 TCGAGGGTGAAAATGTAATTTTTGGACA-T
1 TCGAGGGTAAAAATGTAATTTTTGGA-AGT
* * **
11862327 CCG-GAGGT-AAAATGGTATTTTTTGGAAAAA
1 TCGAG-GGTAAAAAT-GTAATTTTTGG-AAGT
* *
11862357 TC-AAGGTCAAAAATGGAATTTTTGGAAGT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAGT
* * * *
11862386 TCGTGGGTAAAATTGTAATTTTTCGAAAAT
1 TCGAGGGTAAAAATGTAATTTTT-GGAAGT
11862416 T--AGGGTCAAAAATGTAATTTTTGGAAGT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAGT
*
11862444 TCGGGGGTAAAAATGTAATTTTT
1 TCGAGGGTAAAAATGTAATTTTT
11862467 AAAAAATTTG
Statistics
Matches: 157, Mismatches: 27, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
28 20 0.13
29 104 0.66
30 28 0.18
31 5 0.03
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.33
Consensus pattern (29 bp):
TCGAGGGTAAAAATGTAATTTTTGGAAGT
Found at i:11862488 original size:30 final size:28
Alignment explanation
Indices: 11862361--11862585 Score: 111
Period size: 29 Copynumber: 7.7 Consensus size: 28
11862351 GAAAAATCAA
* * * *
11862361 GGTCAAAAATGGAATTTTTGGAAGTTCGTG
1 GGTCAAAAATGTAATTTTTGAAAATT--AG
*
11862391 GGT-AAAATTGTAATTTTTCGAAAATTAG
1 GGTCAAAAATGTAATTTTT-GAAAATTAG
* * *
11862419 GGTCAAAAATGTAATTTTTGGAAGTTCGGG
1 GGTCAAAAATGTAATTTTTGAAAATT--AG
* *
11862449 GGT-AAAAATGTAATTTTTAAAAAATTTG
1 GGTCAAAAATGTAATTTTT-GAAAATTAG
* * * *
11862477 AGGTCAAAAATGGAGTTTTGGAAAGTTTAGG
1 -GGTCAAAAATGTAATTTTTGAAA-ATTA-G
*
11862508 GGT-AAAAATGT-ATTTGTTAGAAACTTTAG
1 GGTCAAAAATGTAATTT-TT-GAAA-ATTAG
* * *
11862537 GGTCAATAATAG-AATTTTGGAAATTTCGAG
1 GGTCAAAAAT-GTAATTTTTGAAAATT--AG
11862567 GG-CAAAAATGTAATTTTTG
1 GGTCAAAAATGTAATTTTTG
11862586 GATAGTTTAG
Statistics
Matches: 151, Mismatches: 27, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
28 17 0.11
29 77 0.51
30 51 0.34
31 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (28 bp):
GGTCAAAAATGTAATTTTTGAAAATTAG
Found at i:11862597 original size:59 final size:58
Alignment explanation
Indices: 11862276--11862584 Score: 247
Period size: 59 Copynumber: 5.3 Consensus size: 58
11862266 CACCCGAGGG
* * ** * * *
11862276 AAAAATGGTAATTTTTAGACACTCGAGGGT-GAAAATGTAATTTTTGGACA-TCCGGAGGT
1 AAAAAT-GTAATTTTTAGAAAATTTAGGGTCAAAAATGGAATTTTTGGA-AGTTCGG-GGT
* * * * *
11862335 -AAAATGGTATTTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGTGGGT
1 AAAAAT-GTAATTTTTAGAAAATTTAGGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGT
* * *
11862394 AAAATTGTAATTTTTCGAAAA-TTAGGGTCAAAAATGTAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGT
* * *
11862452 AAAAATGTAATTTTTAAAAAATTT-GAGGTCAAAAATGG-AGTTTTGGAAAGTTTAGGGGT
1 AAAAATGTAATTTTTAGAAAATTTAG-GGTCAAAAATGGAATTTTTGG-AAG-TTCGGGGT
* * * * *
11862511 AAAAATGT-ATTTGTTAGAAACTTTAGGGTCAATAATAGAA-TTTTGGAAATTTCGAGGGC
1 AAAAATGTAATTT-TTAGAAAATTTAGGGTCAAAAATGGAATTTTTGG-AAGTTCG-GGGT
11862570 AAAAATGTAATTTTT
1 AAAAATGTAATTTTT
11862585 GGATAGTTTA
Statistics
Matches: 206, Mismatches: 30, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
58 87 0.42
59 106 0.51
60 13 0.06
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (58 bp):
AAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:11863778 original size:19 final size:17
Alignment explanation
Indices: 11863733--11863789 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
11863723 TTCAATTTTT
*
11863733 TTATTTAATATTATTAA
1 TTATTTATTATTATTAA
11863750 TTACTATTATTATTATTAA
1 TTA-T-TTATTATTATTAA
*
11863769 TGTTATTTATTACTA-TAA
1 --TTATTTATTATTATTAA
11863787 TTA
1 TTA
11863790 ACATGCATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 4 0.12
19 20 0.59
20 1 0.03
21 3 0.09
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATTTATTATTATTAA
Found at i:11864511 original size:6 final size:6
Alignment explanation
Indices: 11864478--11864587 Score: 56
Period size: 6 Copynumber: 19.5 Consensus size: 6
11864468 TATTTGGACT
*
11864478 TTTAAA GTTTAAA TTT--A TTTAAA -ATAAA TTTAAA TTTAAA -TTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * * * * * *
11864523 TCCAAA CTCAAA -ATAAG TTCAAA TTTAAA -GTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
11864569 --TAAA TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
11864588 TAAAAATGGG
Statistics
Matches: 76, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
4 8 0.11
5 15 0.20
6 47 0.62
7 6 0.08
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:11864514 original size:17 final size:17
Alignment explanation
Indices: 11864494--11864584 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 17
11864484 GTTTAAATTT
*
11864494 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTCAA
* *
11864511 ATTTAAATTAAATCCAA
1 ATTTAAAATAAATTCAA
* * *
11864528 ACTCAAAATAAGTTCAA
1 ATTTAAAATAAATTCAA
*
11864545 ATTTAAAGTAAATTCAA
1 ATTTAAAATAAATTCAA
* *
11864562 ATTT-AAATAAATTTAG
1 ATTTAAAATAAATTCAA
11864578 ATTTAAA
1 ATTTAAA
11864585 TTTTAAAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
16 13 0.22
17 45 0.78
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTCAA
Found at i:11864523 original size:21 final size:22
Alignment explanation
Indices: 11864480--11864522 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11864470 TTTGGACTTT
*
11864480 TAAAGTTTAAATTTATTTAAAA
1 TAAAGTTTAAATTTAATTAAAA
11864502 TAAA-TTTAAATTTAAATTAAA
1 TAAAGTTTAAATTT-AATTAAA
11864523 TCCAAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAAGTTTAAATTTAATTAAAA
Found at i:11864536 original size:34 final size:33
Alignment explanation
Indices: 11864498--11864586 Score: 106
Period size: 34 Copynumber: 2.7 Consensus size: 33
11864488 AAATTTATTT
11864498 AAAATAAATTTAAATTTAAATTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAATTAAATCCAAA-TC
* * * * *
11864532 AAAATAAGTTCAAATTTAAAGTAAATTCAAATT
1 AAAATAAATTTAAATTTAAATTAAATCCAAATC
* *
11864565 TAAATAAATTTAGATTTAAATT
1 AAAATAAATTTAAATTTAAATT
11864587 TTAAAAATGG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 18 0.40
34 27 0.60
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (33 bp):
AAAATAAATTTAAATTTAAATTAAATCCAAATC
Found at i:11874573 original size:12 final size:13
Alignment explanation
Indices: 11874547--11874579 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11874537 GCAAAAATGA
*
11874547 GCAAAGAACATAG
1 GCAAAGAACAGAG
11874560 GCAAA-AACAGAG
1 GCAAAGAACAGAG
11874572 GCAAAGAA
1 GCAAAGAA
11874580 ACAGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.15, G:0.24, T:0.03
Consensus pattern (13 bp):
GCAAAGAACAGAG
Found at i:11875974 original size:30 final size:30
Alignment explanation
Indices: 11875940--11876107 Score: 201
Period size: 30 Copynumber: 5.6 Consensus size: 30
11875930 AAAGTATCCA
* *
11875940 AAAATTACATTATGACCCCTAAACTTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
11875970 AAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
11876000 AAAATTACATTTTAACCCTTAAACTTTCCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * * * *
11876030 AAAGTCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
11876060 AAAATCATATTTTGACCGCTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
11876090 AAAATCACATTTTGACCC
1 AAAATTACATTTTGACCC
11876108 TCGAACTTCT
Statistics
Matches: 121, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 121 1.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:11876023 original size:60 final size:59
Alignment explanation
Indices: 11875940--11876132 Score: 215
Period size: 60 Copynumber: 3.2 Consensus size: 59
11875930 AAAGTATCCA
* * * *
11875940 AAAATTACATTATGACCCCTAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGA-CCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * * * *
11876000 AAAATTACATTTTAACCCTTAAACTTTCCCAAAGTCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTGACCC-TAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * * *
11876060 AAAATCATATTTTGACCGCTAAACTTTTCCAAAATCACATTTTGACCCTCGAACTTCTCT
1 AAAATTACATTTTGACC-CTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
*
11876120 AAAATTTCATTTT
1 AAAATTACATTTT
11876133 CATCCCGAGT
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
59 3 0.03
60 103 0.96
61 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
Found at i:11876132 original size:90 final size:89
Alignment explanation
Indices: 11875940--11876132 Score: 210
Period size: 90 Copynumber: 2.1 Consensus size: 89
11875930 AAAGTATCCA
* * * * * *
11875940 AAAATTACATTATGACCCCTAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCCAAAAT
1 AAAATTTCATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
* *
11876005 TACATTTTAACCCTTAAACTTTCC
66 CACATTTTAACCCTCAAACTTTCC
* * *
11876029 CAAA-GTCATATTTTAACCCCCAAACTTTTCCAAAATCATATTTTGACCGC-TAAACTTTTCCAA
1 AAAATTTC--ATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACC-CTTAAACTTTTCCAA
* * *
11876092 AATCACATTTTGACCCTCGAACTTCTCT
63 AATCACATTTTAACCCTCAAACTT-TCC
11876120 AAAATTTCATTTT
1 AAAATTTCATTTT
11876133 CATCCCGAGT
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
88 1 0.01
89 3 0.04
90 71 0.86
91 6 0.07
92 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (89 bp):
AAAATTTCATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
CACATTTTAACCCTCAAACTTTCC
Found at i:11880677 original size:18 final size:19
Alignment explanation
Indices: 11880640--11880678 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11880630 TTCCAAACAC
*
11880640 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
11880659 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
11880677 AA
1 AA
11880679 AATTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:11880679 original size:19 final size:20
Alignment explanation
Indices: 11880640--11880689 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
11880630 TTCCAAACAC
*
11880640 AATTCAAAATAATTTT-TAA
1 AATTCAAAATAATTTTAAAA
11880659 AATTCAAAAT-ATTTATAAAA
1 AATTCAAAATAATTT-TAAAA
11880679 AATTTCAAAAT
1 AA-TTCAAAAT
11880690 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 4 0.15
21 8 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCAAAATAATTTTAAAA
Found at i:11880760 original size:20 final size:19
Alignment explanation
Indices: 11880701--11880766 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
11880691 TATATTTTTT
11880701 AAAAAATATAAAAATTCTA
1 AAAAAATATAAAAATTCTA
* *
11880720 GAAAATATATAAAAAAT-TA
1 -AAAAAATATAAAAATTCTA
*
11880739 AAAAAATTTAAAAATTTCTA
1 AAAAAATATAAAAA-TTCTA
*
11880759 AAACAATA
1 AAAAAATA
11880767 ATTCTAGAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 22 0.59
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATATAAAAATTCTA
Found at i:11881067 original size:3 final size:3
Alignment explanation
Indices: 11881061--11881094 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11881051 CTACTACTAC
11881061 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11881095 CTATTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11882083 original size:20 final size:19
Alignment explanation
Indices: 11882041--11882086 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11882031 TTTTATATTT
* * *
11882041 TAAAAGAATTATAGTAATT
1 TAAAAAAATTATAGAAATA
11882060 TAAAAAAATTATAGAAAATA
1 TAAAAAAATTATAG-AAATA
11882080 TAAAAAA
1 TAAAAAA
11882087 GTTAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
TAAAAAAATTATAGAAATA
Found at i:11887647 original size:9 final size:9
Alignment explanation
Indices: 11887624--11887652 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
11887614 ATTAAAAGGA
11887624 AAAATGGTG
1 AAAATGGTG
11887633 -AAATGGTG
1 AAAATGGTG
11887641 AAAATGGTG
1 AAAATGGTG
11887650 AAA
1 AAA
11887653 TAGAAGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (9 bp):
AAAATGGTG
Found at i:11892709 original size:31 final size:30
Alignment explanation
Indices: 11892656--11892812 Score: 158
Period size: 30 Copynumber: 5.2 Consensus size: 30
11892646 GAGAAGTTCG
*
11892656 AGGGTCAAAATGTGA-TTTGGAAAAGTTT-
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
*
11892684 AGCGGTCAAAATATGATTTTTGGAAAAGTTTG
1 AG-GGTCAAAATATGA-TTTTGGAAAAGTTTA
* * * *
11892716 GGGGTTAAAATATGACTTTGGGAAAGTTTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* *
11892746 AGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * *
11892776 AGGGTCAAAATGA-AATTTTAGATAAGTTTA
1 AGGGTCAAAAT-ATGATTTTGGAAAAGTTTA
*
11892806 GGGGTCA
1 AGGGTCA
11892813 TAATGTAATT
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.02
29 12 0.11
30 68 0.63
31 25 0.23
32 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (30 bp):
AGGGTCAAAATATGATTTTGGAAAAGTTTA
Found at i:11892726 original size:60 final size:59
Alignment explanation
Indices: 11892656--11892828 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 59
11892646 GAGAAGTTCG
* *
11892656 AGGGTCAAAATGTGA-TTTGGAAAAGTTTAGCGGTCAAAATATGATTTTTGGAAAAGTTTG
1 AGGGTCAAAATGTGACTTTGGAAAAGTTTAG-GGTCAAAATGT-ATTTTTGGAAAAGTTTA
* * * * *
11892716 GGGGTTAAAATATGACTTTGGGAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 AGGGTCAAAATGTGACTTTGGAAAAGTTT-AGGGTCAAAATGTATTTTTGGAAAAGTTTA
** * * * *
11892776 AGGGTCAAAATGAAATTTTAGATAAGTTTAGGGGTCATAATGTAATTTTTGGA
1 AGGGTCAAAATGTGACTTTGGAAAAGTTTA-GGGTCAAAATGT-ATTTTTGGA
11892829 TACTTTAGGA
Statistics
Matches: 91, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
59 1 0.01
60 58 0.64
61 30 0.33
62 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
AGGGTCAAAATGTGACTTTGGAAAAGTTTAGGGTCAAAATGTATTTTTGGAAAAGTTTA
Found at i:11892823 original size:30 final size:30
Alignment explanation
Indices: 11892632--11892824 Score: 156
Period size: 30 Copynumber: 6.4 Consensus size: 30
11892622 ACTCGGGATG
* * **
11892632 AAAATGAAATTTTAGAGAAGTTCGAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
* *
11892662 AAAATGTGA-TTTGGAAAAGTTT-AGCGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAG-GGTC
* * * ** *
11892691 AAAATATGATTTTTGGAAAAGTTTGGGGGTT
1 AAAATGT-AATTTTAGAAAAGTTTAAGGGTC
* * * * *
11892722 AAAATATGACTTTGGGAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
*
11892752 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
* * *
11892782 AAAATGAAATTTTAGATAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
*
11892812 ATAATGTAATTTT
1 AAAATGTAATTTT
11892825 TGGATACTTT
Statistics
Matches: 132, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.02
29 20 0.15
30 86 0.65
31 23 0.17
32 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAAGGGTC
Found at i:11894205 original size:14 final size:14
Alignment explanation
Indices: 11894186--11894223 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
11894176 CACCCAAACC
11894186 CTGTTTCTTTGCCT
1 CTGTTTCTTTGCCT
11894200 CTGTTT-TTTGCCT
1 CTGTTTCTTTGCCT
*
11894213 ATG-TTCTTTGC
1 CTGTTTCTTTGC
11894224 TCATTTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 14 0.64
14 6 0.27
ACGTcount: A:0.03, C:0.24, G:0.16, T:0.58
Consensus pattern (14 bp):
CTGTTTCTTTGCCT
Found at i:11896691 original size:30 final size:30
Alignment explanation
Indices: 11896673--11896841 Score: 198
Period size: 30 Copynumber: 5.6 Consensus size: 30
11896663 GAGAAGTTCG
11896673 AGGGTCAAAATGTGATTTTGGAAAAGTTT-
1 AGGGTCAAAATGTGATTTTGGAAAAGTTTA
* *
11896702 AGCGGTCAAAATATGATTTTGGAAAAGTTTG
1 AG-GGTCAAAATGTGATTTTGGAAAAGTTTA
* * * *
11896733 GGGGTTAAAATATGACTTTGGGAAAA-TTTA
1 AGGGTCAAAATGTGA-TTTTGGAAAAGTTTA
*
11896763 AGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 AGGGTCAAAATGTGATTTTGGAAAAGTTTA
* *
11896793 AGGGTCAAAATGTAATTTTAGAAAAGTTTA
1 AGGGTCAAAATGTGATTTTGGAAAAGTTTA
* * *
11896823 GGGGTCATAATGTAATTTT
1 AGGGTCAAAATGTGATTTT
11896842 TGGATACTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
29 11 0.09
30 102 0.83
31 10 0.08
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AGGGTCAAAATGTGATTTTGGAAAAGTTTA
Found at i:11907873 original size:16 final size:16
Alignment explanation
Indices: 11907852--11907892 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11907842 CATTTTTAAA
11907852 ATTTAAATCTAAATTT
1 ATTTAAATCTAAATTT
* *
11907868 ATTTAAATTTGAATTT
1 ATTTAAATCTAAATTT
11907884 ACTTTAAAT
1 A-TTTAAAT
11907893 TTGAACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTAAATCTAAATTT
Found at i:11907891 original size:17 final size:17
Alignment explanation
Indices: 11907853--11907943 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 17
11907843 ATTTTTAAAA
* *
11907853 TTTAAATCTAAATTTA-
1 TTTAAATTTGAATTTAT
*
11907869 TTTAAATTTGAATTTAC
1 TTTAAATTTGAATTTAT
*
11907886 TTTAAATTTGAACTTAT
1 TTTAAATTTGAATTTAT
* * * *
11907903 TTTGAGTTTGGATTTAA
1 TTTAAATTTGAATTTAT
*
11907920 TTTAAATTTAAATTTAT
1 TTTAAATTTGAATTTAT
11907937 TTTAAAT
1 TTTAAAT
11907944 AAATTTAAAC
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
16 14 0.23
17 46 0.77
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (17 bp):
TTTAAATTTGAATTTAT
Found at i:11907959 original size:7 final size:6
Alignment explanation
Indices: 11907850--11907959 Score: 56
Period size: 6 Copynumber: 19.5 Consensus size: 6
11907840 CCCATTTTTA
* * *
11907850 AAATTT AAATCT AAATTT --ATTT AAATTT GAATTT -ACTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * * ** *
11907895 GAACTT -ATTTT GAGTTT GGATTT -AATTT AAATTT AAATTT -ATTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
11907940 AAA--T AAATTT AAACTTT AAA
1 AAATTT AAATTT AAA-TTT AAA
11907960 AGTCCAAATA
Statistics
Matches: 80, Mismatches: 15, Indels: 17
0.71 0.13 0.15
Matches are distributed among these distances:
4 8 0.10
5 15 0.19
6 51 0.64
7 6 0.08
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:11908682 original size:19 final size:18
Alignment explanation
Indices: 11908658--11908706 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
11908648 TTAATTATAG
11908658 TAATAAATAACATTAATAA
1 TAATAAATAA-ATTAATAA
11908677 TAAT-AATAGTAATTAATAA
1 TAATAAATA--AATTAATAA
*
11908696 TATTAAATAAA
1 TAATAAATAAA
11908707 AAAAATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.23
19 15 0.58
20 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
TAATAAATAAATTAATAA
Found at i:11909887 original size:29 final size:27
Alignment explanation
Indices: 11909841--11910072 Score: 131
Period size: 29 Copynumber: 8.0 Consensus size: 27
11909831 TCCCAAAGGT
*
11909841 CCCTAAACTATCCAAAAATTACATTTTTG
1 CCCTAAA-TTTCC-AAAATTACATTTTTG
* *
11909870 CCCTCGAAATTTCCAAAATTCCATTATTG
1 CCCT--AAATTTCCAAAATTACATTTTTG
* *
11909899 ACCCTAAAGTTTCCAACAAATACATTTTTA
1 -CCCTAAA-TTTCCAA-AATTACATTTTTG
* *
11909929 CCCTAAACTTTCCAAAACTCCATTTTTG
1 CCCTAAA-TTTCCAAAATTACATTTTTG
* ** *
11909957 ACCTCAAATTTTTTAAAAATTACATTTTTAC
1 CCCT-AAA--TTTCCAAAATTACATTTTT-G
** *
11909988 CCCCGAACTTCCAAAAATTACATTTTTG
1 CCCTAAATTTCC-AAAATTACATTTTTG
* * * *
11910016 ACCCTAATTTTCAAAAATTACAATTTTA
1 -CCCTAAATTTCCAAAATTACATTTTTG
* * *
11910044 CCCATGAACTTCCAAAAATTCCATTTTTG
1 CCC-TAAATTTCC-AAAATTACATTTTTG
11910073 ACCTTGATTT
Statistics
Matches: 152, Mismatches: 39, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
27 3 0.02
28 36 0.24
29 74 0.49
30 34 0.22
31 5 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (27 bp):
CCCTAAATTTCCAAAATTACATTTTTG
Found at i:11910053 original size:57 final size:56
Alignment explanation
Indices: 11909853--11910099 Score: 239
Period size: 57 Copynumber: 4.3 Consensus size: 56
11909843 CTAAACTATC
* * * *
11909853 CAAAAATTACATTTTTGCCCTCGAAATTTCCAAAATTCCATTATTGACCCTAAAGTTTC
1 CAAAAATTACATTTTTACCCT-G-AACTTCCAAAATTCCATTTTTGACCCT-AAGTTTT
* * * *
11909912 CAACAAA-TACATTTTTACCCTAAACTTTCCAAAACTCCATTTTTGACCTCAAATTTTT
1 CAA-AAATTACATTTTTACCCTGAAC-TTCCAAAATTCCATTTTTGACC-CTAAGTTTT
* * *
11909970 TAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTACATTTTTGACCCTAA-TTTT
1 CAAAAATTACATTTTTA-CCCTGAACTTCC-AAAATTCCATTTTTGACCCTAAGTTTT
* * *
11910027 CAAAAATTACAATTTTACCCATGAACTTCCAAAAATTCCATTTTTGACCTTGA-TTTT
1 CAAAAATTACATTTTTACCC-TGAACTTCC-AAAATTCCATTTTTGACCCTAAGTTTT
*
11910084 CAAAAAATACCATTTT
1 CAAAAATTA-CATTTT
11910100 ACCTCCGGTG
Statistics
Matches: 158, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.02
57 64 0.41
58 49 0.31
59 39 0.25
60 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (56 bp):
CAAAAATTACATTTTTACCCTGAACTTCCAAAATTCCATTTTTGACCCTAAGTTTT
Found at i:11910089 original size:29 final size:28
Alignment explanation
Indices: 11909999--11910099 Score: 96
Period size: 28 Copynumber: 3.5 Consensus size: 28
11909989 CCCGAACTTC
* *
11909999 CAAAAATTACATTTTTGACCCTAATTTT
1 CAAAAATTACATTTTTGACCATGATTTT
* * *
11910027 CAAAAATTACAATTTT-ACCCATGAACTTC
1 CAAAAATTACATTTTTGA-CCATG-ATTTT
* *
11910056 CAAAAATTCCATTTTTGACCTTGATTTT
1 CAAAAATTACATTTTTGACCATGATTTT
*
11910084 CAAAAAATACCATTTT
1 CAAAAATTA-CATTTT
11910100 ACCTCCGGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.02
28 28 0.49
29 27 0.47
30 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.39
Consensus pattern (28 bp):
CAAAAATTACATTTTTGACCATGATTTT
Found at i:11910139 original size:29 final size:28
Alignment explanation
Indices: 11910084--11910235 Score: 148
Period size: 28 Copynumber: 5.2 Consensus size: 28
11910074 CCTTGATTTT
*
11910084 CAAAAAATACCATTTTACCTCCG-GTGTC
1 CAAAAATTACCATTTTACC-CCGAGTGTC
11910112 CAAAAATTA-CATTTTCACCCTCGAGTGTC
1 CAAAAATTACCATTTT-ACCC-CGAGTGTC
* * * *
11910141 TAAAAATTACCATTTTCTTCCCCAAGTGTT
1 CAAAAATTACCA-TTT-TACCCCGAGTGTC
*
11910171 CAAAAATTACCATTTTACCCCTGAGTGAC
1 CAAAAATTACCATTTTACCCC-GAGTGTC
*
11910200 C-AAAATTACCATTTTACCCCCCGAGTATC
1 CAAAAATTACCATTTTA--CCCCGAGTGTC
11910229 CAAAAAT
1 CAAAAAT
11910236 CACATTTCCA
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.07
28 33 0.32
29 27 0.26
30 28 0.27
31 6 0.06
32 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCCGAGTGTC
Found at i:11910242 original size:29 final size:30
Alignment explanation
Indices: 11910084--11910235 Score: 147
Period size: 30 Copynumber: 5.2 Consensus size: 30
11910074 CCTTGATTTT
* *
11910084 CAAAAAATACCATTTTA-CCTCCG-GTGTC
1 CAAAAATTACCATTTTACCCCCCGAGTGTC
*
11910112 CAAAAATTA-CATTTT-CACCCTCGAGTGTC
1 CAAAAATTACCATTTTAC-CCCCCGAGTGTC
* * * *
11910141 TAAAAATTACCATTTT-CTTCCCCAAGTGTT
1 CAAAAATTACCATTTTAC-CCCCCGAGTGTC
* *
11910171 CAAAAATTACCATTTTA-CCCCTGAGTGAC
1 CAAAAATTACCATTTTACCCCCCGAGTGTC
*
11910200 C-AAAATTACCATTTTACCCCCCGAGTATC
1 CAAAAATTACCATTTTACCCCCCGAGTGTC
11910229 CAAAAAT
1 CAAAAAT
11910236 CACATTTCCA
Statistics
Matches: 99, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
27 6 0.06
28 27 0.27
29 31 0.31
30 35 0.35
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (30 bp):
CAAAAATTACCATTTTACCCCCCGAGTGTC
Found at i:11923257 original size:28 final size:28
Alignment explanation
Indices: 11923226--11923285 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11923216 AAAATGTGAT
**
11923226 TTTTGGATGCCCGGGGGTAAAACGGTAA
1 TTTTGGACACCCGGGGGTAAAACGGTAA
** *
11923254 TTTTGGACATTCGGGGGTAAAATGGTAA
1 TTTTGGACACCCGGGGGTAAAACGGTAA
11923282 TTTT
1 TTTT
11923286 TGGAAGGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (28 bp):
TTTTGGACACCCGGGGGTAAAACGGTAA
Found at i:11923287 original size:29 final size:30
Alignment explanation
Indices: 11923237--11923501 Score: 214
Period size: 29 Copynumber: 9.0 Consensus size: 30
11923227 TTTGGATGCC
* *
11923237 CGGGGGTAAAACGGTAA-TTTTGGACA-TT
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTT
*
11923265 CGGGGGTAAAATGGTAATTTTTGGAAGGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTT
* * *
11923295 C-AGGGTCAAAAAATGG-AATTTTTAGACA-TT
1 CGGGGGT---AAAATGGTAATTTTTGGAAAGTT
*
11923325 CGGGGATAAAATGGTAATTTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTT
* * *
11923355 CGTGGTTAAAAATGG-AATTTTT--AAACATT
1 CGGGGGT-AAAATGGTAATTTTTGGAAA-GTT
*
11923384 CGGGGGTAAAATGGTAATTTTTGGAAGGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTT
* * *
11923414 CAGGGTTAAAAATGG-AA-TTTTGGAAAATT
1 CGGGGGT-AAAATGGTAATTTTTGGAAAGTT
* *
11923443 TGAGGGTAAAAT-GTAATTTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTT
* *
11923472 CGAGGTTAAAAATGG-AA-TTTTGGAAAGTT
1 CGGGGGT-AAAATGGTAATTTTTGGAAAGTT
11923501 C
1 C
11923502 AGGGATCTCC
Statistics
Matches: 190, Mismatches: 29, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 40 0.21
29 77 0.41
30 36 0.19
31 29 0.15
32 7 0.04
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTTGGAAAGTT
Found at i:11923374 original size:59 final size:59
Alignment explanation
Indices: 11923254--11923492 Score: 324
Period size: 59 Copynumber: 4.1 Consensus size: 59
11923244 AAAACGGTAA
* * *
11923254 TTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAAATGGAAT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGT-TAAAAATGGAAT
*
11923314 TTTTAGACATTCGGGGATAAAATGGTAATTTTTGGAAAGTTC-GTGGTTAAAAATGGAAT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAG-GGTTAAAAATGGAAT
* *
11923373 TTTTAAACATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGAA-
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGGAAT
* * * *
11923431 TTTTGGAAAATTTGAGGGTAAAAT-GTAATTTTTGGAAAGTTC-GAGGTTAAAAATGGAAT
1 TTTTAG-ACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAG-GGTTAAAAATGGAAT
11923490 TTT
1 TTT
11923493 GGAAAGTTCA
Statistics
Matches: 161, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
57 1 0.01
58 35 0.22
59 82 0.51
60 43 0.27
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (59 bp):
TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGGAAT
Found at i:11929525 original size:30 final size:30
Alignment explanation
Indices: 11929465--11929678 Score: 203
Period size: 30 Copynumber: 7.2 Consensus size: 30
11929455 AAGTTTCGAA
*
11929465 AAGTTT-GAGGGTCAAAATGTATTTTTTTTGAG
1 AAGTTTAGA-GGTCAAAATGTA--ATTTTTGAG
11929497 AAGTTTAGAGGTCAAAATGTAATTTTTGAG
1 AAGTTTAGAGGTCAAAATGTAATTTTTGAG
* *
11929527 AAGTTTAGGGGTTAAAATGTAATTTTTG-G
1 AAGTTTAGAGGTCAAAATGTAATTTTTGAG
11929556 AAAGTTTATG-GGTCAAAATGTAATTTTT-AGG
1 -AAGTTTA-GAGGTCAAAATGTAATTTTTGA-G
* * * *
11929587 AAGTTTAGGGGTC-TAATGTGATTTTTGAA
1 AAGTTTAGAGGTCAAAATGTAATTTTTGAG
*
11929616 AAGTTTAGAGGTC-AAATGTGATTTTTG-G
1 AAGTTTAGAGGTCAAAATGTAATTTTTGAG
* *
11929644 AAGTTTA-AGGGTTAAAATG-AGATTTTTGGG
1 AAGTTTAGA-GGTCAAAATGTA-ATTTTTGAG
11929674 AAGTT
1 AAGTT
11929679 CGCGGATCTC
Statistics
Matches: 159, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.01
28 10 0.06
29 50 0.31
30 76 0.48
31 2 0.01
32 18 0.11
33 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (30 bp):
AAGTTTAGAGGTCAAAATGTAATTTTTGAG
Found at i:11929571 original size:60 final size:61
Alignment explanation
Indices: 11929465--11929678 Score: 241
Period size: 60 Copynumber: 3.6 Consensus size: 61
11929455 AAGTTTCGAA
* ** *
11929465 AAGTTT-GAGGGTCAAAATGTATTTTTTTTGAGAAGTTTAGAGGTCAAAATGTAATTTTTGAG
1 AAGTTTAG-GGGTTAAAATGTAGATTTTTGGA-AAGTTTAGAGGTCAAAATGTAATTTTTGAG
11929527 AAGTTTAGGGGTTAAAATGTA-ATTTTTGGAAAGTTTATG-GGTCAAAATGTAATTTTT-AGG
1 AAGTTTAGGGGTTAAAATGTAGATTTTTGGAAAGTTTA-GAGGTCAAAATGTAATTTTTGA-G
* *
11929587 AAGTTTAGGGGTCT--AATGT-GATTTTTGAAAAGTTTAGAGGTC-AAATGTGATTTTTG-G
1 AAGTTTAGGGGT-TAAAATGTAGATTTTTGGAAAGTTTAGAGGTCAAAATGTAATTTTTGAG
* *
11929644 AAGTTTAAGGGTTAAAATG-AGATTTTTGGGAAGTT
1 AAGTTTAGGGGTTAAAATGTAGATTTTTGGAAAGTT
11929679 CGCGGATCTC
Statistics
Matches: 134, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
56 1 0.01
57 12 0.09
58 30 0.22
59 25 0.19
60 38 0.28
61 9 0.07
62 18 0.13
63 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (61 bp):
AAGTTTAGGGGTTAAAATGTAGATTTTTGGAAAGTTTAGAGGTCAAAATGTAATTTTTGAG
Found at i:11931902 original size:39 final size:39
Alignment explanation
Indices: 11931793--11932536 Score: 355
Period size: 39 Copynumber: 19.0 Consensus size: 39
11931783 TCATTGCTTC
* * * * * *
11931793 GGATGACTACAATCTACCCCATGATCGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** * * * *
11931832 GGATGATGTCTTCAATCTGCTTCATGATTGGGGTAAGAGATT
1 GGATGA--T-TGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * * * *
11931874 GAATGGTTGCAATCTGCCCTAGGCTTGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
** * ** * *
11931913 GCTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATC
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * * * * ** *
11931952 GAATGGTTACAATCT-ACCTAGGCTCATGGTAATAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * *** * * *
11931990 GGCTGATGGTGGTCTGCCCTAGGTTCGGGGTAAAAGATC
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * * *
11932029 AGATGGTTGCAATCTACCCCAGGCTCGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * * * *
11932068 GGCTGA-TG-ATGATCTTCCCTAGGCTTGGGGTAAAAGATC
1 GGATGATTGCA--ATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** * *
11932107 GGAAGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** * *
11932146 -GACTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATT
1 GGA-TGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * * *
11932185 GGATGATTGCAATCTGCCCCAAGCTCGGCGTAAGAGTTT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * ** *
11932224 GGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** *
11932263 GGATGACTGCAATCTATCCTAGGCTCGGGGTAAAAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * ** * * ** * *
11932302 GGTTGATGGTGATCTACTCCAAACTCAGGGTAAAAGATC
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
** * * * *
11932341 GGATGGCTGTAATTTACCCCAGGCTCGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** * * * *
11932380 -GACTGATGGTGATCTACCCTAGACTCGGGGTAAAAGATC
1 GGA-TGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
** * * *
11932419 GGATGGCTGCAATCTGCCCTAGGCTTGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* * ** * * * * *
11932458 GGCTGATAGTGATATGCCTCAAGCTCGGGATAAAAGATC
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
* ** * *
11932497 GAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATT
1 GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
11932536 G
1 G
11932537 ATTGATAATG
Statistics
Matches: 510, Mismatches: 183, Indels: 24
0.71 0.26 0.03
Matches are distributed among these distances:
37 1 0.00
38 29 0.06
39 441 0.86
40 7 0.01
41 1 0.00
42 31 0.06
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
GGATGATTGCAATCTGCCCCAGGCTCGGGGTAAAAGATT
Found at i:11931965 original size:78 final size:77
Alignment explanation
Indices: 11931861--11932573 Score: 714
Period size: 78 Copynumber: 9.2 Consensus size: 77
11931851 CTTCATGATT
* * * * * *
11931861 GGGGTAAGAGATTGAATGGTTGCAATCTGCCCTAGGCTTGGGGTAAGAGATTGCTTGATGGTGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGC-TGATGGTGAT
11931926 CTGCCCCAAGCTC
65 CTGCCCCAAGCTC
* * * ** * *
11931939 GGGGTAAAAGATCGAATGGTTACAATCTA-CCTAGGCTCATGGTAATAGATTGGCTGATGGTGGT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTGAT
* * *
11932003 CTGCCCTAGGTTC
65 CTGCCCCAAGCTC
* *
11932016 GGGGTAAAAGATC-AGATGGTTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGA
1 GGGGTAAAAGATCGA-ATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTGA
* * * *
11932080 TCTTCCCTAGGCTT
64 TCTGCCCCAAGCTC
11932094 GGGGTAAAAGATCGGAA-GGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGA
1 GGGGTAAAAGATC-GAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTGA
11932158 TCTGCCCCAAGCTC
64 TCTGCCCCAAGCTC
* * * ** * * * *
11932172 GAGGTAAAAGATTGGATGATTGCAATCTGCCCCAAGCTCGGCGTAAGAGTTTGGCTGATGGTGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTGAT
11932237 CTGCCCCAAGCTC
65 CTGCCCCAAGCTC
* * * * * * *
11932250 GGGGTAAAAGATTGGATGACTGCAATCTATCCTAGGCTCGGGGTAAAAGATTGGTTGATGGTGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTGAT
* * *
11932315 CTACTCCAAACTC
65 CTGCCCCAAGCTC
* * * *
11932328 AGGGTAAAAGATCGGATGGCTGTAATTTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTGAT
* *
11932393 CT-ACCCTAGACTC
65 CTGCCCCAAG-CTC
* * * * *
11932406 GGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTGATAGTGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTGAT
* *
11932471 ATGCCTCAAGCTC
65 CTGCCCCAAGCTC
* * * * **
11932484 GGGATAAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGATTGATAATGAT
1 GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTGAT
* *
11932549 CTACCCTAAGCTC
65 CTGCCCCAAGCTC
* *
11932562 AGGGTAAGAGAT
1 GGGGTAAAAGAT
11932574 TGACTGATGG
Statistics
Matches: 534, Mismatches: 88, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
76 1 0.00
77 71 0.13
78 454 0.85
79 7 0.01
80 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (77 bp):
GGGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGCTGATGGTGATC
TGCCCCAAGCTC
Found at i:11932205 original size:156 final size:156
Alignment explanation
Indices: 11931876--11932573 Score: 787
Period size: 156 Copynumber: 4.5 Consensus size: 156
11931866 AAGAGATTGA
* * * *
11931876 ATGGTTGCAATCTGCCCTAGGCTTGGGGTAAGAGATT-GCTTGATGGTGATCTGCCCCAAGCTCG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGC-TGATGGTGATCTACCCTAAGCTCG
* * ** * *
11931940 GGGTAAAAGATC-GAATGGTTACAATCTA-CCTAGGCTCATGGTAATAGATTGGCTGATGGTGGT
65 GGGTAAAAGATCGGAA-GGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGAT
* * * * *
11932003 CTGCCCTAGGTTCGGGGTAAAAGATCAG
129 CTGCCCCAAGCTCGAGGTAAAAGATCGG
* * * * *
11932031 ATGGTTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTTCCCTAGGCTTGG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAGCTCGG
* *
11932096 GGTAAAAGATCGGAAGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT
66 GGTAAAAGATCGGAAGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT
*
11932161 GCCCCAAGCTCGAGGTAAAAGATTGG
131 GCCCCAAGCTCGAGGTAAAAGATCGG
* * * * * *
11932187 ATGATTGCAATCTGCCCCAAGCTCGGCGTAAGAGTTTGGCTGATGGTGATCTGCCCCAAGCTCGG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAGCTCGG
* * * * * *
11932252 GGTAAAAGATTGGATGACTGCAATCTATCCTAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCT
66 GGTAAAAGATCGGAAGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT
* * *
11932317 ACTCCAAACTC-AGGGTAAAAGATCGG
131 GCCCCAAGCTCGA-GGTAAAAGATCGG
* * * * *
11932343 ATGGCTGTAATTTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACCCT-AGACTCG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAG-CTCG
* * * * *
11932407 GGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTGATAGTGATA
65 GGGTAAAAGATCGGAAGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* *
11932472 TGCCTCAAGCTCG-GGATAAAAGATCGA
130 TGCCCCAAGCTCGAGG-TAAAAGATCGG
* * ** ** *
11932499 ATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGATTGATAATGATCTACCCTAAGCTCAG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAGCTCGG
*
11932564 GGTAAGAGAT
66 GGTAAAAGAT
11932574 TGACTGATGG
Statistics
Matches: 457, Mismatches: 78, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
155 80 0.18
156 375 0.82
157 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (156 bp):
ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAGCTCGG
GGTAAAAGATCGGAAGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT
GCCCCAAGCTCGAGGTAAAAGATCGG
Found at i:11932527 original size:117 final size:117
Alignment explanation
Indices: 11932403--11932652 Score: 272
Period size: 117 Copynumber: 2.1 Consensus size: 117
11932393 CTACCCTAGA
* * * * ** *
11932403 CTCGGGGTAAAAGATCGGATGGCTGCA-ATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTGATAG
1 CTCGGGGTAAAAGATCGGATGGAT-AAGATCTACCCTAAGCTCAGGGTAAGAGATTGACTGATAG
* *
11932467 TGATATGCCTCAAG-CTCGGGATAAAAGATCGAATGGCTGCAATCTGCCCCAAG
65 TGATATG-CTCAAGACTCGGGATAAAAGATCAAATGGCTGCAATCTGCACCAAG
* * * *
11932520 CTCGGGGTAAGAGAT-TGATTGATAATGATCTACCCTAAGCTCAGGGTAAGAGATTGACTGATGG
1 CTCGGGGTAAAAGATCGGATGGATAA-GATCTACCCTAAGCTCAGGGTAAGAGATTGACTGATAG
* * * * *
11932584 TGATTTGCTCGAGACTCGGGGTAAGAGATCAAATGGCTGCAATCTGTACCAAG
65 TGATATGCTCAAGACTCGGGATAAAAGATCAAATGGCTGCAATCTGCACCAAG
* *
11932637 CTCGGGCTAACAGATC
1 CTCGGGGTAAAAGATC
11932653 AGAATCTTCA
Statistics
Matches: 109, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
115 1 0.01
116 10 0.09
117 98 0.90
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (117 bp):
CTCGGGGTAAAAGATCGGATGGATAAGATCTACCCTAAGCTCAGGGTAAGAGATTGACTGATAGT
GATATGCTCAAGACTCGGGATAAAAGATCAAATGGCTGCAATCTGCACCAAG
Found at i:11937131 original size:7 final size:7
Alignment explanation
Indices: 11937115--11937153 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
11937105 ACCCAAATTC
11937115 ATTTTT-
1 ATTTTTA
11937121 ATTTTTA
1 ATTTTTA
11937128 ATTTTTA
1 ATTTTTA
11937135 ATTTTTA
1 ATTTTTA
11937142 ATTTTTA
1 ATTTTTA
11937149 ATTTT
1 ATTTT
11937154 CAAGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:11948508 original size:12 final size:13
Alignment explanation
Indices: 11948482--11948514 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11948472 GCAAAAATGA
*
11948482 GCAAAGAACATAG
1 GCAAAGAACAGAG
11948495 GCAAA-AACAGAG
1 GCAAAGAACAGAG
11948507 GCAAAGAA
1 GCAAAGAA
11948515 ACAGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.15, G:0.24, T:0.03
Consensus pattern (13 bp):
GCAAAGAACAGAG
Found at i:11949567 original size:30 final size:30
Alignment explanation
Indices: 11949533--11949700 Score: 203
Period size: 30 Copynumber: 5.6 Consensus size: 30
11949523 AAAGTATCCA
* *
11949533 AAAATTACATTATGACCCCTAAACTTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
11949563 AAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
11949593 AAAATTACATTTTGACCCTTAAA-TTTTCCC
1 AAAATTACATTTTGACCCCTAAACTTTT-CC
* * * * *
11949623 AAAGTCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
11949653 AAAATCATATTTTGACCGCTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
11949683 AAAATCACATTTTGACCC
1 AAAATTACATTTTGACCC
11949701 TCGAACTTCT
Statistics
Matches: 121, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.03
30 113 0.93
31 4 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:11949599 original size:60 final size:60
Alignment explanation
Indices: 11949533--11949725 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
11949523 AAAGTATCCA
* * * *
11949533 AAAATTACATTATGACCCCTAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * * *
11949593 AAAATTACATTTTGACCCTTAAA-TTTTCCCAAAGTCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTT-CCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * * * *
11949653 AAAATCATATTTTGACCGCTAAACTTTTCCAAAATCACATTTTGACCCTCGAACTTCTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
*
11949713 AAAATTTCATTTT
1 AAAATTACATTTT
11949726 CATCCCGAGT
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 4 0.04
60 100 0.93
61 4 0.04
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTTCC
Found at i:11949725 original size:90 final size:89
Alignment explanation
Indices: 11949533--11949725 Score: 210
Period size: 90 Copynumber: 2.1 Consensus size: 89
11949523 AAAGTATCCA
* * * * * *
11949533 AAAATTACATTATGACCCCTAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCCAAAAT
1 AAAATTTCATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
* * *
11949598 TACATTTTGACCCTTAAATTTTCC
66 CACATTTTGACCCTGAAATTCTCC
* * *
11949622 CAAA-GTCATATTTTAACCCCCAAACTTTTCCAAAATCATATTTTGACCGC-TAAACTTTTCCAA
1 AAAATTTC--ATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACC-CTTAAACTTTTCCAA
* *
11949685 AATCACATTTTGACCCTCGAACTTCTCT
63 AATCACATTTTGACCCT-GAAATTCTCC
11949713 AAAATTTCATTTT
1 AAAATTTCATTTT
11949726 CATCCCGAGT
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
88 1 0.01
89 3 0.04
90 67 0.81
91 10 0.12
92 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (89 bp):
AAAATTTCATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
CACATTTTGACCCTGAAATTCTCC
Found at i:11952179 original size:12 final size:13
Alignment explanation
Indices: 11952153--11952185 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11952143 GCAAAAATGA
*
11952153 GCAAAGAACATAG
1 GCAAAGAACAGAG
11952166 GCAAA-AACAGAG
1 GCAAAGAACAGAG
11952178 GCAAAGAA
1 GCAAAGAA
11952186 ACAGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.15, G:0.24, T:0.03
Consensus pattern (13 bp):
GCAAAGAACAGAG
Found at i:11953581 original size:30 final size:30
Alignment explanation
Indices: 11953541--11953739 Score: 168
Period size: 30 Copynumber: 6.6 Consensus size: 30
11953531 GTTCCTAAAG
* *
11953541 TATCCAAAAATTACATTATGACCCCTAAACT
1 TATCC-AAAATTACATTTTGACCCTTAAACT
* *
11953572 TATCTAAAATTTCATTTTGACCCTTAAACT
1 TATCCAAAATTACATTTTGACCCTTAAACT
*
11953602 TTTCCAAAATTACATTTTGACCCTTAAACT
1 TATCCAAAATTACATTTTGACCCTTAAACT
* * * * **
11953632 T-TCCCAAAGTCATATTTTAACCCCCAAACT
1 TAT-CCAAAATTACATTTTGACCCTTAAACT
* * *
11953662 TTTCCAAAATCATATTTTGACCGC-TAAACT
1 TATCCAAAATTACATTTTGACC-CTTAAACT
* * **
11953692 TTTCCAAAATCACATTTTGACCCTCGAACT
1 TATCCAAAATTACATTTTGACCCTTAAACT
* * *
11953722 TCTCTAAAATTTCATTTT
1 TATCCAAAATTACATTTT
11953740 CATCCCGAGT
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
29 2 0.01
30 133 0.94
31 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
TATCCAAAATTACATTTTGACCCTTAAACT
Found at i:11953649 original size:60 final size:60
Alignment explanation
Indices: 11953547--11953739 Score: 201
Period size: 60 Copynumber: 3.2 Consensus size: 60
11953537 AAAGTATCCA
* * * ** *
11953547 AAAATTACATTATGACCCCTAAACTTAT-CTAAAATTTCATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCGCTAAACTT-TCCCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * *
11953607 AAAATTACATTTTGACC-CTTAAACTTTCCCAAAGTCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTGACCGC-TAAACTTTCCCAAAATCACATTTTGACCCTCAAACTTTTCC
* * * * * *
11953667 AAAATCATATTTTGACCGCTAAACTTTTCCAAAATCACATTTTGACCCTCGAACTTCTCT
1 AAAATTACATTTTGACCGCTAAACTTTCCCAAAATCACATTTTGACCCTCAAACTTTTCC
*
11953727 AAAATTTCATTTT
1 AAAATTACATTTT
11953740 CATCCCGAGT
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
59 2 0.02
60 105 0.97
61 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (60 bp):
AAAATTACATTTTGACCGCTAAACTTTCCCAAAATCACATTTTGACCCTCAAACTTTTCC
Found at i:11957901 original size:18 final size:19
Alignment explanation
Indices: 11957864--11957902 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11957854 TTCCAAACAC
*
11957864 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
11957883 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
11957901 AA
1 AA
11957903 AAATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:11957922 original size:26 final size:26
Alignment explanation
Indices: 11957891--11957941 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
11957881 AAAATTCAAA
* *
11957891 ATATTTATAAAAAAATTTCAAAATTT
1 ATATTTATAAAAAAATATAAAAATTT
* *
11957917 ATATTTTTTAAAAAATATAAAAATT
1 ATATTTATAAAAAAATATAAAAATT
11957942 CTAGAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTTATAAAAAAATATAAAAATTT
Found at i:11957985 original size:20 final size:19
Alignment explanation
Indices: 11957926--11957991 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
11957916 TATATTTTTT
11957926 AAAAAATATAAAAATTCTA
1 AAAAAATATAAAAATTCTA
* *
11957945 GAAAATATATAAAAAAT-TA
1 -AAAAAATATAAAAATTCTA
*
11957964 AAAAAATTTAAAAATTTCTA
1 AAAAAATATAAAAA-TTCTA
*
11957984 AAACAATA
1 AAAAAATA
11957992 ATTCTAGAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 22 0.59
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATATAAAAATTCTA
Found at i:11958295 original size:3 final size:3
Alignment explanation
Indices: 11958289--11958322 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11958279 CTACTACTAC
11958289 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11958323 CTATTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11970930 original size:2 final size:2
Alignment explanation
Indices: 11970923--11970951 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11970913 TTTACATACG
11970923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11970952 GTTCTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11971716 original size:7 final size:7
Alignment explanation
Indices: 11971704--11971742 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
11971694 ATTAAACTTG
11971704 AAAATTA
1 AAAATTA
11971711 AAAATTA
1 AAAATTA
11971718 AAAATTA
1 AAAATTA
11971725 AAAATTA
1 AAAATTA
11971732 AAAA-TA
1 AAAATTA
11971738 AAAAT
1 AAAAT
11971743 GAATTTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:11976377 original size:39 final size:38
Alignment explanation
Indices: 11976323--11976998 Score: 329
Period size: 39 Copynumber: 17.4 Consensus size: 38
11976313 CATTATCAAT
* *
11976323 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATT
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCA-CCATC
* * * * ** * *
11976362 CGATCTTTTATCCCGAGCTTGAGGCATATCACTATCAGC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGC-ACCATC
* * * *
11976401 CAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCA-CCATC
* * *
11976440 CGATCTTTTACCCCGAG-TCTAGGGTAGA-T-CACCATC
1 CAATCTTTTACCCCGAGCT-TGGGGCAGATTGCACCATC
* * * * *
11976476 AGTCAATCTCTTACCCCGAGCCTGGGGTAAATTACAGCCATC
1 ---CAATCTTTTACCCCGAGCTTGGGGCAGATTGCA-CCATC
* * * * *
11976518 CGATCTTTTACCCTGAGTTTGGAGTAGA-T-CACCATCAAC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCAT---C
* * ** *
11976557 CAATCTTTTACCCCGAGCCTAGGATAGATTGCAGTCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCA-CCATC
11976596 CAATCTTTTACCCCGAGCTTGGGGCAGA-T-CACCATCAGC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCAT---C
* * * *
11976635 CAAACTCTTACGCCGAGCTTGGGGCAGATTGCAATCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGC-ACCATC
*
11976674 CAATCTTTTACCTCGAGCTTGGGGCAGA-T-CACCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCATC
* * * *
11976710 AGTCAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCTTC
1 ---CAATCTTTTACCCCGAGCTTGGGGCAGATTGCA-CCATC
* * * * * * *
11976752 CGATCTTTTACCCCAAGCCTAGGGAAGATCAT-CATCAGC
1 CAATCTTTTACCCCGAGCTTGGGGCAGAT--TGCACCATC
* * *
11976791 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGC-ACCATC
** * * * *
11976830 TGATCTTTTACCCCGAACCTAGGGCAGA--CCACCATCAGC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCAT---C
* ** * * * * *
11976869 CAATCTATTACCATGAGCCT-AGGTAGATTGTAACCATT
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTG-CACCATC
*
11976907 CGATCTTTTACCCCGAGCTTGGGGCAGA-T-CACCATC
1 CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCATC
* * * *
11976943 AAGCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATT
1 ---CAATCTTTTACCCCGAGCTTGGGGCAGATTGC-ACCATC
*
11976985 CAATCTCTTACCCC
1 CAATCTTTTACCCC
11976999 AATCATGAAG
Statistics
Matches: 479, Mismatches: 113, Indels: 90
0.70 0.17 0.13
Matches are distributed among these distances:
36 27 0.06
37 9 0.02
38 27 0.06
39 373 0.78
40 8 0.02
41 14 0.03
42 21 0.04
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (38 bp):
CAATCTTTTACCCCGAGCTTGGGGCAGATTGCACCATC
Found at i:11976398 original size:78 final size:78
Alignment explanation
Indices: 11976323--11977057 Score: 730
Period size: 78 Copynumber: 9.4 Consensus size: 78
11976313 CATTATCAAT
* * *
11976323 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTATCCCGAGCTTGAGGCA
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
* *
11976388 TATCACTATCAGC
66 GATCACCATCAGC
* * * * * *
11976401 CAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGTCTAG-GGT
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAG-CTTGAGGC
*
11976465 AGATCACCATCAGT
65 AGATCACCATCAGC
* * * * * *
11976479 CAATCTCTTACCCCGAGCCTGGGGTAAATTACAGCCATCCGATCTTTTACCCTGAGTTTG-GAGT
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAG-GC
*
11976543 AGATCACCATCAAC
65 AGATCACCATCAGC
* * * * * * *
11976557 CAATCTTTTACCCCGAGCCTAGGATAGATTGCAGTCATCCAATCTTTTACCCCGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
11976622 GATCACCATCAGC
66 GATCACCATCAGC
* * * * ** * * * *
11976635 CAAACTCTTACGCCGAGCTTGGGGCAGATTGCAATCATCCAATCTTTTACCTCGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
*
11976700 GATCACCATCAGT
66 GATCACCATCAGC
* *
11976713 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCC-TTCCGATCTTTTACCCCAAGCCT-AGGG
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATT-CGATCTTTTACCCCGAGCTTGA-GG
* *
11976776 AAGATCATCATCAGC
64 CAGATCACCATCAGC
* * *
11976791 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCA-TCTGATCTTTTACCCCGAACCT-AGGG
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTC-GATCTTTTACCCCGAGCTTGA-GG
*
11976854 CAGACCACCATCAGC
64 CAGATCACCATCAGC
* ** * * * *
11976869 CAATCTATTACCATGAGCCT-AGGTAGATTGTAACCATTCGATCTTTTACCCCGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
11976933 GATCACCATCAAG-
66 GATCACCATC-AGC
* * * * * * * * *
11976946 CAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATTCAATCTCTTACCCCAATCATGAAGCA
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
* * *
11977011 GATTGAAGACATCATC
66 GA-T-CA-CCATCAGC
* *
11977027 CAATCTCTTACCCCGATCATGGGGTAGATTG
1 CAATCTCTTACCCCGAGCCTGGGGTAGATTG
11977058 TAGTCATCCG
Statistics
Matches: 551, Mismatches: 91, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
77 66 0.12
78 447 0.81
79 5 0.01
80 2 0.00
81 31 0.06
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
CAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGAGGCA
GATCACCATCAGC
Found at i:11976424 original size:117 final size:117
Alignment explanation
Indices: 11976208--11976429 Score: 293
Period size: 117 Copynumber: 1.9 Consensus size: 117
11976198 GAAGATTCTG
* * * *
11976208 ATCTGTTAGCCCGAGCTTGGTACAGATTGCAGCCATTTGATCTCTTACCCCGAGTCTCGAGCAAA
1 ATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGAGCAAA
* ** * *
11976273 TCACCATCAGTCAATCTCTTACCCTGAGCTTAGGGTAGATCATTATCAATCA
66 TCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGATCATTATCAATCA
* * * * *
11976325 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTATCCCGAG-CTTGAGGCAT
1 ATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGA-GCAA
*
11976389 ATCACTATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGAT
65 ATCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGAT
11976430 TGCAGCCATC
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 4 0.04
117 85 0.96
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (117 bp):
ATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGAGCAAA
TCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGATCATTATCAATCA
Found at i:11976451 original size:117 final size:116
Alignment explanation
Indices: 11976207--11976456 Score: 270
Period size: 117 Copynumber: 2.1 Consensus size: 116
11976197 TGAAGATTCT
* * * *
11976207 GATCTGTTAGCCCGAGCTTGGTACAGATTGCAGCCATTTGATCTCTTACCCCGAGTCTCGAGCAA
1 GATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGAGCAA
* ** * * * *
11976272 ATCACCATCAGTCAATCTCTTACCCTGAGCTTAGGGTAGATCATTATCAATC
66 ATCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGAT-ATCAGCAATC
* * * * *
11976324 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTATCCCGAG-CTTGAGGCA
1 GATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGA-GCA
* * *
11976388 TATCACTATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGAT-TGCAGCCATCC
65 AATCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGATAT-CAGCAAT-C
*
11976441 GATCTTTTACCCCGAG
1 GATCTCTTACCCCGAG
11976457 TCTAGGGTAG
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
115 1 0.01
116 8 0.07
117 100 0.92
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (116 bp):
GATCTCTTACCCCGAGCTTGGGACAGATTGCAGCCATTCGATCTCTTACCCCGAGTCTCGAGCAA
ATCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGATATCAGCAATC
Found at i:11977056 original size:42 final size:39
Alignment explanation
Indices: 11976946--11977057 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 39
11976936 CACCATCAAG
* * * * *
11976946 CAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATT
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAACCATC
* **
11976985 CAATCTCTTACCCCAATCATGAAGCAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAA-AC--CATC
*
11977027 CAATCTCTTACCCCGATCATGGGGTAGATTG
1 CAATCTCTTACCCCGATCATGGGGCAGATTG
11977058 TAGTCATCCG
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 26 0.45
40 2 0.03
42 30 0.52
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (39 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAACCATC
Found at i:11979216 original size:30 final size:30
Alignment explanation
Indices: 11979182--11979395 Score: 172
Period size: 30 Copynumber: 7.2 Consensus size: 30
11979172 GAGATCCGCG
11979182 AACTTCCCAAAAATCT-CATTTTAACCCTTA
1 AACTTCCCAAAAAT-TACATTTTAACCCTTA
* *
11979212 AACTT-CCAAAAATCACA-TTTGA-CCTCTA
1 AACTTCCCAAAAATTACATTTTAACCCT-TA
** * *
11979240 AACTTTTCAAAAATCACA--TTAGACCCCTA
1 AACTTCCCAAAAATTACATTTTA-ACCCTTA
* * *
11979269 AACTTCCTAAAAATTACATTTTGACCCATA
1 AACTTCCCAAAAATTACATTTTAACCCTTA
* *
11979299 AACTTTCCAAAAATTACATTTTAACCCCTA
1 AACTTCCCAAAAATTACATTTTAACCCTTA
* *
11979329 AACTTCTCAAAAATTACATTTTGA-CCTCTA
1 AACTTCCCAAAAATTACATTTTAACCCT-TA
* * * *
11979359 AACTTCTCAAAAAAAATACATTTTGACCCTCA
1 AACTTC-C-CAAAAATTACATTTTAACCCTTA
11979391 AACTT
1 AACTT
11979396 TTCGAAACTT
Statistics
Matches: 150, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.02
28 13 0.09
29 40 0.27
30 68 0.45
31 2 0.01
32 21 0.14
33 3 0.02
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (30 bp):
AACTTCCCAAAAATTACATTTTAACCCTTA
Found at i:11979350 original size:60 final size:59
Alignment explanation
Indices: 11979182--11979395 Score: 242
Period size: 60 Copynumber: 3.6 Consensus size: 59
11979172 GAGATCCGCG
* * *
11979182 AACTTCCCAAAAATCT-CATTTTAACCCTTAAACTTCCAAAAATCACA-TTTGACCTCTA
1 AACTTTCCAAAAAT-TACATTTTAACCCCTAAACTTCCAAAAATTACATTTTGACCTCTA
* *
11979240 AACTTTTCAAAAATCACA--TTAGACCCCTAAACTTCCTAAAAATTACATTTTGACC-CATA
1 AACTTTCCAAAAATTACATTTTA-ACCCCTAAACTTCC-AAAAATTACATTTTGACCTC-TA
11979299 AACTTTCCAAAAATTACATTTTAACCCCTAAACTTCTCAAAAATTACATTTTGACCTCTA
1 AACTTTCCAAAAATTACATTTTAACCCCTAAACTTC-CAAAAATTACATTTTGACCTCTA
* * *
11979359 AACTTCTCAAAAAAAATACATTTTGA-CCCTCAAACTT
1 AACTT-TC-CAAAAATTACATTTTAACCCCT-AAACTT
11979396 TTCGAAACTT
Statistics
Matches: 134, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
56 3 0.02
57 13 0.10
58 24 0.18
59 25 0.19
60 38 0.28
61 11 0.08
62 20 0.15
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (59 bp):
AACTTTCCAAAAATTACATTTTAACCCCTAAACTTCCAAAAATTACATTTTGACCTCTA
Found at i:11985408 original size:30 final size:29
Alignment explanation
Indices: 11985358--11985587 Score: 161
Period size: 29 Copynumber: 7.8 Consensus size: 29
11985348 GGAGATCCCT
*
11985358 GAACTTTCC-AAAATTCCATTTTTAACCTC
1 GAACTTTCCAAAAATTACATTTTTAACC-C
*
11985387 GAACTTTCCAAAAATTACA-TTTTACCCTC
1 GAACTTTCCAAAAATTACATTTTTAACC-C
* * *
11985416 AAATTTTCC-AAAATTCCATTTTTAACCC
1 GAACTTTCCAAAAATTACATTTTTAACCC
* *
11985444 TGAACCTTCCAAAAATTACCA-TTTTACCCCC
1 -GAACTTTCCAAAAATTA-CATTTTTA-ACCC
* *
11985475 GAA-TGTT-TAAAAATTCCATTTTTAACCAC
1 GAACT-TTCCAAAAATTACATTTTTAACC-C
*
11985504 GAACTTTCCAAAAATTACCA-TTTTATCCCC
1 GAACTTTCCAAAAATTA-CATTTTTA-ACCC
* * * *
11985534 GAA-TGTCTAAAAATTCCATTTTTTGACCC
1 GAACTTTCCAAAAATTACA-TTTTTAACCC
*
11985563 TGAACCTTCCAAAAATTACCATTTT
1 -GAACTTTCCAAAAATTA-CATTTT
11985588 ACCCCCGAAT
Statistics
Matches: 156, Mismatches: 27, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
28 15 0.10
29 69 0.44
30 48 0.31
31 22 0.14
32 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
GAACTTTCCAAAAATTACATTTTTAACCC
Found at i:11985409 original size:29 final size:30
Alignment explanation
Indices: 11985358--11985609 Score: 186
Period size: 30 Copynumber: 8.6 Consensus size: 30
11985348 GGAGATCCCT
* *
11985358 GAACTTTCC-AAAATTCCATTTTTAACCTC
1 GAACTTTCCAAAAATTACATTTTTAACCCC
11985387 GAACTTTCCAAAAATTACA-TTTT-ACCCTC
1 GAACTTTCCAAAAATTACATTTTTAACCC-C
* * * *
11985416 AAATTTTCC-AAAATTCCATTTTTAACCCT
1 GAACTTTCCAAAAATTACATTTTTAACCCC
* *
11985445 GAACCTTCCAAAAATTACCA-TTTTACCCCC
1 GAACTTTCCAAAAATTA-CATTTTTAACCCC
* * *
11985475 GAA-TGTT-TAAAAATTCCATTTTTAACCAC
1 GAACT-TTCCAAAAATTACATTTTTAACCCC
*
11985504 GAACTTTCCAAAAATTACCA-TTTTATCCCC
1 GAACTTTCCAAAAATTA-CATTTTTAACCCC
* * * * *
11985534 GAA-TGTCTAAAAATTCCATTTTTTGACCCT
1 GAACTTTCCAAAAATTACA-TTTTTAACCCC
* *
11985564 GAACCTTCCAAAAATTACCA-TTTTACCCCC
1 GAACTTTCCAAAAATTA-CATTTTTAACCCC
*
11985594 GAA-TGTCC-AAAATTAC
1 GAACTTTCCAAAAATTAC
11985610 CGTTTTACCC
Statistics
Matches: 172, Mismatches: 36, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
27 1 0.01
28 22 0.13
29 64 0.37
30 70 0.41
31 13 0.08
32 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACATTTTTAACCCC
Found at i:11985496 original size:59 final size:59
Alignment explanation
Indices: 11985367--11985599 Score: 330
Period size: 59 Copynumber: 3.9 Consensus size: 59
11985357 TGAACTTTCC
* * * *
11985367 AAAATTCCATTTTTAA-CCTCGAACTTTCCAAAAATTA-CATTTTACCCTCAAAT-TTTCC
1 AAAATTCCATTTTTAACCCT-GAACCTTCCAAAAATTACCATTTTACCCCCGAATGTTT-A
11985425 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTTTA
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTTTA
* * *
11985484 AAAATTCCATTTTTAACCAC-GAACTTTCCAAAAATTACCATTTTATCCCCGAATGTCTA
1 AAAATTCCATTTTTAACC-CTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTTTA
*
11985543 AAAATTCCATTTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGT
1 AAAATTCCA-TTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGT
11985600 CCAAAATTAC
Statistics
Matches: 159, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
58 32 0.20
59 81 0.51
60 46 0.29
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTTTA
Found at i:11985635 original size:29 final size:29
Alignment explanation
Indices: 11985367--11985643 Score: 131
Period size: 29 Copynumber: 9.5 Consensus size: 29
11985357 TGAACTTTCC
* * *
11985367 AAAATT-CCATTTTTAACCTCGAACTTTCCA
1 AAAATTACCA-TTTTACCCCCGAAC-ATCCA
* * **
11985397 AAAATTA-CATTTTACCCTCAAATTTTCC-
1 AAAATTACCATTTTACCCCCGAA-CATCCA
* * *
11985425 AAAATT-CCATTTTTAACCCTGAACCTTCCA
1 AAAATTACCA-TTTTACCCCCGAA-CATCCA
** **
11985455 AAAATTACCATTTTACCCCCGAATGTTTA
1 AAAATTACCATTTTACCCCCGAACATCCA
* * *
11985484 AAAATT-CCATTTTTAACCACGAACTTTCCA
1 AAAATTACCA-TTTTACCCCCGAAC-ATCCA
* ** *
11985514 AAAATTACCATTTTATCCCCGAATGTCTA
1 AAAATTACCATTTTACCCCCGAACATCCA
* *
11985543 AAAATT-CCATTTTTTGA-CCCTGAACCTTCCA
1 AAAATTACCA--TTTT-ACCCCCGAA-CATCCA
**
11985574 AAAATTACCATTTTACCCCCGAATGTCC-
1 AAAATTACCATTTTACCCCCGAACATCCA
* **
11985602 AAAATTACCGTTTTACCCCCGGGCATCCA
1 AAAATTACCATTTTACCCCCGAACATCCA
*
11985631 AAAATCA-CATTTT
1 AAAATTACCATTTT
11985644 GACTCCGTCT
Statistics
Matches: 191, Mismatches: 40, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
28 42 0.22
29 66 0.35
30 64 0.34
31 16 0.08
32 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAACATCCA
Found at i:11992563 original size:18 final size:19
Alignment explanation
Indices: 11992524--11992574 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
11992514 TTTCAAATAC
11992524 AATTCAAAATAAATTTCAAA
1 AATTCAAAAT-AATTTCAAA
* *
11992544 AATTCAAAATATTTATAAAAA
1 AATTCAAAATAATT-T-CAAA
11992565 AATTCAAAAT
1 AATTCAAAAT
11992575 TTATATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 11 0.41
21 13 0.48
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTCAAAATAATTTCAAA
Found at i:11998960 original size:94 final size:94
Alignment explanation
Indices: 11998799--11998986 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
11998789 CCCGTCATGC
** *
11998799 ATTTAAGAGTGTTGAGTTTGAAGGTGATGGTAAGATCGGAGTATTGTAACAATCAACTTTGTTGA
1 ATTTAAGAGTGTTGACCTTGAAGGTGATGGTAAGATCGAAGTATTGTAACAATCAACTTTGTTGA
11998864 AGGTTAGTTAGTTCTTTAATTTCAAGTTT
66 AGGTTAGTTAGTTCTTTAATTTCAAGTTT
*
11998893 ATTTAAGAGTGTTGACCTTGAAGGTGATGGTAAGCTCGAAGTATTGTAACAATCAACTTTGTTGA
1 ATTTAAGAGTGTTGACCTTGAAGGTGATGGTAAGATCGAAGTATTGTAACAATCAACTTTGTTGA
11998958 AGGTTAGTTAGTTCTTTAATTTCAAGTTT
66 AGGTTAGTTAGTTCTTTAATTTCAAGTTT
11998987 TTTTTAGTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (94 bp):
ATTTAAGAGTGTTGACCTTGAAGGTGATGGTAAGATCGAAGTATTGTAACAATCAACTTTGTTGA
AGGTTAGTTAGTTCTTTAATTTCAAGTTT
Found at i:12000990 original size:29 final size:28
Alignment explanation
Indices: 12000896--12001382 Score: 309
Period size: 30 Copynumber: 16.5 Consensus size: 28
12000886 AAAGGGATTG
* * *
12000896 AAAATG-AAGTTTCAAAGAGTTCGGGGTT
1 AAAATGTAATTTTGAAA-AGTTTGGGGTT
** *
12000924 AAAACATAATTTTGGAAAGTTTTAGGGGTT
1 AAAATGTAATTTTGAAAAG-TTT-GGGGTT
* *
12000954 AAAAATGTCATTTTGAAAAAGTTTGGGGTG
1 -AAAATGTAATTTTG-AAAAGTTTGGGGTT
* * * *
12000984 AAAATGTGATTTTTGAGAAGTTTGAGG-C
1 AAAATGT-AATTTTGAAAAGTTTGGGGTT
* * *
12001012 AAAAT-TATGCTTTTTG-GAAGTTTGGGG-G
1 AAAATGTA---ATTTTGAAAAGTTTGGGGTT
* *
12001040 AAAATGTAATTTTTGAAAAGTTTAGGGTC
1 AAAATGTAA-TTTTGAAAAGTTTGGGGTT
** **
12001069 AAAATAAAATTTTGGAAAAGTTTAATGGTT
1 AAAATGTAATTTT-GAAAAGTTT-GGGGTT
12001099 AAAATGTAATTTTGAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTG-AAAAGTTT-GGGGTT
*
12001129 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
1 AAAATGTAATTTT-GAAAAGTTTG-GGGTT
* * * *
12001159 AAAATGTAGTTTTGGAAAAAAATTAGGGGTC
1 AAAATGTAATTTT-G--AAAAGTTTGGGGTT
*
12001190 AAAATTTAATTTTTGAAAAGTTTAGGGGTT
1 AAAATGTAA-TTTTGAAAAGTTT-GGGGTT
**
12001220 AAAATGTAATTTTTGAAAAGTTTGGCAATT
1 AAAATGTAA-TTTTGAAAAGTTTGG-GGTT
* *
12001250 AAAATGTAATTTTTGAGAAGTTTGGGGGT
1 AAAATGTAA-TTTTGAAAAGTTTGGGGTT
* *
12001279 CAAATGTAATTCTTGAGAAGTTTTAGGGGTT
1 AAAATGTAATT-TTGAAAAG-TTT-GGGGTT
* * *
12001310 AAAATGTTATTTTTAAGAAGTTCGGAGGTT
1 AAAATGTAATTTTGAA-AAGTTTGG-GGTT
* *
12001340 AAAATATAATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTT-GAAAAGTTT-GGGGTT
*
12001370 AAAATGTGATTTT
1 AAAATGTAATTTT
12001383 TAAAGAGAAC
Statistics
Matches: 369, Mismatches: 60, Indels: 58
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 41 0.11
29 79 0.21
30 179 0.49
31 48 0.13
32 15 0.04
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTGAAAAGTTTGGGGTT
Found at i:12002374 original size:28 final size:30
Alignment explanation
Indices: 12002302--12002374 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
12002292 TTACTCCGAA
12002302 ATAATAAATAAATAAAGTCAACAAATATAT
1 ATAATAAATAAATAAAGTCAACAAATATAT
* * * *
12002332 ATAATATAATGAATAAATATAAACATATATAT
1 ATAATA-AATAAATAAA-GTCAACAAATATAT
12002364 ATAAATAAATA
1 AT-AATAAATA
12002375 TACCTTCAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.17
31 9 0.26
32 16 0.46
33 4 0.11
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (30 bp):
ATAATAAATAAATAAAGTCAACAAATATAT
Found at i:12003429 original size:39 final size:39
Alignment explanation
Indices: 12003384--12004144 Score: 334
Period size: 39 Copynumber: 19.5 Consensus size: 39
12003374 AATCTACCTC
* * *
12003384 AAGCTCGGGGCAAAAGATTGGCTGATGATGATCTTCCCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* * * *
12003423 AGGCTCGGGGTAAGAGATTGGTTAATGATGATCTGCCCC
1 AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* * * ** * * *
12003462 AAGCTCGAGGTAAAAGATCGAATGGTTG-TAATCTGCCCC
1 AAGCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCT
* *
12003501 AAGCTTGGCGTAAGAGATTGGCTGATGATGATCTGCCCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
** * * * * * **
12003540 CGGCTTGGGGTAAAAGATTGGATGCCT--TCAAT-TTACCT
1 AAGCTCGGGGTAAGAGATTGGCTG-ATGAT-GATCTGCCCT
* * * *
12003578 CAAGTTTGGGTTAAGAGATTGGCTGATGATGATCAG-CCT
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
12003617 CAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCC-
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCT
* * ** * * *
12003657 AAGCTCGGGGTAAAAGATCGAATGGCTGA-AATCT-ACCT
1 AAGCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCT
*
12003695 CAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* * ** *
12003735 AGGCTCGGGGTAAGAGATCGAATG--GCTGCAATCTG-CCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGATG--ATCTGCCCT
* * * *
12003773 CAGGCTCGGGGTAAGAGATTGGATGATGATG-TACTACCCC
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGAT-CTGCCCT
* * * * * * *
12003813 AAACTCGAGGCAAAAGA-T--CAGATGACTTCAATCT-ACCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGA--T-GATCTGCCCT
* * *
12003851 CAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCC
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* * ** * *
12003891 AAGCTCGGGGTAAAATATTGAATG--GTTGCAATCT-ACCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGATG--ATCTGCCCT
* * *
12003929 CAAGCTTGGTGTAAGAGATTGGCTGATGATGAT-T-CGTCT
1 -AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGC-CCT
* * * ** * * *
12003968 CAGGCTCGGGATAAGAGATCGAATGGCTGA-AATCTACCCT
1 -AAGCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCT
* * *
12004008 AGGCTCGGGGTAAGAGATTGGCTTATGATGATCTACCC-
1 AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* *
12004046 AAGCTCGGGGTAAAAGATCAGATGGCT--TCA--ATCTGCCCT
1 AAGCTCGGGGTAAGAGAT----TGGCTGATGATGATCTGCCCT
** *
12004085 AAGCTCGGGGTAAGAGATTGATTGATGGTGATCTGCCCT
1 AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
* * *
12004124 AGGCTCGAGGTAAAAGATTGG
1 AAGCTCGGGGTAAGAGATTGG
12004145 ATGACTTCAA
Statistics
Matches: 533, Mismatches: 139, Indels: 100
0.69 0.18 0.13
Matches are distributed among these distances:
35 3 0.01
36 5 0.01
37 9 0.02
38 50 0.09
39 419 0.79
40 27 0.05
41 9 0.02
42 11 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCT
Found at i:12003519 original size:117 final size:115
Alignment explanation
Indices: 12003298--12003560 Score: 319
Period size: 117 Copynumber: 2.3 Consensus size: 115
12003288 GATGGTTGCA
* * * * * *
12003298 ATCTGCCCCTGGCTCGGGATAAGAGATTAGCTGATGGTGTTCTGCCTAAGCTCGAGGTAAAAGAT
1 ATCTG-CCCTGGCTCGGGGTAAGAGATTGGCTAATGATGATCTGCCCAAGCTCGAGGTAAAAGAT
* *
12003363 CGAATGGCTACAATCTACCTCAAGCTCGGGGCAAAAGATTGGCTGATGATG
65 CGAATGGCTACAATCTACCCCAAGCTCGGCGCAAAAGATTGGCTGATGATG
* *
12003414 ATCTTCCCTAGGCTCGGGGTAAGAGATTGGTTAATGATGATCTGCCCCAAGCTCGAGGTAAAAGA
1 ATCTGCCCT-GGCTCGGGGTAAGAGATTGGCTAATGATGATCTG-CCCAAGCTCGAGGTAAAAGA
* ** * * * *
12003479 TCGAATGGTTGTAATCTGCCCCAAGCTTGGCGTAAGAGATTGGCTGATGATG
64 TCGAATGGCTACAATCTACCCCAAGCTCGGCGCAAAAGATTGGCTGATGATG
* *
12003531 ATCTGCCCTCGGCTTGGGGTAAAAGATTGG
1 ATCTGCCCT-GGCTCGGGGTAAGAGATTGG
12003561 ATGCCTTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
115 4 0.03
116 32 0.26
117 88 0.71
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (115 bp):
ATCTGCCCTGGCTCGGGGTAAGAGATTGGCTAATGATGATCTGCCCAAGCTCGAGGTAAAAGATC
GAATGGCTACAATCTACCCCAAGCTCGGCGCAAAAGATTGGCTGATGATG
Found at i:12003749 original size:156 final size:155
Alignment explanation
Indices: 12003309--12004141 Score: 633
Period size: 156 Copynumber: 5.4 Consensus size: 155
12003299 TCTGCCCCTG
* * * * * *
12003309 GCTCGGGATAAGAGATTAGCTGATGGTGTTCTG-CCTAAGCTCGAGGTAAAAGATCGAATGGCT-
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTG
* * * * *
12003372 ACAATCTACCTCAAGCTCGGGGCAAAAGATTGGCTGATGATGATCTTCCCTAGGCTCGGGGTAAG
66 A-AATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAG
* *
12003437 AGATTGGTTAAT-GATG-ATCTGCCCCAA
130 AGATT-G--AATGGATGAATCAGCCTCAA
* * * ** * * * * * * ** *
12003464 GCTCGAGGTAAAAGATCGAATGGTTG-TAATCTGCCCCAAGCTTGGCGTAAGAGATTGGCT-GAT
1 GCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCT
* * * * * * * * * *
12003527 GATGATCTGCCCTC-GGCTTGGGGTAAAAGATTGGATGCCT--TCAATTTA-CCTCAAGTTTGGG
65 GA-AATCT-ACCTCAGGCTCGGGGTAAGAGATTGGCTG-ATGAT-GATCTACCCT-AAGCTCGGG
* **
12003588 TTAAGAGATTGGCT-GATGATGATCAGCCTCAA
125 GTAAGAGATTGAATGGATGA--ATCAGCCTCAA
*
12003620 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCCAAGCTCGGGGTAAAAGATCGAATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTG
* *
12003685 AAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAGA
66 AAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAGA
* * * *
12003750 GATCGAATGGCTGCAATCTGCCTCAG
131 GATTGAATGGATG-AATCAGCCTCAA
* * * * * *
12003776 GCTCGGGGTAAGAGATTGGATGATGATG-TACTACCCCAAACTCGAGGCAAAAGATC-AGATGAC
1 GCTCGGGGTAAGAGATTGGCTGATGATGAT-CTGCCCCAAGCTCGGGGTAAAAGATCGA-ATGGC
** *
12003839 TTCAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGCTCGGGGTAA
64 TGAAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAA
* * *
12003904 AATATTGAATGGTTGCAATCTA-CCTCAA
129 GAGATTGAATGGATG-AATC-AGCCTCAA
* * * * * * *
12003932 GCTTGGTGTAAGAGATTGGCTGATGATGAT-TCGTCTCAGGCTCGGGATAAGAGATCGAATGGCT
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCT-GCCCCAAGCTCGGGGTAAAAGATCGAATGGCT
*
12003996 GAAATCTACC-CTAGGCTCGGGGTAAGAGATTGGCTTATGATGATCTACCC-AAGCTCGGGGTAA
65 GAAATCTACCTC-AGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAA
* * * * *
12004059 AAGA-TCAGATGGCTTCAATCTGCC-CTAA
129 GAGATTGA-ATGG-ATGAATCAGCCTC-AA
** * * * *
12004087 GCTCGGGGTAAGAGATTGATTGATGGTGATCTGCCCTAGGCTCGAGGTAAAAGAT
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGAT
12004142 TGGATGACTT
Statistics
Matches: 527, Mismatches: 121, Indels: 60
0.74 0.17 0.08
Matches are distributed among these distances:
153 5 0.01
154 3 0.01
155 108 0.20
156 392 0.74
157 18 0.03
158 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (155 bp):
GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTG
AAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAGA
GATTGAATGGATGAATCAGCCTCAA
Found at i:12004158 original size:39 final size:38
Alignment explanation
Indices: 12004038--12004180 Score: 132
Period size: 39 Copynumber: 3.7 Consensus size: 38
12004028 GCTTATGATG
* * * *
12004038 ATCTACCC-AAGCTCGGGGTAAAAGATCAGATGGCTTCA
1 ATCTGCCCTAAGCTCGAGGTAAAAGAT-TGATGACTTCA
* * *
12004076 ATCTGCCCTAAGCTCGGGGTAAGAGATTGATTGA-TGGT-G
1 ATCTGCCCTAAGCTCGAGGTAAAAGATTGA-TGACT--TCA
*
12004115 ATCTGCCCTAGGCTCGAGGTAAAAGATTGGATGACTTCA
1 ATCTGCCCTAAGCTCGAGGTAAAAGATT-GATGACTTCA
12004154 ATCTG-CCTCAAGCTCGAGGTAAAAGAT
1 ATCTGCCCT-AAGCTCGAGGTAAAAGAT
12004181 CGAAATCTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
38 14 0.16
39 69 0.79
40 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (38 bp):
ATCTGCCCTAAGCTCGAGGTAAAAGATTGATGACTTCA
Found at i:12004167 original size:78 final size:78
Alignment explanation
Indices: 12003614--12004180 Score: 596
Period size: 78 Copynumber: 7.3 Consensus size: 78
12003604 TGATGATCAG
*
12003614 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCC-AAGCTCGGGGTAAAAGATCGA
1 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCT-ACCCTAAGCTCGGGGTAAAAGATCGA
**
12003678 ATGGCTGAAATCTA
65 ATGGCTTCAATCTA
* * * *
12003692 CCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAA
1 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAAAGATCGAA
* *
12003757 TGGCTGCAATCTG
66 TGGCTTCAATCTA
* * * * * *
12003770 CCTCAGGCTCGGGGTAAGAGATTGGATGATGATG-TACTACCCCAAACTCGAGGCAAAAGATC-A
1 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGAT-CTACCCTAAGCTCGGGGTAAAAGATCGA
*
12003833 GATGACTTCAATCTA
65 -ATGGCTTCAATCTA
* * * *
12003848 CCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGCTCGGGGTAAAATATTGAA
1 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAAAGATCGAA
12003913 TGG-TTGCAATCTA
66 TGGCTT-CAATCTA
* * * * * *
12003926 CCTCAAGCTTGGTGTAAGAGATTGGCTGATGATGAT-T-CGTCTCAGGCTCGGGATAAGAGATCG
1 CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTAC-CCT-AAGCTCGGGGTAAAAGATCG
**
12003989 AATGGCTGAAATCTA
64 AATGGCTTCAATCTA
* *
12004004 CC-CTAGGCTCGGGGTAAGAGATTGGCTTATGATGATCTACCC-AAGCTCGGGGTAAAAGATC-A
1 CCTC-AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAAAGATCGA
*
12004066 GATGGCTTCAATCTG
65 -ATGGCTTCAATCTA
** * * * * * *
12004081 CC-CTAAGCTCGGGGTAAGAGATTGATTGATGGTGATCTGCCCTAGGCTCGAGGTAAAAGATTGG
1 CCTC-AAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAAAGATCGA
* *
12004145 ATGACTTCAATCTG
65 ATGGCTTCAATCTA
* *
12004159 CCTCAAGCTCGAGGTAAAAGAT
1 CCTCAAGCTCGGGGTAAGAGAT
12004181 CGAAATCTTC
Statistics
Matches: 413, Mismatches: 60, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
76 2 0.00
77 73 0.18
78 331 0.80
79 6 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
CCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCTAAGCTCGGGGTAAAAGATCGAA
TGGCTTCAATCTA
Found at i:12004263 original size:41 final size:40
Alignment explanation
Indices: 12004171--12004267 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 40
12004161 TCAAGCTCGA
* *
12004171 GGTAAAAGATCGAAATCTTCATTCTGTCCTTCTTGATTAAG
1 GGTAAAAGA-CTAAATCTTCAATCTGTCCTTCTTGATTAAG
*
12004212 CGTAAAAGACTATAATCTTCAATCTGTCCTTCTTGATTAAG
1 GGTAAAAGACTA-AATCTTCAATCTGTCCTTCTTGATTAAG
12004253 GGTAAAAGACTAAAT
1 GGTAAAAGACTAAAT
12004268 GATAATGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (40 bp):
GGTAAAAGACTAAATCTTCAATCTGTCCTTCTTGATTAAG
Found at i:12004482 original size:50 final size:50
Alignment explanation
Indices: 12004421--12004760 Score: 257
Period size: 50 Copynumber: 6.9 Consensus size: 50
12004411 CCATCTTGTT
* *
12004421 TTCTAAGGTACCAAGTTCGCCGTTGCGACCTCAACCTTTCCCTTCATATC
1 TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
* ** * * *
12004471 TTCTAAGGTACCAGGTTTACCGTTGCAGCCTCAACCTTTCCCTTAAAATC
1 TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
* * ** * * *
12004521 TTC-ATGGTATCGGGTTCGCCATTACGGCCTCAACCTTTCCCATCACAT-
1 TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * * * *
12004569 TTC-ATGGTA-CAGAATTCGTCGTTGCGGCCTCAATCTTTCCCATCATATC
1 TTCTAAGGTACCA-AGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
* ** ** * *
12004618 TTCTGAGGTACTGAGTTCGCTATTGTGGCCTCAACCTTTCCCGTCACATC
1 TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * *
12004668 TTTTAAGGTACC-GGATTCGCTGTTGCGGTCTCAATCC-TTCCCTTCA-A-C
1 TTCTAAGGTACCAAG-TTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCACATC
* * ** *
12004716 TTC-ATGGTACCGAGTTCGCTATTGCGGCCTTAACCTTTCCCTTCA
1 TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA
12004761 AATATGTAAA
Statistics
Matches: 230, Mismatches: 52, Indels: 19
0.76 0.17 0.06
Matches are distributed among these distances:
46 2 0.01
47 33 0.14
48 42 0.18
49 39 0.17
50 112 0.49
51 2 0.01
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.34
Consensus pattern (50 bp):
TTCTAAGGTACCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATC
Found at i:12004619 original size:97 final size:95
Alignment explanation
Indices: 12004434--12004756 Score: 278
Period size: 97 Copynumber: 3.3 Consensus size: 95
12004424 TAAGGTACCA
** * * * **
12004434 AGTTCGCCGTTGCGACCTCAACCTTTCCCTTCATA-TCTTCTAAGGTACCAGGTTTAC-CGTTGC
1 AGTTCGCTATTGCGGCCTCAACCTTTCCCATCACACT-TTC-AAGGTA-CAGAATT-CGCGTTGC
* * *
12004497 AGCCTCAACCTTTCCCTTAAAATCTTCATGGTATCG
62 GGCCTCAATCTTTCCCTT-CAATCTTCATGGTA-CG
* * * *
12004533 GGTTCGCCATTACGGCCTCAACCTTTCCCATCACA-TTTCATGGTACAGAATTCGTCGTTGCGGC
1 AGTTCGCTATTGCGGCCTCAACCTTTCCCATCACACTTTCAAGGTACAGAATTCG-CGTTGCGGC
*
12004597 CTCAATCTTTCCCATCATATCTTC-TGAGGTACTG
65 CTCAATCTTTCCCTTCA-ATCTTCAT--GGTAC-G
* * * * *
12004631 AGTTCGCTATTGTGGCCTCAACCTTTCCCGTCACATCTTTTAAGGTACCGGATTCGCTGTTGCGG
1 AGTTCGCTATTGCGGCCTCAACCTTTCCCATCACA-CTTTCAAGGTACAGAATTCGC-GTTGCGG
* *
12004696 TCTCAATCCTTCCCTTCAA-CTTCATGGTACCG
64 CCTCAATCTTTCCCTTCAATCTTCATGGTA-CG
*
12004728 AGTTCGCTATTGCGGCCTTAACCTTTCCC
1 AGTTCGCTATTGCGGCCTCAACCTTTCCC
12004757 TTCAAATATG
Statistics
Matches: 186, Mismatches: 27, Indels: 24
0.78 0.11 0.10
Matches are distributed among these distances:
95 1 0.01
96 7 0.04
97 65 0.35
98 43 0.23
99 33 0.18
100 37 0.20
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.33
Consensus pattern (95 bp):
AGTTCGCTATTGCGGCCTCAACCTTTCCCATCACACTTTCAAGGTACAGAATTCGCGTTGCGGCC
TCAATCTTTCCCTTCAATCTTCATGGTACG
Found at i:12005692 original size:7 final size:6
Alignment explanation
Indices: 12005665--12005734 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
12005655 CGACCTCTCC
* *
12005665 TTTTCTT TTTCTCAT TTTTCT ATTTTCT TTTTCCT TTTCCT TTTTCT CTTT-T
1 TTTTC-T TTT-TC-T TTTTCT -TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT
*
12005717 TTTTCT TTAT-T TTTTCT T
1 TTTTCT TTTTCT TTTTCT T
12005735 CATTGAATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
5 8 0.16
6 21 0.41
7 16 0.31
8 6 0.12
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:12005730 original size:34 final size:34
Alignment explanation
Indices: 12005662--12005730 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
12005652 CCTCGACCTC
*
12005662 TCCTTTTCTTTTTCTCATTTTTCTATTTTCTTTT
1 TCCTTTTCTTTTTCTCATTTTTCTATTTTATTTT
*
12005696 TCCTTTTCCTTTTTCTC-TTTTT-TTTCTTTATTTT
1 TCCTTTT-CTTTTTCTCATTTTTCTAT-TTTATTTT
12005730 T
1 T
12005731 TCTTCATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.06
34 20 0.65
35 9 0.29
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.75
Consensus pattern (34 bp):
TCCTTTTCTTTTTCTCATTTTTCTATTTTATTTT
Found at i:12010548 original size:30 final size:30
Alignment explanation
Indices: 12010514--12010834 Score: 310
Period size: 30 Copynumber: 10.8 Consensus size: 30
12010504 TTTCGAAGAG
* * *
12010514 TTAGGGGTAAAAATGTGATTTTTGAGAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * * *
12010544 TTA-GGATAAAAATGTGATTTTTTG-GAAGT
1 TTAGGGGTTAAAATGT-AATTTTTGAAAAGT
** *
12010573 TT-GGGGGCAAAATTTAATTTTTGAAAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * *
12010602 TTTGGGGCTAAAATGTAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * *
12010632 TTAAGGGTTAAAATGTAATTTTAGAAAAAT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * *
12010662 TTAGGGGTCAAAATGTAATATTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * *
12010692 TT-GGTAGTTAAAATGTAAATTTTGAGAAGT
1 TTAGG-GGTTAAAATGTAATTTTTGAAAAGT
* *
12010722 TCTA-GGGTTAAAATGTATTTTTTGAGAAGT
1 T-TAGGGGTTAAAATGTAATTTTTGAAAAGT
*
12010752 TTAGGGGTTAAAATGTAATTTTTGAGAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* *
12010782 TTAAGGGTTAAAATGTAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
* * *
12010812 TTAAGGGTTAAAATATGATTTTT
1 TTAGGGGTTAAAATGTAATTTTT
12010835 AAAGAGAACA
Statistics
Matches: 244, Mismatches: 39, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
28 7 0.03
29 36 0.15
30 199 0.82
31 2 0.01
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (30 bp):
TTAGGGGTTAAAATGTAATTTTTGAAAAGT
Found at i:12011562 original size:16 final size:16
Alignment explanation
Indices: 12011543--12011573 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12011533 TTTTATTTGA
12011543 AATCTGTTTTTTTTAC
1 AATCTGTTTTTTTTAC
12011559 AATCTGTTTTTTTTA
1 AATCTGTTTTTTTTA
12011574 TTCTAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (16 bp):
AATCTGTTTTTTTTAC
Found at i:12013072 original size:26 final size:26
Alignment explanation
Indices: 12013043--12013099 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
12013033 AATGAAAGCA
*
12013043 GTTATCAGCAGTTGTTGGTTAAGTTG
1 GTTATCAGCAATTGTTGGTTAAGTTG
*
12013069 GTTAGCAGCAATTGTTGGTTAAGTTG
1 GTTATCAGCAATTGTTGGTTAAGTTG
12013095 GTTAT
1 GTTAT
12013100 TAGAAGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.42
Consensus pattern (26 bp):
GTTATCAGCAATTGTTGGTTAAGTTG
Found at i:12014383 original size:3 final size:3
Alignment explanation
Indices: 12014375--12014413 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12014365 CTTAATTGTT
12014375 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
12014414 AATATCATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:12016591 original size:39 final size:39
Alignment explanation
Indices: 12016548--12016679 Score: 158
Period size: 39 Copynumber: 3.4 Consensus size: 39
12016538 GCTCTAGTAG
* * *
12016548 TGTTTATAGTGTCAGTACAACTGAGTTATAGTCGTGCGA
1 TGTTTACAGTGTCACTACAACTGAGTTATAATCGTGCGA
* * * * *
12016587 TGTTTACAGTGTCACTACTACAGAGTTATAACCATGTGA
1 TGTTTACAGTGTCACTACAACTGAGTTATAATCGTGCGA
*
12016626 TGTTTACAGTGTCACTA-ATACTGAGTTATAATCGTACGA
1 TGTTTACAGTGTCACTACA-ACTGAGTTATAATCGTGCGA
*
12016665 TATTTACAGTGTCAC
1 TGTTTACAGTGTCAC
12016680 CGTCAAATCA
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (39 bp):
TGTTTACAGTGTCACTACAACTGAGTTATAATCGTGCGA
Found at i:12016714 original size:39 final size:39
Alignment explanation
Indices: 12016667--12016845 Score: 164
Period size: 39 Copynumber: 4.6 Consensus size: 39
12016657 TCGTACGATA
* * **
12016667 TTTACAGTGTCACCGTCAAATCAAGATAGTATCGCAGTG
1 TTTACAGTGTCACCGTCAATTCAAGACAGTATTACAGTG
* *** *
12016706 TTTGCAGTGTCACTACCAATTC-AGTACAGTATTACGGTG
1 TTTACAGTGTCACCGTCAATTCAAG-ACAGTATTACAGTG
* * * *
12016745 TTTACAGTGTCACCGTCAATTCAGTGA-TGCATTGCAGTG
1 TTTACAGTGTCACCGTCAATTCA-AGACAGTATTACAGTG
* * * *
12016784 TTTACAGTGTCACTGCCATTTCAATACAGTATTACAGTG
1 TTTACAGTGTCACCGTCAATTCAAGACAGTATTACAGTG
*
12016823 TTTACAGTGTCACCGTCATTTCA
1 TTTACAGTGTCACCGTCAATTCA
12016846 GTGTTGAAAT
Statistics
Matches: 108, Mismatches: 28, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
38 3 0.03
39 103 0.95
40 1 0.01
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (39 bp):
TTTACAGTGTCACCGTCAATTCAAGACAGTATTACAGTG
Found at i:12016846 original size:78 final size:79
Alignment explanation
Indices: 12016667--12016848 Score: 260
Period size: 78 Copynumber: 2.3 Consensus size: 79
12016657 TCGTACGATA
* * * * *
12016667 TTTACAGTGTCACCGTCAAATCA-AGATAGTATCGCAGTGTTTGCAGTGTCACTACCAATTCAGT
1 TTTACAGTGTCACCGTCAATTCAGTGATAGCATCGCAGTGTTTACAGTGTCACTACCAATTCAAT
*
12016731 ACAGTATTACGGTG
66 ACAGTATTACAGTG
* * *
12016745 TTTACAGTGTCACCGTCAATTCAGTGAT-GCATTGCAGTGTTTACAGTGTCACTGCCATTTCAAT
1 TTTACAGTGTCACCGTCAATTCAGTGATAGCATCGCAGTGTTTACAGTGTCACTACCAATTCAAT
12016809 ACAGTATTACAGTG
66 ACAGTATTACAGTG
*
12016823 TTTACAGTGTCACCGTCATTTCAGTG
1 TTTACAGTGTCACCGTCAATTCAGTG
12016849 TTGAAATCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
78 90 0.97
79 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (79 bp):
TTTACAGTGTCACCGTCAATTCAGTGATAGCATCGCAGTGTTTACAGTGTCACTACCAATTCAAT
ACAGTATTACAGTG
Found at i:12017158 original size:64 final size:63
Alignment explanation
Indices: 12017075--12017288 Score: 257
Period size: 64 Copynumber: 3.3 Consensus size: 63
12017065 GTCAAACATT
* * * * *
12017075 CACACGGTCTAGCACACACGCCCGTGTCCCCAGGCCGTGTAACTCACTGTTTCTTACTTATATGA
1 CACACGGTCTAG-ACACACGCCCATGGCCCCAGACCGTGTAACTCACTATTTCTTA-TTGTATGA
* * * *
12017140 CACATGGTCTAGACACACGCACATGGCCCCAGATCGTGTAACTCGCTATTTCTTATTGTATGA
1 CACACGGTCTAGACACACGCCCATGGCCCCAGACCGTGTAACTCACTATTTCTTATTGTATGA
** * * *
12017203 CACACGGTCTAGACACACGCTTATGGCCCCACACCATATAACTCACTATTTCTTATTTGTATGA
1 CACACGGTCTAGACACACGCCCATGGCCCCAGACCGTGTAACTCACTATTTCTTA-TTGTATGA
**
12017267 CACACGACCTAGACACACGCCC
1 CACACGGTCTAGACACACGCCC
12017289 GTGTGTCCAC
Statistics
Matches: 127, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
63 54 0.43
64 62 0.49
65 11 0.09
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (63 bp):
CACACGGTCTAGACACACGCCCATGGCCCCAGACCGTGTAACTCACTATTTCTTATTGTATGA
Found at i:12019152 original size:24 final size:24
Alignment explanation
Indices: 12019124--12019176 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12019114 GGTGGAAAAT
12019124 TTTATATAAAAAATTTACAAATAA
1 TTTATATAAAAAATTTACAAATAA
* * *
12019148 TTTATATTAAAATTTTATAAATAA
1 TTTATATAAAAAATTTACAAATAA
*
12019172 CTTAT
1 TTTAT
12019177 TAATGTGTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTATATAAAAAATTTACAAATAA
Found at i:12029193 original size:30 final size:29
Alignment explanation
Indices: 12029159--12029258 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
12029149 AAATAGATCT
12029159 CTTAAAAGTTGGTAAAAAAAATTTTGAGCC
1 CTTAAAAGTTGGTAAAAAAAATTTTG-GCC
* *
12029189 CTTAAAAGCT--AAAAATAATAATTTTTGGGGCC
1 CTTAAAAGTTGGTAAAA-AA-AA-TTTT--GGCC
* *
12029221 ACTTAAAAATTGGTAAAAAAAAATTTGGCC
1 -CTTAAAAGTTGGTAAAAAAAATTTTGGCC
*
12029251 TTTAAAAG
1 CTTAAAAG
12029259 ATTAATTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
28 4 0.07
29 8 0.15
30 15 0.28
31 4 0.07
32 6 0.11
33 11 0.20
34 2 0.04
35 4 0.07
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (29 bp):
CTTAAAAGTTGGTAAAAAAAATTTTGGCC
Found at i:12031691 original size:5 final size:5
Alignment explanation
Indices: 12031681--12031709 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12031671 CCAATAGAAC
12031681 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
12031710 AAGCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:12032439 original size:64 final size:64
Alignment explanation
Indices: 12032360--12032487 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
12032350 CTGTTTCAAA
12032360 CCTAAATTCCAAGCTACTTGGAAGTCCTCAAGTGCACCCCAAAGCTCAGCATTAATAACAGAGC
1 CCTAAATTCCAAGCTACTTGGAAGTCCTCAAGTGCACCCCAAAGCTCAGCATTAATAACAGAGC
12032424 CCTAAATTCCAAGCTACTTGGAAGTCCTCAAGTGCACCCCAAAGCTCAGCATTAATAACAGAGC
1 CCTAAATTCCAAGCTACTTGGAAGTCCTCAAGTGCACCCCAAAGCTCAGCATTAATAACAGAGC
12032488 ATGATCCAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (64 bp):
CCTAAATTCCAAGCTACTTGGAAGTCCTCAAGTGCACCCCAAAGCTCAGCATTAATAACAGAGC
Found at i:12035775 original size:2 final size:2
Alignment explanation
Indices: 12035770--12035813 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
12035760 CTTAATTTTT
* * *
12035770 TA TA TA TA TA TA TA TA TA TA TT TA TA T- TT TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12035811 TA T
1 TA T
12035814 TTAAACTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:12035813 original size:17 final size:17
Alignment explanation
Indices: 12035782--12035815 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12035772 TATATATATA
**
12035782 TATATATATTTATATTT
1 TATATATATAAATATTT
12035799 TATATATATAAATATTT
1 TATATATATAAATATTT
12035816 AAACTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATATAAATATTT
Found at i:12037545 original size:58 final size:58
Alignment explanation
Indices: 12037464--12037580 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
12037454 TACAACCTTA
12037464 TTTTGCGAGGTATTTTTACGAACTCGCGTTGCTATCTTCTCGCGATCTGCCTTATACT
1 TTTTGCGAGGTATTTTTACGAACTCGCGTTGCTATCTTCTCGCGATCTGCCTTATACT
*
12037522 TTTTGCGAGGTATTTTTACGAACTCGTGTTGCTATCTTCTCGCGATCTGCCTTATACT
1 TTTTGCGAGGTATTTTTACGAACTCGCGTTGCTATCTTCTCGCGATCTGCCTTATACT
12037580 T
1 T
12037581 AATCTTCGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (58 bp):
TTTTGCGAGGTATTTTTACGAACTCGCGTTGCTATCTTCTCGCGATCTGCCTTATACT
Found at i:12040902 original size:19 final size:21
Alignment explanation
Indices: 12040861--12040911 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12040851 ATTATAAACT
* *
12040861 TAAAAAGTCAAAAATGATATA
1 TAAAAATTAAAAAATGATATA
*
12040882 TAAAATTTAAAAAATG-T-TA
1 TAAAAATTAAAAAATGATATA
12040901 TAAAAATTAAA
1 TAAAAATTAAA
12040912 GAGGTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.46
20 1 0.04
21 13 0.50
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (21 bp):
TAAAAATTAAAAAATGATATA
Found at i:12049883 original size:15 final size:16
Alignment explanation
Indices: 12049845--12049886 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12049835 AAACTAAAAG
12049845 AATTAAATTAAATTAT
1 AATTAAATTAAATTAT
12049861 AA--ACAATTAAATT-T
1 AATTA-AATTAAATTAT
12049875 AATTAAATTAAA
1 AATTAAATTAAA
12049887 ATGTTCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.17
15 16 0.70
16 3 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAATTAAATTAT
Found at i:12050560 original size:18 final size:18
Alignment explanation
Indices: 12050523--12050562 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12050513 TGAAATAACA
** *
12050523 ATTTTGATCAGTTTTTAT
1 ATTTTGATCAAATTTGAT
12050541 ATTTTGATCAAATTTGAT
1 ATTTTGATCAAATTTGAT
12050559 ATTT
1 ATTT
12050563 AATCTTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (18 bp):
ATTTTGATCAAATTTGAT
Found at i:12054049 original size:31 final size:31
Alignment explanation
Indices: 12054009--12054073 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
12053999 CTTAATACAA
12054009 GAACCTAATATTTTTATAAGGAAGAAAGTGG
1 GAACCTAATATTTTTATAAGGAAGAAAGTGG
*
12054040 GAACGTAATATTTTTATAAGGAAGAAAGTGG
1 GAACCTAATATTTTTATAAGGAAGAAAGTGG
12054071 GAA
1 GAA
12054074 GATGAGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.28
Consensus pattern (31 bp):
GAACCTAATATTTTTATAAGGAAGAAAGTGG
Found at i:12063225 original size:29 final size:30
Alignment explanation
Indices: 12063192--12063249 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12063182 AAAAATATAA
* *
12063192 ATTTTAAAGG-ATTAAATTAAAATTTTATC
1 ATTTTAAAGGAATCAAAATAAAATTTTATC
*
12063221 ATTTTAAAGGAATCAAAATATAATTTTAT
1 ATTTTAAAGGAATCAAAATAAAATTTTAT
12063250 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (30 bp):
ATTTTAAAGGAATCAAAATAAAATTTTATC
Found at i:12063622 original size:2 final size:2
Alignment explanation
Indices: 12063617--12063661 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12063607 AAAAATTGTT
12063617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12063659 TA T
1 TA T
12063662 TTTTCGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12066838 original size:24 final size:24
Alignment explanation
Indices: 12066811--12066911 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
12066801 TTAAACTCTG
12066811 TCTAGGCTCGAATGAGCTAACTTA
1 TCTAGGCTCGAATGAGCTAACTTA
* * *
12066835 TCTAGGCTC-ATAAGAGTTAACCTA
1 TCTAGGCTCGA-ATGAGCTAACTTA
* * * *
12066859 TCTGGGCTCGTATGAGCTAATTTTG
1 TCTAGGCTCGAATGAGCTAA-CTTA
* * *
12066884 TCTAGGCTTGTATGAGCTAAATT-
1 TCTAGGCTCGAATGAGCTAACTTA
12066907 TCTAG
1 TCTAG
12066912 AAGATTCAGT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
23 6 0.10
24 36 0.59
25 19 0.31
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (24 bp):
TCTAGGCTCGAATGAGCTAACTTA
Found at i:12082129 original size:27 final size:26
Alignment explanation
Indices: 12082082--12082142 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
12082072 AAGAGAAAGG
*
12082082 AGAAAGAAGGAATAAAGG-AAATGGGAA
1 AGAAA-AAGGAATAAAGGAAAAT-GAAA
12082109 AGAAAAAGGAA-AAACGAGAAAATGAAA
1 AGAAAAAGGAATAAA-G-GAAAATGAAA
12082136 AGAAAAA
1 AGAAAAA
12082143 AAAAAGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.10
26 7 0.23
27 16 0.53
28 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.05
Consensus pattern (26 bp):
AGAAAAAGGAATAAAGGAAAATGAAA
Found at i:12082157 original size:26 final size:29
Alignment explanation
Indices: 12082097--12082157 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
12082087 GAAGGAATAA
*
12082097 AGGAAATGGGAAAGAAAAAGGAAAAACGAG
1 AGGAAATGGAAAAGAAAAA-GAAAAACGAG
12082127 A--AAAT-GAAAAGAAAAA-AAAAA-GAG
1 AGGAAATGGAAAAGAAAAAGAAAAACGAG
12082151 AGGAAAT
1 AGGAAAT
12082158 AATAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 4 0.14
25 5 0.18
26 4 0.14
27 10 0.36
28 4 0.14
30 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.05
Consensus pattern (29 bp):
AGGAAATGGAAAAGAAAAAGAAAAACGAG
Found at i:12085629 original size:23 final size:23
Alignment explanation
Indices: 12085578--12085629 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12085568 AAGACAGAAA
* *
12085578 TGTGTCACAAGGTAGAGGAAAAG
1 TGTGCCACAAGGTAGAGAAAAAG
**
12085601 CATGCCACAAGGTAGAGAAAAAG
1 TGTGCCACAAGGTAGAGAAAAAG
12085624 TGTGCC
1 TGTGCC
12085630 GAAAAAAAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (23 bp):
TGTGCCACAAGGTAGAGAAAAAG
Found at i:12098306 original size:61 final size:61
Alignment explanation
Indices: 12098238--12098417 Score: 184
Period size: 61 Copynumber: 2.9 Consensus size: 61
12098228 TTTTTTCTAA
* * *
12098238 TTTTTAGAGTTAGGACTAAATTGATAGATTTTGTAAATATTGAGGATTAAATTTATT-AATT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGG-CTAAATTTATTGAATT
* * * * *
12098299 TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGCTAAATTTGTTGAATT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGGCTAAATTTATTGAATT
* * * * * *
12098360 TTTTTATATTTAGGA-TCCAATTGATAGAATCTGTAAACATTAGAGGGCTAATTTTATT
1 TTTTTAGAATTAGGACT-AAATTGATAGATTTTGTAAACATT-GA-GGCTAAATTTATT
12098418 ACAAGACAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
60 10 0.10
61 73 0.76
62 2 0.02
63 11 0.11
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.43
Consensus pattern (61 bp):
TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGGCTAAATTTATTGAATT
Found at i:12108100 original size:16 final size:16
Alignment explanation
Indices: 12108079--12108120 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
12108069 AATAAATCAT
12108079 TAAAAAATTATAAAAA
1 TAAAAAATTATAAAAA
*
12108095 TAAAAAATATTTTAAAAA
1 T-AAAAA-ATTATAAAAA
12108113 TAAAAAAT
1 TAAAAAAT
12108121 CAGTTCAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAAATTATAAAAA
Found at i:12108120 original size:18 final size:18
Alignment explanation
Indices: 12108080--12108120 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12108070 ATAAATCATT
12108080 AAAAA-ATTATAAAAATA
1 AAAAATATTATAAAAATA
*
12108097 AAAAATATTTTAAAAATA
1 AAAAATATTATAAAAATA
12108115 AAAAAT
1 AAAAAT
12108121 CAGTTCAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATATTATAAAAATA
Found at i:12109842 original size:23 final size:22
Alignment explanation
Indices: 12109800--12109847 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
12109790 TTTTCCTTAA
*
12109800 TTTTTTTATATTTAGTTTTTACT
1 TTTTTTTATATTTAGATTTTA-T
*
12109823 TTTTTTTATATTTTGATTTTAT
1 TTTTTTTATATTTAGATTTTAT
12109845 TTT
1 TTT
12109848 AGTTTTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTTTTATATTTAGATTTTAT
Found at i:12109908 original size:23 final size:24
Alignment explanation
Indices: 12109856--12109921 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
12109846 TTAGTTTTTA
* *
12109856 TCTGCCTTTGTGACACGCTTTTCT
1 TCTGTCTTTGTGGCACGCTTTTCT
*
12109880 TCTGTCTTTGTGGCACG-TTTTTT
1 TCTGTCTTTGTGGCACGCTTTTCT
* *
12109903 TTTGTC-TTGTGGTACGCTT
1 TCTGTCTTTGTGGCACGCTT
12109922 CTACCTTCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.25
23 12 0.33
24 15 0.42
ACGTcount: A:0.06, C:0.21, G:0.21, T:0.52
Consensus pattern (24 bp):
TCTGTCTTTGTGGCACGCTTTTCT
Found at i:12112814 original size:18 final size:18
Alignment explanation
Indices: 12112791--12112828 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12112781 CTGGTTAAAG
12112791 TGAAAGGTTATTAGGACC
1 TGAAAGGTTATTAGGACC
12112809 TGAAAGGTTATTAGGACC
1 TGAAAGGTTATTAGGACC
12112827 TG
1 TG
12112829 CTTTTCTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (18 bp):
TGAAAGGTTATTAGGACC
Found at i:12113934 original size:27 final size:27
Alignment explanation
Indices: 12113903--12113957 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12113893 CCAATAGACG
12113903 TCAAATGCAGGGATGGGTAAATCTACA
1 TCAAATGCAGGGATGGGTAAATCTACA
** *
12113930 TCAAATGTGGGGATGGGTAAATTTACA
1 TCAAATGCAGGGATGGGTAAATCTACA
12113957 T
1 T
12113958 TTTGGTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (27 bp):
TCAAATGCAGGGATGGGTAAATCTACA
Found at i:12114279 original size:12 final size:12
Alignment explanation
Indices: 12114245--12114297 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
12114235 TAAGCACAAT
12114245 AAAAGCAAACAAA
1 AAAAGCAAA-AAA
* *
12114258 AATA-CCAAAAA
1 AAAAGCAAAAAA
12114269 AAAAGCAAAAAA
1 AAAAGCAAAAAA
12114281 AAAAG-AAAAAA
1 AAAAGCAAAAAA
12114292 AGAAAG
1 A-AAAG
12114298 TATCCTCGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 13 0.38
12 18 0.53
13 3 0.09
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.02
Consensus pattern (12 bp):
AAAAGCAAAAAA
Found at i:12115924 original size:56 final size:56
Alignment explanation
Indices: 12115840--12116176 Score: 389
Period size: 56 Copynumber: 6.0 Consensus size: 56
12115830 AAAATGTATC
* *
12115840 AACC-TTACATTGATGCTCC-TTCGAACATCCCATTTCATAATATCC-CTACGGATAT
1 AACCTTTACATTGATG-TCCTTTCGGACATCCCTTTTCATAATATCCTC-ACGGATAT
* * *
12115895 AA-CTATTACATTGATGTCCATTCGGACATCCCTTTTCATGATACCCTCACGGATAT
1 AACCT-TTACATTGATGTCCTTTCGGACATCCCTTTTCATAATATCCTCACGGATAT
* * * * *
12115951 AACCTTTACGTTAATATCCTTTCAGACATCTCTTTTCATAATATCC-CTACGGATAT
1 AACCTTTACATTGATGTCCTTTCGGACATCCCTTTTCATAATATCCTC-ACGGATAT
* * * *
12116007 AACCTTTACATTGATGT-TTATTCGGGCATCCCTTTTCATGATATCCTCACGGATTT
1 AACCTTTACATTGATGTCCT-TTCGGACATCCCTTTTCATAATATCCTCACGGATAT
* * **
12116063 AACCTTTACGTTAAAATCCTTTCGGACATCCCTTTTCATAATATCCTCACGGATAT
1 AACCTTTACATTGATGTCCTTTCGGACATCCCTTTTCATAATATCCTCACGGATAT
* * * *
12116119 AATCTTTACGTTGATGTCCTTTCGAACATCCCTTTTCACAATATCCTCACGGATAT
1 AACCTTTACATTGATGTCCTTTCGGACATCCCTTTTCATAATATCCTCACGGATAT
12116175 AA
1 AA
12116177 AGAAAATCAA
Statistics
Matches: 238, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
54 1 0.00
55 7 0.03
56 225 0.95
57 5 0.02
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.36
Consensus pattern (56 bp):
AACCTTTACATTGATGTCCTTTCGGACATCCCTTTTCATAATATCCTCACGGATAT
Found at i:12116066 original size:112 final size:111
Alignment explanation
Indices: 12115864--12116176 Score: 450
Period size: 112 Copynumber: 2.8 Consensus size: 111
12115854 GCTCCTTCGA
* *
12115864 ACATCCCATTTCATAATATCCCTACGGATATAACTATTACATTGATGTCCATTCGGACATCCCTT
1 ACATCCCTTTTCATAATATCCCTACGGATATAACT-TTACATTGATGTCTATTCGGACATCCCTT
* *
12115929 TTCATGATACCCTCACGGATATAACCTTTACGTTAATATCCTTTCAG
65 TTCATGATATCCTCACGGATATAACCTTTACGTTAAAATCCTTTCAG
* * *
12115976 ACATCTCTTTTCATAATATCCCTACGGATATAACCTTTACATTGATGTTTATTCGGGCATCCCTT
1 ACATCCCTTTTCATAATATCCCTACGGATATAA-CTTTACATTGATGTCTATTCGGACATCCCTT
* *
12116041 TTCATGATATCCTCACGGATTTAACCTTTACGTTAAAATCCTTTCGG
65 TTCATGATATCCTCACGGATATAACCTTTACGTTAAAATCCTTTCAG
* *
12116088 ACATCCCTTTTCATAATAT-CCTCACGGATATAATCTTTACGTTGATGTCCT-TTCGAACATCCC
1 ACATCCCTTTTCATAATATCCCT-ACGGATATAA-CTTTACATTGATGT-CTATTCGGACATCCC
**
12116151 TTTTCACAATATCCTCACGGATATAA
63 TTTTCATGATATCCTCACGGATATAA
12116177 AGAAAATCAA
Statistics
Matches: 180, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
111 3 0.02
112 174 0.97
113 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (111 bp):
ACATCCCTTTTCATAATATCCCTACGGATATAACTTTACATTGATGTCTATTCGGACATCCCTTT
TCATGATATCCTCACGGATATAACCTTTACGTTAAAATCCTTTCAG
Found at i:12116115 original size:27 final size:27
Alignment explanation
Indices: 12116033--12116115 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
12116023 TTTATTCGGG
*
12116033 CATCCCTTTTCATGATATCCTCACGGA
1 CATCCCTTTTCATAATATCCTCACGGA
** * * * * **
12116060 TTTAACCTTTACGTTAAAATCCTTTCGGA
1 CAT-CCCTTTTC-ATAATATCCTCACGGA
12116089 CATCCCTTTTCATAATATCCTCACGGA
1 CATCCCTTTTCATAATATCCTCACGGA
12116116 TATAATCTTT
Statistics
Matches: 37, Mismatches: 17, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
27 13 0.35
28 12 0.32
29 12 0.32
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (27 bp):
CATCCCTTTTCATAATATCCTCACGGA
Done.