Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011783.1 Kokia drynarioides strain JFW-HI SEQ_126778, whole genome shotgun sequence
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: 143117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 449 characters in sequence are not A, C, G, or T
Found at i:11485 original size:29 final size:28
Alignment explanation
Indices: 11453--11515 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
11443 AAAATGAGAC
11453 TTTTCGGATACCCGGGGACAAAATAGTAA
1 TTTT-GGATACCCGGGGACAAAATAGTAA
* * * *
11482 TTTTGGATTCTCGGGGGCAAAATAGTGA
1 TTTTGGATACCCGGGGACAAAATAGTAA
11510 TTTTGG
1 TTTTGG
11516 GAAAATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGGGGACAAAATAGTAA
Found at i:11648 original size:58 final size:59
Alignment explanation
Indices: 11531--11815 Score: 321
Period size: 59 Copynumber: 4.8 Consensus size: 59
11521 TTTTGGGGTT
* *** *
11531 AATGGAATTTTTGGAAGTTAAGGGGTAAAAATGTAATTTTCAAAAGTTTC-AGGGTTAAA
1 AATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGA-GGTAAAA
*
11590 AATGGAAATTTTGGAAGTTTAGGGGT-AAAATGTAATTTTTGGAAGTTTCGAGGCT-AAA
1 AATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGG-TAAAA
* * * *
11648 AATGGAATTTTTGGAAG-TTCGAGGGTAAAAATATAATTTTTGGAAGTTTTGGGGTAAAA
1 AATGGAATTTTTGGAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTAAAA
* ** *
11707 AATGGAATTTTTGGAAGTTT-GAGGGT-AAAATGTAATGTTTGGAAGTTTTTAGGTCAAA
1 AATGGAATTTTTGGAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTAAAA
* * *
11765 AATGGAATTTTGGAGAAGTTTAGGGGTGAAAATATAATTTTTGGATAGTTT
1 AATGGAATTTTTG-GAAGTTTAGGGGTAAAAATGTAATTTTTGGA-AGTTT
11816 AGGGACCTCT
Statistics
Matches: 198, Mismatches: 18, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
57 3 0.02
58 85 0.43
59 87 0.44
60 18 0.09
61 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
AATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTAAAA
Found at i:11675 original size:117 final size:117
Alignment explanation
Indices: 11531--11805 Score: 358
Period size: 117 Copynumber: 2.3 Consensus size: 117
11521 TTTTGGGGTT
* *
11531 AATGGAATTTTTGGAAGTTAAGGGGTAAAAATGTAATTTTCAAAAGTTTCAGGGTTAAAAATGGA
1 AATGGAATTTTTGGAAGTTAAGGGGTAAAAATATAATTTTCAAAAGTTTCAGGGTAAAAAATGGA
*
11596 AATTTTGGAAGTTT-AGGGGTAAAATGTAATTTTTGGAAGTTTCGAGG-CTAAA
66 AATTTTGGAAGTTTGA-GGGTAAAATGTAATGTTTGGAAGTTTCGAGGTC-AAA
* *** **
11648 AATGGAATTTTTGGAAGTT-CGAGGGTAAAAATATAATTTTTGGAAGTTTTGGGGTAAAAAATGG
1 AATGGAATTTTTGGAAGTTAAG-GGGTAAAAATATAATTTTCAAAAGTTTCAGGGTAAAAAATGG
* **
11712 AATTTTTGGAAGTTTGAGGGTAAAATGTAATGTTTGGAAGTTTTTAGGTCAAA
65 AAATTTTGGAAGTTTGAGGGTAAAATGTAATGTTTGGAAGTTTCGAGGTCAAA
* * *
11765 AATGGAATTTTGGAGAAGTTTAGGGGTGAAAATATAATTTT
1 AATGGAATTTTTG-GAAGTTAAGGGGTAAAAATATAATTTT
11806 TGGATAGTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
116 1 0.01
117 111 0.80
118 25 0.18
119 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (117 bp):
AATGGAATTTTTGGAAGTTAAGGGGTAAAAATATAATTTTCAAAAGTTTCAGGGTAAAAAATGGA
AATTTTGGAAGTTTGAGGGTAAAATGTAATGTTTGGAAGTTTCGAGGTCAAA
Found at i:11815 original size:30 final size:29
Alignment explanation
Indices: 11531--11819 Score: 271
Period size: 30 Copynumber: 9.8 Consensus size: 29
11521 TTTTGGGGTT
* *
11531 AATGGAATTTTTGGAAGTTAAGGGGTAAA
1 AATGTAATTTTTGGAAGTTTAGGGGTAAA
*** *
11560 AATGTAATTTTCAAAAGTTTCAGGGTTAAA
1 AATGTAATTTTTGGAAGTTT-AGGGGTAAA
* *
11590 AATGGAAATTTTGGAAGTTTAGGGGT-AA
1 AATGTAATTTTTGGAAGTTTAGGGGTAAA
* *
11618 AATGTAATTTTTGGAAGTTTCGAGGCTAAA
1 AATGTAATTTTTGGAAGTTTAG-GGGTAAA
* *
11648 AATGGAATTTTTGGAAG-TTCGAGGGTAAA
1 AATGTAATTTTTGGAAGTTTAG-GGGTAAA
* *
11677 AATATAATTTTTGGAAGTTTTGGGGTAAAA
1 AATGTAATTTTTGGAAGTTTAGGGGT-AAA
*
11707 AATGGAATTTTTGGAAGTTT-GAGGGT-AA
1 AATGTAATTTTTGGAAGTTTAG-GGGTAAA
* ***
11735 AATGTAATGTTTGGAAGTTTTTAGGTCAAA
1 AATGTAATTTTTGGAAGTTTAGGGGT-AAA
* * *
11765 AATGGAATTTTGGAGAAGTTTAGGGGTGAA
1 AATGTAATTTTTG-GAAGTTTAGGGGTAAA
*
11795 AATATAATTTTTGGATAGTTTAGGG
1 AATGTAATTTTTGGA-AGTTTAGGG
11820 ACCTCTAAGG
Statistics
Matches: 212, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
28 44 0.21
29 56 0.26
30 102 0.48
31 10 0.05
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AATGTAATTTTTGGAAGTTTAGGGGTAAA
Found at i:12305 original size:79 final size:78
Alignment explanation
Indices: 12174--12330 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 78
12164 CTTTTCTCAA
*
12174 AAACACGTGGATCTGAGGTCGAGTCGGGTCGGATTTCGGGTCATGGGTCAAATATGGCAAAACGG
1 AAACACGTGGATCTGAGGTCGAGTCGGGTCGGATTTCGGGTCATGGGTCAAATATGGCAAAACGA
12239 CGTCGTTTTGGGT
66 CGTCGTTTTGGGT
12252 NAAACACGTGGATCTGAGGTCGAGTCGGGTCGGATTTCGGGTCATGGGTCAAATATGGCAAAACG
1 -AAACACGTGGATCTGAGGTCGAGTCGGGTCGGATTTCGGGTCATGGGTCAAATATGGCAAAACG
12317 ACGTCGTTTTGGGT
65 ACGTCGTTTTGGGT
12331 CTTTATGCAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.25
Consensus pattern (78 bp):
AAACACGTGGATCTGAGGTCGAGTCGGGTCGGATTTCGGGTCATGGGTCAAATATGGCAAAACGA
CGTCGTTTTGGGT
Found at i:13015 original size:16 final size:16
Alignment explanation
Indices: 12994--13052 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
12984 TCTTCAGTTT
12994 TTATTATTATTTAATA
1 TTATTATTATTTAATA
*
13010 TTATTAATATATTTACTA
1 TTATT-AT-TATTTAATA
* *
13028 TTA-AACCTATTTAATA
1 TTATTA-TTATTTAATA
13044 TTATTATTA
1 TTATTATTA
13053 ATGGTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 19 0.58
17 3 0.09
18 11 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTATTTAATA
Found at i:13845 original size:29 final size:29
Alignment explanation
Indices: 13812--13871 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
13802 ATAATAAGTT
*
13812 TTAAATTTAAA-TATAAATCTAAATTTATA
1 TTAAATTTAAATTATAAAAC-AAATTTATA
*
13841 TTAAATTTAAATTTTAAAACAAATTTATA
1 TTAAATTTAAATTATAAAACAAATTTATA
13870 TT
1 TT
13872 CAAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAATTTAAATTATAAAACAAATTTATA
Found at i:13856 original size:18 final size:18
Alignment explanation
Indices: 13811--13900 Score: 80
Period size: 17 Copynumber: 5.2 Consensus size: 18
13801 TATAATAAGT
13811 TTTAAATTTAAATATAAA
1 TTTAAATTTAAATATAAA
* *
13829 TCTAAATTTATAT-TAAA
1 TTTAAATTTAAATATAAA
*
13846 TTTAAATTTTAAA-ACAAA
1 TTTAAA-TTTAAATATAAA
* *
13864 TTTATATTCAAA-ATAAA
1 TTTAAATTTAAATATAAA
**
13881 TTTAACCTTAAA-ATAAA
1 TTTAAATTTAAATATAAA
13898 TTT
1 TTT
13901 TAGAATGAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
17 34 0.59
18 24 0.41
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAATTTAAATATAAA
Found at i:13858 original size:7 final size:6
Alignment explanation
Indices: 13811--13854 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
13801 TATAATAAGT
* * *
13811 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
13855 TAAAACAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:14716 original size:207 final size:199
Alignment explanation
Indices: 14293--14838 Score: 716
Period size: 207 Copynumber: 2.7 Consensus size: 199
14283 TTCAATCCGA
*
14293 TTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
1 TTCTCAGTATCTCATCAGGAAGCT-ACCATTTTATTGCTTCG-CCTGCTTCTCAGTATCTCATCA
* * *
14358 GGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCAT
64 GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCCTGAGTTGGTATACTTCTCAGTATCTCAT
* * * * *
14423 CAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATTTCATCAGGAAGACGAATTTG
129 CAGGAAGATGACCGCATCACTTGCTTCAATCCGCTCCTCTATATCTCATCAGGAAGACGAATTTG
14488 GTCCAC
194 GTCCAC
* *** *
14494 TTCTCAGTGTCTCATCAGGAAGCTATTTTTTTTATCGCTTCGCTCTGCTTCTCAGTATCTCATCA
1 TTCTCAGTATCTCATCAGGAAGCTA-CCATTTTATTGCTTCGC-CTGCTTCTCAGTATCTCATCA
* * ** * * *
14559 GGAAGCTGGGATTTGAAGATTTGCTCGCTTTGAGCTTGGGTTTGATTTTGGTCTTCTTCTCAGTA
64 GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGC-----CCTGA-GTTGGTATACTTCTCAGTA
* *
14624 TCTCATCAGGAAGATGATCGCATCGCTTGCTTCAATCCGCTCCTCTATATCTCATCAGGAAGACG
123 TCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCGCTCCTCTATATCTCATCAGGAAGACG
14689 AATTTGGTCCAC
188 AATTTGGTCCAC
*
14701 TTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCA
1 TTCTCAGTATCTCATCAGGAAGCT-ACCATTTTATTGCTTC-GCCTGCTTCTCAGTATCTCATCA
* * * *
14766 GGAAGCTGAGG-TTCGAAGATGTGTTCACTTTGAGCCTTGAGTTGGTATACTTCTCTGTATCTCA
64 GGAAGCTG-GGATTCGAAGATTTGCTCACTTTGAGCCCTGAGTTGGTATACTTCTCAGTATCTCA
14830 TCAGGAAGA
128 TCAGGAAGA
14839 CGAATTTGGT
Statistics
Matches: 296, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
200 2 0.01
201 115 0.39
202 4 0.01
206 3 0.01
207 168 0.57
208 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (199 bp):
TTCTCAGTATCTCATCAGGAAGCTACCATTTTATTGCTTCGCCTGCTTCTCAGTATCTCATCAGG
AAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCCTGAGTTGGTATACTTCTCAGTATCTCATCA
GGAAGATGACCGCATCACTTGCTTCAATCCGCTCCTCTATATCTCATCAGGAAGACGAATTTGGT
CCAC
Found at i:14851 original size:152 final size:152
Alignment explanation
Indices: 14666--14990 Score: 587
Period size: 152 Copynumber: 2.1 Consensus size: 152
14656 CAATCCGCTC
* *
14666 CTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCAT
1 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCAT
*
14731 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATGTGTTCACTT
66 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATGTGCTCACTT
14796 TGAGCCTTGAGTTGGTATACTT
131 TGAGCCTTGAGTTGGTATACTT
*
14818 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGATGACCAT
1 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCAT
* *
14883 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTT
66 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATGTGCTCACTT
14948 TGAGCCTTGAGTTGGTATACTT
131 TGAGCCTTGAGTTGGTATACTT
*
14970 CTATGTATCTCATCAGGAAGA
1 CTCTGTATCTCATCAGGAAGA
14991 TAACCGCCTC
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 166 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (152 bp):
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCAT
TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATGTGCTCACTT
TGAGCCTTGAGTTGGTATACTT
Found at i:26408 original size:60 final size:57
Alignment explanation
Indices: 26334--26468 Score: 137
Period size: 58 Copynumber: 2.3 Consensus size: 57
26324 ACCCAGGCGC
* *
26334 AAAATGGTAATTTTGGACTCTCGAGGGC-AAAATAGTGATTTTAAGAAAATTTTGGGGTTA
1 AAAATGGAAATTTTGGACT-TCGAGGGCAAAAAT-GT-ATTTT-AGAAAATTTTAGGGTTA
* * * ** *
26394 AAAATGGAAATTTTGAAAGTTCGAGGGTAAAAATGTATTTTTTAAAGTTTTAGGGTTA
1 AAAATGGAAATTTTG-GACTTCGAGGGCAAAAATGTATTTTAGAAAATTTTAGGGTTA
*
26452 AAAATGGAATTTTTGGA
1 AAAATGGAAATTTTGGA
26469 AGTTTGGGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 1 0.02
58 27 0.43
59 5 0.08
60 23 0.37
61 7 0.11
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (57 bp):
AAAATGGAAATTTTGGACTTCGAGGGCAAAAATGTATTTTAGAAAATTTTAGGGTTA
Found at i:26436 original size:29 final size:29
Alignment explanation
Indices: 26392--26554 Score: 127
Period size: 28 Copynumber: 5.6 Consensus size: 29
26382 ATTTTGGGGT
* *
26392 TAAAAATGGAAATTTTGAAAGTTCGAGGG
1 TAAAAATGTAATTTTTGAAAGTTCGAGGG
* **
26421 TAAAAATGT-ATTTTTTAAAGTTTTAGGG
1 TAAAAATGTAATTTTTGAAAGTTCGAGGG
* * *
26449 TTAAAAATGGAATTTTTGGAAGTTTG-GGG
1 -TAAAAATGTAATTTTTGAAAGTTCGAGGG
*
26478 TAAAAATGTAATTTTTGGAAGTTTCGA-GG
1 TAAAAATGTAATTTTTGAAAG-TTCGAGGG
* * *
26507 TCAAAAATGGAA-TTTTGAAGAAGTTTGGGGG
1 T-AAAAATGTAATTTTTG-A-AAGTTCGAGGG
* *
26538 TCAAAATATAATTTTTG
1 TAAAAATGTAATTTTTG
26555 GATAGTTTAG
Statistics
Matches: 107, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
28 35 0.33
29 30 0.28
30 31 0.29
31 11 0.10
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGAAAGTTCGAGGG
Found at i:26460 original size:58 final size:58
Alignment explanation
Indices: 26378--26554 Score: 180
Period size: 58 Copynumber: 3.0 Consensus size: 58
26368 GTGATTTTAA
* *
26378 GAAAATTTTGGGGTTAAAAATGGAAATTTTGAAAGTTCGAGGGTAAAAATGT-ATTTTT
1 GAAAGTTTTAGGGTTAAAAATGGAAATTTTGAAAGTTCG-GGGTAAAAATGTAATTTTT
* * * *
26436 TAAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGTAATTTTT
1 GAAAGTTTTAGGGTTAAAAATGGAAATTTTGAAAGTTCGGGGTAAAAATGTAATTTTT
* * * * * *
26494 GGAAG-TTTCGAGGTCAAAAATGG-AATTTTGAAGAAGTTTGGGGGTCAAAATATAATTTTT
1 GAAAGTTTTAG-GGTTAAAAATGGAAATTTTG-A-AAG-TTCGGGGTAAAAATGTAATTTTT
26554 G
1 G
26555 GATAGTTTAG
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 22 0.22
58 53 0.54
59 3 0.03
60 21 0.21
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (58 bp):
GAAAGTTTTAGGGTTAAAAATGGAAATTTTGAAAGTTCGGGGTAAAAATGTAATTTTT
Found at i:26526 original size:28 final size:27
Alignment explanation
Indices: 26384--26526 Score: 112
Period size: 29 Copynumber: 5.0 Consensus size: 27
26374 TTAAGAAAAT
26384 TTTG-GGGTTAAAAATGGAAATTTTGAAAG
1 TTTGAGGG-TAAAAATGG-AATTTTG-AAG
* * * *
26413 TTCGAGGGTAAAAATGTATTTTTTAAAG
1 TTTGAGGGTAAAAATGGA-ATTTTGAAG
*
26441 TTTTAGGGTTAAAAATGGAATTTTTGGAAG
1 TTTGAGGG-TAAAAATGGAA-TTTT-GAAG
*
26471 TTTG-GGGTAAAAATGTAATTTTTGGAAG
1 TTTGAGGGTAAAAATGGAA-TTTT-GAAG
26499 TTTCGA-GGTCAAAAATGGAATTTTGAAG
1 TTT-GAGGGT-AAAAATGGAATTTTGAAG
26527 AAGTTTGGGG
Statistics
Matches: 94, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
28 37 0.39
29 39 0.41
30 18 0.19
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (27 bp):
TTTGAGGGTAAAAATGGAATTTTGAAG
Found at i:26554 original size:31 final size:28
Alignment explanation
Indices: 26459--26562 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 28
26449 TTAAAAATGG
* *
26459 AATTTTTGGAAGTTTGGGGTAAAAATGT
1 AATTTTTGGAAGTTTGGGGTCAAAATAT
*
26487 AATTTTTGGAAGTTTCGAGGTCAAAA-AT
1 AATTTTTGGAAGTTT-GGGGTCAAAATAT
26515 GGAA-TTTTGAAGAAGTTTGGGGGTCAAAATAT
1 --AATTTTTG--GAAGTTT-GGGGTCAAAATAT
26547 AATTTTTGGATAGTTT
1 AATTTTTGGA-AGTTT
26563 AGGGACCTCT
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
28 16 0.25
29 15 0.24
30 9 0.14
31 21 0.33
32 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (28 bp):
AATTTTTGGAAGTTTGGGGTCAAAATAT
Found at i:27681 original size:16 final size:16
Alignment explanation
Indices: 27660--27718 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
27650 TCCTCAGTTT
27660 TTATTATTATTTAATA
1 TTATTATTATTTAATA
*
27676 TTATTAATATATTTACTA
1 TTATT-AT-TATTTAATA
* *
27694 TTA-AACCTATTTAATA
1 TTATTA-TTATTTAATA
27710 TTATTATTA
1 TTATTATTA
27719 ATGGTATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 19 0.58
17 3 0.09
18 11 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTATTTAATA
Found at i:28502 original size:18 final size:17
Alignment explanation
Indices: 28466--28585 Score: 114
Period size: 17 Copynumber: 6.9 Consensus size: 17
28456 GATTTTCAAT
* *
28466 ATTTATAATAAGTTGTAA
1 ATTTAAAATAAATT-TAA
*
28484 ATTTAAATATAAATCTAA
1 ATTTAAA-ATAAATTTAA
** *
28502 ATTTGTATTAAATTTAA
1 ATTTAAAATAAATTTAA
*
28519 ATTTTAAAACAAATTTAA
1 A-TTTAAAATAAATTTAA
28537 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
**
28554 CCTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
**
28571 CCTTAAAATAAATTT
1 ATTTAAAATAAATTT
28586 TAGAATGACT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
17 54 0.63
18 27 0.31
19 5 0.06
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:28526 original size:7 final size:6
Alignment explanation
Indices: 28481--28553 Score: 53
Period size: 6 Copynumber: 12.5 Consensus size: 6
28471 TAATAAGTTG
* * ** *
28481 TAAATT TAAATA TAAATC TAAATT TGTA-T TAAATT TAAATTT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT
* *
28528 CAAATT TAAATT TAAA-A TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAA
28554 CCTTAAAATA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
5 10 0.20
6 34 0.68
7 6 0.12
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:30935 original size:41 final size:41
Alignment explanation
Indices: 30878--30960 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
30868 TATACTTTAT
*
30878 CAAATCTTCTAATGTGCAAGCCCCTCGAGGTTCTCCATGGA
1 CAAATCTTCAAATGTGCAAGCCCCTCGAGGTTCTCCATGGA
*
30919 CAAATCTTCAAATGTGCGAGCCCCTCGAGGTTCTCCATGGA
1 CAAATCTTCAAATGTGCAAGCCCCTCGAGGTTCTCCATGGA
30960 C
1 C
30961 TCAAAAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (41 bp):
CAAATCTTCAAATGTGCAAGCCCCTCGAGGTTCTCCATGGA
Found at i:36472 original size:18 final size:18
Alignment explanation
Indices: 36449--36483 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36439 AATATTATCA
*
36449 TTGTTTCGTACAATTCAC
1 TTGTTTCATACAATTCAC
*
36467 TTGTTTTATACAATTCA
1 TTGTTTCATACAATTCA
36484 TATTCGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (18 bp):
TTGTTTCATACAATTCAC
Found at i:44825 original size:61 final size:61
Alignment explanation
Indices: 44758--44907 Score: 158
Period size: 61 Copynumber: 2.5 Consensus size: 61
44748 TATTTTAAAA
* * * *
44758 TTTTTAGAGTTAGGACTAAATTAATAGATTTTGTAAATATTGAGGGCCAAATTTATTAATT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTAAGGGCCAAATTTATTAATT
* * * * ** * *
44819 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTAAGGGTTAAATTTGTTTATT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTAAGGGCCAAATTTATTAATT
* *
44880 TTTTTATATTTAGGA-TCAAATTGATAGA
1 TTTTTAGAATTAGGACT-AAATTGATAGA
44908 ATGTGTAGAC
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
60 1 0.01
61 69 0.99
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (61 bp):
TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTAAGGGCCAAATTTATTAATT
Found at i:64602 original size:31 final size:31
Alignment explanation
Indices: 64564--64632 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 31
64554 ACTACAAAAA
*
64564 TAGTCACTTTTAT-TTGTCTCAA-GTTACATTT
1 TAGTCACTTTTATGTT-T-TAAATGTTACATTT
64595 TAGTCAC--TTATGTTTTAAATGTTACATTT
1 TAGTCACTTTTATGTTTTAAATGTTACATTT
64624 TAGTCACTT
1 TAGTCACTT
64633 ATGTTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 3 0.09
29 21 0.64
30 2 0.06
31 7 0.21
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (31 bp):
TAGTCACTTTTATGTTTTAAATGTTACATTT
Found at i:64975 original size:6 final size:6
Alignment explanation
Indices: 64955--64996 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
64945 CAAAAGGGAA
64955 GAAGAT GAA-ACT GAAGAT GAAGAT GAAGAT GAAGAT G-AGAT G
1 GAAGAT GAAGA-T GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT G
64997 TGTGTGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 6 0.18
6 27 0.79
7 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (6 bp):
GAAGAT
Found at i:65998 original size:11 final size:11
Alignment explanation
Indices: 65982--66010 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
65972 TTAAATATAT
65982 AAAAATAATAA
1 AAAAATAATAA
65993 AAAAATAATAA
1 AAAAATAATAA
66004 AAAAATA
1 AAAAATA
66011 CGTATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:66127 original size:35 final size:36
Alignment explanation
Indices: 66081--66149 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
66071 ATTTTAGTAA
66081 ATAATAATTT-GGGTACCATTTTGATTATTAATTAT
1 ATAATAATTTGGGGTACCATTTTGATTATTAATTAT
*
66116 ATAATAATTTGGGGTATCATTTTGATTATTAATT
1 ATAATAATTTGGGGTACCATTTTGATTATTAATT
66150 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (36 bp):
ATAATAATTTGGGGTACCATTTTGATTATTAATTAT
Found at i:75363 original size:2 final size:2
Alignment explanation
Indices: 75356--75380 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75346 AAATTATCAT
75356 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 T
75381 TTTCCCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78852 original size:16 final size:16
Alignment explanation
Indices: 78831--78862 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
78821 AAATAAAATA
78831 TAAGTTAATGTTGAAC
1 TAAGTTAATGTTGAAC
78847 TAAGTTAATGTTGAAC
1 TAAGTTAATGTTGAAC
78863 CAAGCAGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
TAAGTTAATGTTGAAC
Found at i:85983 original size:13 final size:13
Alignment explanation
Indices: 85967--86007 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
85957 AACAACTTAA
85967 AAAAATAAAAAAT
1 AAAAATAAAAAAT
*
85980 AAAAAT-AAAAAC
1 AAAAATAAAAAAT
85992 AAAAATAAGAAAAT
1 AAAAATAA-AAAAT
86006 AA
1 AA
86008 CAATCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 7 0.29
14 6 0.25
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:92990 original size:26 final size:26
Alignment explanation
Indices: 92935--92986 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
92925 AGACGACTAT
* *
92935 ATAAAATTTTTAATAAATAAAAATAT
1 ATAAAATTATTAATAAATAAAAATAA
* *
92961 ATAAAATTATTAA-ATATTAAAATAA
1 ATAAAATTATTAATAAATAAAAATAA
92986 A
1 A
92987 ATAATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAAATTATTAATAAATAAAAATAA
Found at i:93039 original size:29 final size:29
Alignment explanation
Indices: 92970--93049 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
92960 TATAAAATTA
*
92970 TTAAATATTAAAATAAAATAATATATTTC
1 TTAAAAATTAAAATAAAATAATATATTTC
** * *
92999 ACAAAAAATAAAATAAAATAA-ATATTTTT
1 TTAAAAATTAAAATAAAATAATATA-TTTC
93028 TTAAAAATT-AAA-AAAATAATAT
1 TTAAAAATTAAAATAAAATAATAT
93050 GAACAAGCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 7 0.17
28 8 0.20
29 26 0.63
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
TTAAAAATTAAAATAAAATAATATATTTC
Found at i:94143 original size:11 final size:11
Alignment explanation
Indices: 94127--94151 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
94117 CAGTTTAGTC
94127 CTTAAATTAAG
1 CTTAAATTAAG
94138 CTTAAATTAAG
1 CTTAAATTAAG
94149 CTT
1 CTT
94152 TAAAGACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (11 bp):
CTTAAATTAAG
Found at i:96366 original size:20 final size:19
Alignment explanation
Indices: 96341--96379 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
96331 TAATATATAT
*
96341 AATTTTAAAATATTTTTTAA
1 AATTTTAAAA-ATTATTTAA
96361 AATTTTAAAAATTATTTAA
1 AATTTTAAAAATTATTTAA
96380 TTACTAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTAAAAATTATTTAA
Found at i:98780 original size:26 final size:26
Alignment explanation
Indices: 98751--98813 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
98741 TAAATAGATG
98751 TTAATTTTAAAGTGGATAATTATTTT
1 TTAATTTTAAAGTGGATAATTATTTT
*** * *
98777 TTAA-AAAATAAGTGGGTAGTTATTTT
1 TTAATTTTA-AAGTGGATAATTATTTT
98803 TTAATTTTAAA
1 TTAATTTTAAA
98814 TTTTTATTGG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
25 1 0.04
26 25 0.93
27 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (26 bp):
TTAATTTTAAAGTGGATAATTATTTT
Found at i:101461 original size:24 final size:24
Alignment explanation
Indices: 101432--101478 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
101422 ATTTATATTA
101432 TTTAAA-ATATAAAATATAATTTAT
1 TTTAAATATATAAAA-ATAATTTAT
*
101456 TTTAAATATGTAAAAATAATTTA
1 TTTAAATATATAAAAATAATTTA
101479 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTAAATATATAAAAATAATTTAT
Found at i:105212 original size:21 final size:22
Alignment explanation
Indices: 105186--105226 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
105176 TGTCATCTCA
105186 AGATTTTT-TTTTTGTCAGGAC
1 AGATTTTTGTTTTTGTCAGGAC
105207 AGATTTTTGTTTTTGTCAGG
1 AGATTTTTGTTTTTGTCAGG
105227 CTCCCGCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (22 bp):
AGATTTTTGTTTTTGTCAGGAC
Found at i:112761 original size:29 final size:30
Alignment explanation
Indices: 112729--112797 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
112719 AAATAAAAAA
*
112729 TTATGTATAAAATTACACA-AAATCAAAGT
1 TTATGTATAAAATTACACATAAACCAAAGT
** * *
112758 TTATACATACAATTACACATTAAACCATAGT
1 TTATGTATAAAATTACACA-TAAACCAAAGT
112789 TTATGTATA
1 TTATGTATA
112798 GATTTGATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (30 bp):
TTATGTATAAAATTACACATAAACCAAAGT
Found at i:112969 original size:15 final size:15
Alignment explanation
Indices: 112949--112977 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
112939 TGTGATTCTC
112949 TTTTTTAAATATTTG
1 TTTTTTAAATATTTG
112964 TTTTTTAAATATTT
1 TTTTTTAAATATTT
112978 TATTATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTG
Found at i:116995 original size:42 final size:42
Alignment explanation
Indices: 116936--117022 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
116926 GGGCTTTAAC
116936 TTTACAAAGTATATTTGAGTATTGAGTTTAATTTCTTTTTTA
1 TTTACAAAGTATATTTGAGTATTGAGTTTAATTTCTTTTTTA
116978 TTTACAAAGTATATTTGAGTATTGAGTTTAATTTCTTTTTTA
1 TTTACAAAGTATATTTGAGTATTGAGTTTAATTTCTTTTTTA
117020 TTT
1 TTT
117023 TGGACTTGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (42 bp):
TTTACAAAGTATATTTGAGTATTGAGTTTAATTTCTTTTTTA
Found at i:122166 original size:30 final size:30
Alignment explanation
Indices: 122132--122282 Score: 138
Period size: 30 Copynumber: 5.2 Consensus size: 30
122122 AAAAAATCAT
*
122132 ATTTTGACCCCCAAACTCTTCCAAAATTAC
1 ATTTTGACCCCTAAACTCTTCCAAAATTAC
* * * *
122162 ATTTTGACCCCTAAACTTTTCTAACATCAC
1 ATTTTGACCCCTAAACTCTTCCAAAATTAC
122192 ATTTT--CCCCTAAA--CTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTCTTCC-AAAATTAC
*
122219 ATTTTTACCCCTAAA--CTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTCTTCC-AAAATTAC
* *
122248 ATTTTTG-CCCCTTAACT-TCTCAAAAATTAC
1 A-TTTTGACCCCTAAACTCT-TCCAAAATTAC
122278 ATTTT
1 ATTTT
122283 TACTCTCAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.03
27 11 0.11
28 8 0.08
29 34 0.33
30 44 0.43
31 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTCTTCCAAAATTAC
Found at i:122219 original size:57 final size:58
Alignment explanation
Indices: 122123--122428 Score: 252
Period size: 59 Copynumber: 5.2 Consensus size: 58
122113 TGAATTGACA
* * *
122123 AAAAATCATA-TTTTGACCCCCAAACTCTTCC-AAAATTACATTTTGACCCCTAAACTTTTC
1 AAAAATCACATTTTTG-CCCCTAAA--CTTCCAAAAATTACATTTTGACCCCTAAAC-TTCC
* * *
122183 TAACATCACA-TTTT-CCCCTAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCC
1 AAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTGACCCCTAAACTTCC
* * * *
122239 AAAAATTACATTTTTGCCCCTTAACTTCTCAAAAATTACATTTTTA-CTCTCAAACTTCC
1 AAAAATCACATTTTTGCCCCTAAACTTC-CAAAAATTACATTTTGACCCCT-AAACTTCC
* * * * * * * *
122298 AAAAATCATATTTTTACCTCTGATCTTCTCAAAAATTACATTTTG-CCTCAAAACTTCT
1 AAAAATCACATTTTTGCCCCTAAACTTC-CAAAAATTACATTTTGACCCCTAAACTTCC
* * *
122356 AAAAATCACATTTTTACCCTTGATA-TAT-CAAAAATTACATTGTT-ACCCCTAAACTTCTC
1 AAAAATCACATTTTTGCCCCT-AAACT-TCCAAAAATTACATT-TTGACCCCTAAACTTC-C
*
122415 AAAAATTACATTTT
1 AAAAATCACATTTT
122429 GCCTCCGAAC
Statistics
Matches: 205, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
56 15 0.07
57 40 0.20
58 59 0.29
59 80 0.39
60 11 0.05
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (58 bp):
AAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTGACCCCTAAACTTCC
Found at i:122229 original size:87 final size:87
Alignment explanation
Indices: 122123--122489 Score: 292
Period size: 87 Copynumber: 4.2 Consensus size: 87
122113 TGAATTGACA
* * *
122123 AAAAATCATATTTTGACCCCCAAACTCTTCC-AAAATTACATTTTGACCCCTAAACTTTTCTAAC
1 AAAAATCACATTTTTACCCCCAAA-TCTTCCAAAAATTACATTTTG-CCCCTAAAC--TTCTAAA
122187 ATCACA-TTTT-CCCCT-AAACTTCC
62 ATCACATTTTTACCCCTCAAACTTCC
* * *
122210 AAAAATTACATTTTTACCCCTAAA-CTTCCAAAAATTACATTTTTGCCCCTTAACTTCTCAAAAA
1 AAAAATCACATTTTTACCCCCAAATCTTCCAAAAATTACA-TTTTGCCCCTAAACTTCT--AAAA
* *
122274 TTACATTTTTA-CTCTCAAACTTCC
63 TCACATTTTTACCCCTCAAACTTCC
* * ** * *
122298 AAAAATCATATTTTTA-CCTCTGATCTTCTCAAAAATTACATTTTGCCTCAAAACTTCTAAAAAT
1 AAAAATCACATTTTTACCCCCAAATCTTC-CAAAAATTACATTTTGCCCCTAAACTTCT-AAAAT
* * *
122362 CACATTTTTACCCTTGATA-TAT-C
64 CACATTTTTACCCCTCAAACT-TCC
* * * * **
122385 AAAAATTACATTGTTACCCCTAAA-CTTCTCAAAAATTACATTTTGCCTCC-GAACTTCTAACTT
1 AAAAATCACATTTTTACCCCCAAATCTTC-CAAAAATTACATTTTGCC-CCTAAACTTCTAAAAT
* * *
122448 CACATTTTT-GCTC-CGAACTTCTC
64 CACATTTTTACCCCTCAAACTTC-C
122471 AAAAATCACATTTTTACCC
1 AAAAATCACATTTTTACCC
122490 TGAATTTTCT
Statistics
Matches: 223, Mismatches: 41, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
84 6 0.03
85 7 0.03
86 54 0.24
87 95 0.43
88 50 0.22
89 11 0.05
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (87 bp):
AAAAATCACATTTTTACCCCCAAATCTTCCAAAAATTACATTTTGCCCCTAAACTTCTAAAATCA
CATTTTTACCCCTCAAACTTCC
Found at i:122235 original size:29 final size:29
Alignment explanation
Indices: 122149--122428 Score: 259
Period size: 29 Copynumber: 9.7 Consensus size: 29
122139 CCCCCAAACT
*
122149 CTTCC-AAAATTACATTTTGACCCCTAAA
1 CTTCCAAAAATTACATTTTTACCCCTAAA
* * * *
122177 CTTTTCTAACATCACA-TTTT-CCCCTAAA
1 C-TTCCAAAAATTACATTTTTACCCCTAAA
122205 CTTCCAAAAATTACATTTTTACCCCTAAA
1 CTTCCAAAAATTACATTTTTACCCCTAAA
* *
122234 CTTCCAAAAATTACATTTTTGCCCCTTAA
1 CTTCCAAAAATTACATTTTTACCCCTAAA
*
122263 CTTCTCAAAAATTACATTTTTA-CTCTCAAA
1 CTTC-CAAAAATTACATTTTTACCCCT-AAA
* * * * *
122293 CTTCCAAAAATCATATTTTTACCTCTGAT
1 CTTCCAAAAATTACATTTTTACCCCTAAA
* * *
122322 CTTCTCAAAAATTACA-TTTTGCCTCAAAA
1 CTTC-CAAAAATTACATTTTTACCCCTAAA
* * * *
122351 CTTCTAAAAATCACATTTTTACCCTTGATA
1 CTTCCAAAAATTACATTTTTACCCCT-AAA
*
122381 -TAT-CAAAAATTACATTGTTACCCCTAAA
1 CT-TCCAAAAATTACATTTTTACCCCTAAA
122409 CTTCTCAAAAATTACATTTT
1 CTTC-CAAAAATTACATTTT
122429 GCCTCCGAAC
Statistics
Matches: 202, Mismatches: 36, Indels: 26
0.77 0.14 0.10
Matches are distributed among these distances:
27 10 0.05
28 26 0.13
29 107 0.53
30 59 0.29
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
CTTCCAAAAATTACATTTTTACCCCTAAA
Found at i:122280 original size:59 final size:58
Alignment explanation
Indices: 122154--122428 Score: 281
Period size: 59 Copynumber: 4.7 Consensus size: 58
122144 AAACTCTTCC
* * * * *
122154 AAAATTACATTTTGACCCCTAAACTTTTCTAACATCACA-TTTTCCCCTAAACTTC-CA
1 AAAATTACATTTTTACCCCTAAAC-TTCCAAAAATCACATTTTTCCCCTTAACTTCTCA
*
122211 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGCCCCTTAACTTCTCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTT-CCCCTTAACTTCTCA
* * * * *
122270 AAAATTACATTTTTA-CTCTCAAACTTCCAAAAATCATATTTTTACCTCTGATCTTCTCA
1 AAAATTACATTTTTACCCCT-AAACTTCCAAAAATCACATTTTT-CCCCTTAACTTCTCA
* * * * * * *
122329 AAAATTACA-TTTTGCCTCAAAACTTCTAAAAATCACATTTTTACCCTTGA-TATATCA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTCCCCTTAACT-TCTCA
* *
122386 AAAATTACATTGTTACCCCTAAACTTCTCAAAAATTACATTTT
1 AAAATTACATTTTTACCCCTAAACTTC-CAAAAATCACATTTT
122429 GCCTCCGAAC
Statistics
Matches: 181, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
56 11 0.06
57 43 0.24
58 52 0.29
59 75 0.41
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTCCCCTTAACTTCTCA
Found at i:122440 original size:29 final size:30
Alignment explanation
Indices: 122123--122488 Score: 225
Period size: 29 Copynumber: 12.6 Consensus size: 30
122113 TGAATTGACA
* * * *
122123 AAAAATCATATTTTGACCCCCAAAC-TCTTC
1 AAAAATTACATTTTTACCTCCAAACTTC-TC
* * *
122153 CAAAATTACATTTTGACC-CCTAAACTTTTC
1 AAAAATTACATTTTTACCTCC-AAACTTCTC
* * *
122183 TAACATCACA-TTTT-CC-CCTAAACTTC-C
1 AAAAATTACATTTTTACCTCC-AAACTTCTC
122210 AAAAATTACATTTTTACC-CCTAAACTTC-C
1 AAAAATTACATTTTTACCTCC-AAACTTCTC
* *
122239 AAAAATTACATTTTTGCC-CCTTAACTTCTC
1 AAAAATTACATTTTTACCTCC-AAACTTCTC
122269 AAAAATTACATTTTTA-CTCTCAAACTTC-C
1 AAAAATTACATTTTTACCTC-CAAACTTCTC
* * ** *
122298 AAAAATCATATTTTTACCTCTGATCTTCTC
1 AAAAATTACATTTTTACCTCCAAACTTCTC
* *
122328 AAAAATTACA-TTTTGCCTCAAAACTTCT-
1 AAAAATTACATTTTTACCTCCAAACTTCTC
* *** *
122356 AAAAATCACATTTTTACC-CTTGA-TATATC
1 AAAAATTACATTTTTACCTCCAAACT-TCTC
*
122385 AAAAATTACATTGTTACC-CCTAAACTTCTC
1 AAAAATTACATTTTTACCTCC-AAACTTCTC
* *
122415 AAAAATTACA-TTTTGCCTCCGAACTTCT-
1 AAAAATTACATTTTTACCTCCAAACTTCTC
* * *
122443 --AACTTCACATTTTT-GCTCCGAACTTCTC
1 AAAAATT-ACATTTTTACCTCCAAACTTCTC
*
122471 AAAAATCACATTTTTACC
1 AAAAATTACATTTTTACC
122489 CTGAATTTTC
Statistics
Matches: 268, Mismatches: 47, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
26 4 0.01
27 24 0.09
28 32 0.12
29 122 0.46
30 83 0.31
31 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTTACCTCCAAACTTCTC
Found at i:122718 original size:16 final size:15
Alignment explanation
Indices: 122670--122719 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
122660 TTGATTCATA
122670 ATTCGTAT-TTTATT
1 ATTCGTATATTTATT
* * *
122684 TTTCTTATATTTAAT
1 ATTCGTATATTTATT
122699 -TTCGTATATTTATT
1 ATTCGTATATTTATT
122713 CATTCGT
1 -ATTCGT
122720 GCTTTGTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 18 0.64
15 5 0.18
16 5 0.18
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTCGTATATTTATT
Found at i:127233 original size:17 final size:17
Alignment explanation
Indices: 127198--127265 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 17
127188 GGCCTATTGG
* *
127198 ATTTTGAATTT-ATTTT
1 ATTTTAAATTTAAATTT
127214 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
127231 ATTTGAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
127248 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
127265 A
1 A
127266 AAATGTCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 10 0.22
17 36 0.78
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:127241 original size:7 final size:6
Alignment explanation
Indices: 127216--127267 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
127206 TTTATTTTAT
127216 TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
127262 TTTAAA
1 TTTAAA
127268 ATGTCCAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 7 0.17
5 1 0.03
6 25 0.62
7 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:129037 original size:30 final size:29
Alignment explanation
Indices: 129001--129320 Score: 207
Period size: 30 Copynumber: 10.8 Consensus size: 29
128991 CCCTAAATTG
*
129001 TCCAAAAATCTCATTTTTGACCCAAAAACT
1 TCCAAAAATCCCATTTTT-ACCCAAAAACT
**
129031 TCCAAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATCCCATTTTT-ACCCAAAAACT
* * ***
129061 TCCAAAAAATCTCGTTTTTACCCTCGAACT
1 TCC-AAAAATCCCATTTTTACCCAAAAACT
* * *
129091 TCCAAAAATCCCATTTTTAATCTC-GAAGCT
1 TCCAAAAATCCCATTTTT-A-CCCAAAAACT
* * * *
129121 TCCAAAAATCTCGTTTTTA-TCACTAAACT
1 TCCAAAAATCCCATTTTTACCCA-AAAACT
* * ***
129150 TCCAAAAAACCCAATTTTACCCCTGAACT
1 TCCAAAAATCCCATTTTTACCCAAAAACT
* * *
129179 TTCAAAAATTCCATTTTTTACCTC-GAAACT
1 TCCAAAAATCCCA-TTTTTACC-CAAAAACT
**
129209 TTAAAAAATCCCATTTTTTACCCAAAAACT
1 TCCAAAAATCCCA-TTTTTACCCAAAAACT
*
129239 TCCAAAAATCCCATTTTTGACCGAAAAACT
1 TCCAAAAATCCCATTTTT-ACCCAAAAACT
* * * *
129269 TGCAAAGATCCCGTTTTTAGCCC-TAAACT
1 TCCAAAAATCCCATTTTTA-CCCAAAAACT
** *
129298 TTAAAAAATCACATTTTTGACCC
1 TCCAAAAATCCCATTTTT-ACCC
129321 CGAATTTTCC
Statistics
Matches: 231, Mismatches: 47, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.01
29 76 0.33
30 137 0.59
31 16 0.07
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTACCCAAAAACT
Found at i:129094 original size:60 final size:59
Alignment explanation
Indices: 129004--129307 Score: 226
Period size: 59 Copynumber: 5.1 Consensus size: 59
128994 TAAATTGTCC
* **
129004 AAAAATCTCATTTTTGACCCAAAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCA
1 AAAAATCTCGTTTTT-ACCCTCAAACTTCCAAAAATCCCATTTTT-ACCCCGAAACTTCCA
* * * *
129065 AAAAATCTCGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAATCTCGAAGCTTCC-
1 AAAAATCTCGTTTTTACCCTCAAACTTCCAAAAATCCCATTTTT-ACCCCGAAACTTCCA
* * * *
129124 AAAAATCTCGTTTTTATCACT-AAACTTCCAAAAAACCCAATTTTACCCCTG-AACTTTCA
1 AAAAATCTCGTTTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTACCCC-GAAACTTCCA
* * ** **
129183 AAAATTC-CATTTTTTA-CCTCGAAACTTTAAAAAATCCCATTTTTTACCCAAAAACTTCC-
1 AAAAATCTC-GTTTTTACCCTC-AAACTTCCAAAAATCCCA-TTTTTACCCCGAAACTTCCA
* * *** * * * * * *
129242 AAAAATCCCATTTTTGACCGAAAAACTTGCAAAGATCCCGTTTTTAGCCCTAAACTT-TA
1 AAAAATCTCGTTTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCCA
129301 AAAAATC
1 AAAAATC
129308 ACATTTTTGA
Statistics
Matches: 192, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
57 2 0.01
58 9 0.05
59 96 0.50
60 70 0.36
61 15 0.08
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (59 bp):
AAAAATCTCGTTTTTACCCTCAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCCA
Found at i:129784 original size:90 final size:90
Alignment explanation
Indices: 129620--129793 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
129610 AAAACTTTAA
* * *
129620 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGGGCAATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGGGCAACT
*
129685 TTTTCTCAAATCGAAATAAACCCTT
66 TTCTCTCAAATCGAAATAAACCCTT
*
129710 AATCGAGGCAATATT-TCCTTATCTTCGA--TTCTG-AAATATTGCGCCTTAACTTACTAGGTGC
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTC-GAAAAT-TTGCGCCTTAACTTACTAGGGGC
*
129771 AACCTTTCT-TCAAATCGAGATAA
62 AA-CTTTCTCTCAAATCGAAATAA
129794 TCGAATATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
89 8 0.11
90 56 0.77
91 9 0.12
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (90 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGGGCAACT
TTCTCTCAAATCGAAATAAACCCTT
Found at i:134575 original size:11 final size:11
Alignment explanation
Indices: 134559--134614 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
134549 TGTTTAAAAA
134559 TTTAAATTTAT
1 TTTAAATTTAT
*
134570 TTTAAATTTAAA
1 TTTAAATTT-AT
** *
134582 TTTATTTTTAG
1 TTTAAATTTAT
134593 TTTAAATTTAT
1 TTTAAATTTAT
134604 TTTCAAATTTA
1 TTT-AAATTTA
134615 AAATTGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:134578 original size:17 final size:17
Alignment explanation
Indices: 134541--134616 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
134531 AATTCATTTT
* *
134541 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
134559 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
134576 TTTAAATTTATTTTTAG
1 TTTAAATTTATTTTAAA
134593 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
134611 TTTAAA
1 TTTAAA
134617 ATTGTTAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
17 32 0.63
18 19 0.37
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:134614 original size:23 final size:23
Alignment explanation
Indices: 134556--134602 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
134546 ATTTGTTTAA
*
134556 AAATTTAAATTTATTTTAAATTT
1 AAATTTAAATTTAGTTTAAATTT
**
134579 AAATTTATTTTTAGTTTAAATTT
1 AAATTTAAATTTAGTTTAAATTT
134602 A
1 A
134603 TTTTCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTTAAATTTAGTTTAAATTT
Found at i:134745 original size:17 final size:18
Alignment explanation
Indices: 134712--134753 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
134702 TACAAAATGG
*
134712 CCCAAAATCAGCCCTAAA
1 CCCAAAATCAACCCTAAA
134730 CCCAAAAT-AACCCTAAA
1 CCCAAAATCAACCCTAAA
*
134747 CCTAAAA
1 CCCAAAA
134754 GGGCCCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.50, C:0.36, G:0.02, T:0.12
Consensus pattern (18 bp):
CCCAAAATCAACCCTAAA
Found at i:135340 original size:16 final size:18
Alignment explanation
Indices: 135319--135355 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
135309 AGTGATAAGT
135319 ATTAAT-AG-TAATATTA
1 ATTAATCAGATAATATTA
135335 ATTAATCAGAATAATATTA
1 ATTAATCAG-ATAATATTA
135354 AT
1 AT
135356 AATGGACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
19 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTAATCAGATAATATTA
Found at i:135439 original size:17 final size:18
Alignment explanation
Indices: 135407--135443 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
135397 GCGGTTTTTC
*
135407 AAAATTTTTATTAATAAT
1 AAAATTTTTATAAATAAT
135425 AAAATTTTT-TAAATAAT
1 AAAATTTTTATAAATAAT
135442 AA
1 AA
135444 TAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTTTATAAATAAT
Found at i:136650 original size:89 final size:89
Alignment explanation
Indices: 136552--136730 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 89
136542 CCATTTTTGA
* * *
136552 CCCGAGCCTTCTAAAAATTACCATTTTA-CCCTAAATCTTCCAAAAATCCCATTTTTGACCCCGA
1 CCCGAGCCTTCTAAAAATTACCATTTTACCCCCAAA-CTTCCAAAAATCCCATTTTTAACCCCAA
* *
136616 GCCTTCTAAAAATTACCATTTTACC
65 ACCTTCCAAAAATTACCATTTTACC
* * *
136641 CCCGAGCCTTCTAAAAATTGCCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAA
1 CCCGAGCCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAA
*
136706 CTTTCCAAAAATTACCATTTTACC
66 CCTTCCAAAAATTACCATTTTACC
136730 C
1 C
136731 TTAAACTTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 75 0.94
90 5 0.06
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (89 bp):
CCCGAGCCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAA
CCTTCCAAAAATTACCATTTTACC
Found at i:136668 original size:30 final size:30
Alignment explanation
Indices: 136441--136791 Score: 195
Period size: 30 Copynumber: 11.9 Consensus size: 30
136431 AGTCCCTAAA
*
136441 CCTTCTAAAAGTTACCATTTTACCCCCGA-
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
* * * * * *
136470 ACTTCCAAAAA-TCCCAATACTGA-CCCTGAG
1 CCTTCTAAAAATTACC-AT-TTTACCCCCGAG
136500 CCTTCTAAAAATTACCATTTTACCCCCGA-
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
* * * * ***
136529 ACATCCAAAAA-TCCCATTTTTGACCCGAG
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
** *
136558 CCTTCTAAAAATTACCATTTTA-CCCTAAA
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
* * *
136587 TCTTCCAAAAA-TCCCATTTTTGA-CCCCGAG
1 CCTTCTAAAAATTACCA-TTTT-ACCCCCGAG
136617 CCTTCTAAAAATTACCATTTTACCCCCGAG
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
*
136647 CCTTCTAAAAATTGCCATTTTACCCCCGA-
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
* * * * ** *
136676 ACTTCCAAAAA-TCCCATTTTTAACCCTAAA
1 CCTTCTAAAAATTACCA-TTTTACCCCCGAG
* * ** *
136706 CTTTCCAAAAATTACCATTTTA-CCCTTAA
1 CCTTCTAAAAATTACCATTTTACCCCCGAG
* * * * * *
136735 ACTTCCAAAAA-TCCCATTTTTAACCCTGAA
1 CCTTCTAAAAATTACCA-TTTTACCCCCGAG
* *
136765 CGTTCTAAAAATTATCATTTTACCCCC
1 CCTTCTAAAAATTACCATTTTACCCCC
136792 AAACTTCCAA
Statistics
Matches: 245, Mismatches: 60, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
28 28 0.11
29 88 0.36
30 115 0.47
31 14 0.06
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (30 bp):
CCTTCTAAAAATTACCATTTTACCCCCGAG
Found at i:136672 original size:59 final size:59
Alignment explanation
Indices: 136441--136645 Score: 315
Period size: 59 Copynumber: 3.5 Consensus size: 59
136431 AGTCCCTAAA
* * ** *
136441 CCTTCTAAAAGTTACCATTTTACCCCCGAACTTCCAAAAATCCCAATACTGACCCTGAG
1 CCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAG
*
136500 CCTTCTAAAAATTACCATTTTACCCCCGAACATCCAAAAATCCCATTTTTGA-CCCGAG
1 CCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAG
**
136558 CCTTCTAAAAATTACCATTTTA-CCCTAAATCTTCCAAAAATCCCATTTTTGACCCCGAG
1 CCTTCTAAAAATTACCATTTTACCCCCGAA-CTTCCAAAAATCCCATTTTTGACCCCGAG
136617 CCTTCTAAAAATTACCATTTTACCCCCGA
1 CCTTCTAAAAATTACCATTTTACCCCCGA
136646 GCCTTCTAAA
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
57 5 0.04
58 48 0.36
59 75 0.57
60 4 0.03
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.29
Consensus pattern (59 bp):
CCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAG
Found at i:136686 original size:59 final size:59
Alignment explanation
Indices: 136501--136805 Score: 228
Period size: 59 Copynumber: 5.2 Consensus size: 59
136491 GACCCTGAGC
* * * * * *** *
136501 CTTCTAAAAATTACCATTTTACCCCCGAA-CATCCAAAAA-TCCCATTTTTGACCCGAGC
1 CTTCCAAAAATTACCATTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGA-A
* * * * *
136559 CTTCTAAAAATTACCATTTT-ACCCTAAATCTTCCAAAAA-TCCCATTTTTGA-CCCCGAGC
1 CTTCCAAAAATTACCATTTTAACCCTGAACCTTCCAAAAATTACCA-TTTT-ACCCCCGA-A
* * * * * *
136618 CTTCTAAAAATTACCATTTTACCCCCGAGCCTTCTAAAAATTGCCATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAA
* * * ***
136677 CTTCCAAAAA-TCCCATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTTAAA
1 CTTCCAAAAATTACCA-TTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAA
* * * * *
136736 CTTCCAAAAA-TCCCATTTTTAACCCTGAACGTTCTAAAAATTATCATTTTACCCCCAAA
1 CTTCCAAAAATTACCA-TTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAA
136795 CTTCCAAAAAT
1 CTTCCAAAAAT
136806 CCCAATTTTG
Statistics
Matches: 207, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
57 5 0.02
58 38 0.18
59 137 0.66
60 23 0.11
61 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
CTTCCAAAAATTACCATTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:136806 original size:59 final size:59
Alignment explanation
Indices: 136649--136814 Score: 251
Period size: 59 Copynumber: 2.8 Consensus size: 59
136639 CCCCCGAGCC
* * *
136649 TTCTAAAAATTGCCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTAAACG
* ** *
136708 TTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCCCATTTTTAACCCTGAACG
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTAAACG
* *
136767 TTCTAAAAATTATCATTTTACCCCCAAACTTCCAAAAATCCCAATTTT
1 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
136815 GACTCCGAAC
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 95 1.00
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTAAACG
Found at i:140284 original size:24 final size:24
Alignment explanation
Indices: 140257--140306 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
140247 TTTAAGAGTT
140257 CCAAGATATCTTTGCATGGTCTTA
1 CCAAGATATCTTTGCATGGTCTTA
140281 CCAAGATATCTTTGCATGGTCTTA
1 CCAAGATATCTTTGCATGGTCTTA
140305 CC
1 CC
140307 GTGAAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (24 bp):
CCAAGATATCTTTGCATGGTCTTA
Done.