Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003926.1 Hibiscus syriacus cultivar Beakdansim tig00008486_pilon, 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: 92617
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:4422 original size:3 final size:3
Alignment explanation
Indices: 4408--4440 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4398 CCATTGCAAA
*
4408 GAG GAG GCG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
4441 ATGAAGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:11420 original size:16 final size:17
Alignment explanation
Indices: 11401--11433 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11391 ATATGATCCT
11401 AATAATTCAT-ATTCTG
1 AATAATTCATGATTCTG
*
11417 AATAATTGATGATTCTG
1 AATAATTCATGATTCTG
11434 TCAGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAATTCATGATTCTG
Found at i:11656 original size:24 final size:24
Alignment explanation
Indices: 11620--11682 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
11610 TGATTTCGGA
* * *
11620 TCTGATTTCTGATCTAAATTCTGT
1 TCTGATATATGATATAAATTCTGT
*
11644 TCTGATATATGATATGAATTCTGT
1 TCTGATATATGATATAAATTCTGT
* * *
11668 TTTGATTTTTGATAT
1 TCTGATATATGATAT
11683 CTCTATTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (24 bp):
TCTGATATATGATATAAATTCTGT
Found at i:20258 original size:29 final size:29
Alignment explanation
Indices: 20217--20274 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
20207 TATTAATAAA
20217 TTTAATTTAAATTAAAATATATATATATT
1 TTTAATTTAAATTAAAATATATATATATT
*
20246 TTTATATTTAATTTAAATATATATATATA
1 TTTA-ATTTAAATTAAA-ATATATATATA
20275 CCCAGCCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 11 0.42
31 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAATTTAAATTAAAATATATATATATT
Found at i:21581 original size:14 final size:15
Alignment explanation
Indices: 21556--21584 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21546 AGTTTCCAGA
21556 TTTCTCTTCTTCTTC
1 TTTCTCTTCTTCTTC
21571 TTTCT-TTCTTCTTC
1 TTTCTCTTCTTCTTC
21585 ACCGTGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCTCTTCTTCTTC
Found at i:22954 original size:23 final size:23
Alignment explanation
Indices: 22909--22969 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
22899 CAATCTTATA
*
22909 TGGCACTATGGTGCAATTCTACG
1 TGGCACTTTGGTGCAATTCTACG
22932 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTTGGTGCAATTCTACG
* *
22955 TGCCACTTCGGTGCA
1 TGGCACTTTGGTGCA
22970 TTTATACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTTGGTGCAATTCTACG
Found at i:29892 original size:23 final size:23
Alignment explanation
Indices: 29866--29925 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
29856 AATCTTATAT
*
29866 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
29889 GGCACTTCAGTACAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
29912 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
29926 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:31799 original size:45 final size:44
Alignment explanation
Indices: 31682--31876 Score: 178
Period size: 45 Copynumber: 4.4 Consensus size: 44
31672 TAGCCAGGCA
* * * * *
31682 AGGTGCCGATGCTGTGTGACCCAGACCTAGCCTAAGGTA-TTAAG
1 AGGTGCCGATGCTATGTGACACAGACCTCGCCTAAGATACTT-GG
* * * *
31726 AGGTGCCAATGTTATATG-CACGGACCTCGCCTAAGATACTTGG
1 AGGTGCCGATGCTATGTGACACAGACCTCGCCTAAGATACTTGG
* *
31769 TAGGTGTCGATGCTATGTGACACAGACCTCGCCTGAGATACTTGGG
1 -AGGTGCCGATGCTATGTGACACAGACCTCGCCTAAGATACTT-GG
* * * *
31815 AGGTGTCGATGCTATGTGACACGGACCTCACCTGAGATACTTGGG
1 AGGTGCCGATGCTATGTGACACAGACCTCGCCTAAGATACTT-GG
* **
31860 AGATGCTAATGCTATGT
1 AGGTGCCGATGCTATGT
31877 AACCCATGTC
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
43 17 0.13
44 30 0.24
45 77 0.61
46 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (44 bp):
AGGTGCCGATGCTATGTGACACAGACCTCGCCTAAGATACTTGG
Found at i:37233 original size:44 final size:44
Alignment explanation
Indices: 37154--37343 Score: 169
Period size: 43 Copynumber: 4.4 Consensus size: 44
37144 TTGCAAAGGT
* * * *
37154 AAAATGTGATATTG-AAAATTTTAGGGGCCTAAATTATATAAGC
1 AAAAAGTGATATTGAAAAAATTTAGGGGCCTCAATTATAAAAGC
* **
37197 AAAAAGTGATATTGAAAAAATTTAGGGGTCTCAATTATAAAAAT
1 AAAAAGTGATATTGAAAAAATTTAGGGGCCTCAATTATAAAAGC
* * **
37241 AAAAATTG-TGATT-AAAAAAATTAATGGCCTCAATTAT-AAAGC
1 AAAAAGTGAT-ATTGAAAAAATTTAGGGGCCTCAATTATAAAAGC
* * * *
37283 TAGAAAGTGATATTGAAAAAA-TTATGAG-CTCAATTATAAAAGT
1 -AAAAAGTGATATTGAAAAAATTTAGGGGCCTCAATTATAAAAGC
*
37326 AAAAA-TGAGATTGAAAAA
1 AAAAAGTGATATTGAAAAA
37344 CTTAGGGTAA
Statistics
Matches: 119, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
41 12 0.10
42 16 0.13
43 51 0.43
44 40 0.34
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (44 bp):
AAAAAGTGATATTGAAAAAATTTAGGGGCCTCAATTATAAAAGC
Found at i:37576 original size:12 final size:12
Alignment explanation
Indices: 37544--37576 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
37534 TTTAATCAGT
37544 GATAACATTTAG
1 GATAACATTTAG
37556 GATAA-ATTTAG
1 GATAACATTTAG
37567 GATAACATTT
1 GATAACATTT
37577 TTTTAATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (12 bp):
GATAACATTTAG
Found at i:40333 original size:41 final size:41
Alignment explanation
Indices: 40288--40457 Score: 134
Period size: 41 Copynumber: 4.1 Consensus size: 41
40278 ATAGTGGCGT
** *
40288 TTTTTCAAAAAATACTGCAATAGATTAGTAATTTAGCGGCA
1 TTTTTCAAAAAACGCCGCAATAGATTAGTAATTTAGCGGCA
* *
40329 TTTTT-ATACAAAA-GCCGCAATAGATTGGTAATTTAGCGGCG
1 TTTTTCA-A-AAAACGCCGCAATAGATTAGTAATTTAGCGGCA
* * *
40370 TTTATCAAACAAACGCCGCAATATGATT-GT--TTATAGTGGCG
1 TTTTTCAAA-AAACGCCGCAATA-GATTAGTAATT-TAGCGGCA
* * * * *
40411 TTTGTGCAAAAAACACCCCAATAGAGTAATAATTTAGCGGCA
1 TTT-TTCAAAAAACGCCGCAATAGATTAGTAATTTAGCGGCA
40453 TTTTT
1 TTTTT
40458 TGAAAAAAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 22
0.74 0.11 0.16
Matches are distributed among these distances:
40 7 0.07
41 61 0.59
42 29 0.28
43 6 0.06
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (41 bp):
TTTTTCAAAAAACGCCGCAATAGATTAGTAATTTAGCGGCA
Found at i:40373 original size:124 final size:124
Alignment explanation
Indices: 40212--40457 Score: 325
Period size: 124 Copynumber: 2.0 Consensus size: 124
40202 GTGTTTTTCA
* * ** * *
40212 ACAAATGCCGCAATAGAGTGGTAATGTAGCGGTGTTTAT-AGCTCAAACGTCGGAATA-GAGTTG
1 ACAAAAGCCGCAATAGAGTGGTAATGTAGCGGCGTTTATCA-AACAAACGCCGCAATATGA-TTG
* * * ** * *
40275 TTTATAGTGGCGTTTTTTCAAAAAATACTGCAATAGATTAGTAATTTAGCGGCATTTTTAT
64 TTTATAGTGGCGTTTGTGCAAAAAACACCCCAATAGAGTAATAATTTAGCGGCATTTTTAT
* *
40336 ACAAAAGCCGCAATAGATTGGTAATTTAGCGGCGTTTATCAAACAAACGCCGCAATATGATTGTT
1 ACAAAAGCCGCAATAGAGTGGTAATGTAGCGGCGTTTATCAAACAAACGCCGCAATATGATTGTT
40401 TATAGTGGCGTTTGTGCAAAAAACACCCCAATAGAGTAATAATTTAGCGGCATTTTT
66 TATAGTGGCGTTTGTGCAAAAAACACCCCAATAGAGTAATAATTTAGCGGCATTTTT
40458 TGAAAAAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
124 102 0.97
125 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (124 bp):
ACAAAAGCCGCAATAGAGTGGTAATGTAGCGGCGTTTATCAAACAAACGCCGCAATATGATTGTT
TATAGTGGCGTTTGTGCAAAAAACACCCCAATAGAGTAATAATTTAGCGGCATTTTTAT
Found at i:40946 original size:22 final size:22
Alignment explanation
Indices: 40918--40965 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40908 TGTTTTTCTT
40918 CTTTCGAATAGAAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
*
40940 CTTTCGAATAGGAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
40962 CTTT
1 CTTT
40966 TGAAAACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTTCGAATAGAAAAATAATAG
Found at i:42305 original size:41 final size:41
Alignment explanation
Indices: 42244--42433 Score: 193
Period size: 41 Copynumber: 4.6 Consensus size: 41
42234 TTAATTTTGT
** *
42244 GCGTTTGTGGCAAAACGCCGCAATAGCCATATACTTTAGTG
1 GCGTTTGTGAAAAAACGCCGCAATAGCCATGTACTTTAGTG
* * * * *
42285 GTGTTTCTGAGAAAATGCCGCAATAGCCTTGTACTTTAGTG
1 GCGTTTGTGAAAAAACGCCGCAATAGCCATGTACTTTAGTG
** * * *
42326 GCGTTTGTGACCAAACACCGCAATATCCATGTACTTTAGCG
1 GCGTTTGTGAAAAAACGCCGCAATAGCCATGTACTTTAGTG
* * * * *
42367 ACGTTTGTAAAAAAATGCCGCAATATCTATGTACTTTAGTG
1 GCGTTTGTGAAAAAACGCCGCAATAGCCATGTACTTTAGTG
*
42408 GCGTTTGT-AAAGACACGCCGCAATAG
1 GCGTTTGTGAAA-AAACGCCGCAATAG
42434 TTTTGCCCTT
Statistics
Matches: 120, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
40 3 0.03
41 117 0.98
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
GCGTTTGTGAAAAAACGCCGCAATAGCCATGTACTTTAGTG
Found at i:42333 original size:82 final size:82
Alignment explanation
Indices: 42244--42415 Score: 220
Period size: 82 Copynumber: 2.1 Consensus size: 82
42234 TTAATTTTGT
* * * ** * *
42244 GCGTTTGTGGCAAAACGCCGCAATAGCCATATACTTTAGTGGTGTTTCTGAGAAAATGCCGCAAT
1 GCGTTTGTGACAAAACACCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAAT
42309 AGCCT-TGTACTTTAGTG
66 A-CCTATGTACTTTAGTG
* * * *
42326 GCGTTTGTGACCAAACACCGCAATATCCATGTACTTTAGCGACGTTTGTAAAAAAATGCCGCAAT
1 GCGTTTGTGACAAAACACCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAAT
*
42391 ATCTATGTACTTTAGTG
66 ACCTATGTACTTTAGTG
42408 GCGTTTGT
1 GCGTTTGT
42416 AAAGACACGC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 2 0.03
82 75 0.97
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (82 bp):
GCGTTTGTGACAAAACACCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAAT
ACCTATGTACTTTAGTG
Found at i:42429 original size:82 final size:82
Alignment explanation
Indices: 42256--42433 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 82
42246 GTTTGTGGCA
* ** * *
42256 AAACGCCGCAATAGCCATATACTTTAGTGGTGTTTCTGAGAAAATGCCGCAATAGCCTTGTACTT
1 AAACGCCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAATAGCCTTGTACTT
* *
42321 TAGTGGCGTTTGTGACC
66 TAGTGGCGTTTGTAAAC
* * * * *
42338 AAACACCGCAATATCCATGTACTTTAGCGACGTTTGTAAAAAAATGCCGCAATA-TCTATGTACT
1 AAACGCCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAATAGCCT-TGTACT
*
42402 TTAGTGGCGTTTGTAAAG
65 TTAGTGGCGTTTGTAAAC
*
42420 ACACGCCGCAATAG
1 AAACGCCGCAATAG
42434 TTTTGCCCTT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
81 2 0.03
82 77 0.97
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (82 bp):
AAACGCCGCAATAGCCATATACTTTAGCGACGTTTCTAAAAAAATGCCGCAATAGCCTTGTACTT
TAGTGGCGTTTGTAAAC
Found at i:42477 original size:42 final size:44
Alignment explanation
Indices: 42431--42542 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
42421 CACGCCGCAA
42431 TAGTTTTGCCCTTTAGTGGTG-TTTTT-T-TAATAAACGCCATAG
1 TAGTTTTGCCCTTTAGTGG-GATTTTTGTGTAATAAACGCCATAG
* *
42473 TAGTTTTGTCCTTTA-TGGGCATTTTTGTGTAATAAACGCCGTAG
1 TAGTTTTGCCCTTTAGTGGG-ATTTTTGTGTAATAAACGCCATAG
* * *
42517 AAGTTTGGTCCC-TTAGTGGCATTTTT
1 TAGTTTTG-CCCTTTAGTGGGATTTTT
42543 AATATAAACG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 19 0.33
43 1 0.02
44 29 0.50
45 5 0.09
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.45
Consensus pattern (44 bp):
TAGTTTTGCCCTTTAGTGGGATTTTTGTGTAATAAACGCCATAG
Found at i:42522 original size:44 final size:44
Alignment explanation
Indices: 42458--42542 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
42448 GGTGTTTTTT
* * *
42458 TAATAAACGCCATAGTAGTTTTGTCCTTTA-TGGGCATTTTTGTG
1 TAATAAACGCCATAGAAGTTTGGTCCCTTAGT-GGCATTTTTGTG
*
42502 TAATAAACGCCGTAGAAGTTTGGTCCCTTAGTGGCATTTTT
1 TAATAAACGCCATAGAAGTTTGGTCCCTTAGTGGCATTTTT
42543 AATATAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (44 bp):
TAATAAACGCCATAGAAGTTTGGTCCCTTAGTGGCATTTTTGTG
Found at i:49975 original size:18 final size:19
Alignment explanation
Indices: 49952--50032 Score: 89
Period size: 18 Copynumber: 4.3 Consensus size: 19
49942 TTTACTTAAT
49952 TTATTATTATTA-AAATTA
1 TTATTATTATTATAAATTA
49970 TTATTATTATTATAAA-TA
1 TTATTATTATTATAAATTA
*
49988 TTATTATTA-TATTATATATA
1 TTATTATTATTA-TAAAT-TA
*
50008 TTA-TATTATTATTAAATAA
1 TTATTATTATTA-TAAATTA
50027 TTATTA
1 TTATTA
50033 CAAGCCCAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 26 0.48
19 12 0.22
20 14 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTATTATAAATTA
Found at i:50032 original size:3 final size:3
Alignment explanation
Indices: 49952--50021 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
49942 TTTACTTAAT
** * *
49952 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49999 TTA -TA TATA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
50022 AATAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:50797 original size:9 final size:9
Alignment explanation
Indices: 50783--50811 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
50773 CGGAGGCTTT
50783 AAGAGAGAA
1 AAGAGAGAA
50792 AAGAGAGAA
1 AAGAGAGAA
50801 AAGAGAGAA
1 AAGAGAGAA
50810 AA
1 AA
50812 AAAAATTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (9 bp):
AAGAGAGAA
Found at i:51677 original size:15 final size:15
Alignment explanation
Indices: 51628--51679 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
51618 TTTTTAAATA
51628 AATAAATATTTTACTTT
1 AATAAATATTTTA--TT
*
51645 TATAAATTATATTT-TT
1 AATAAA-TAT-TTTATT
51661 AATAAATATTTTATT
1 AATAAATATTTTATT
51676 AATA
1 AATA
51680 TTTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 9 0.30
16 7 0.23
17 5 0.17
18 3 0.10
19 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAAATATTTTATT
Found at i:58979 original size:23 final size:22
Alignment explanation
Indices: 58935--58979 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58925 AATCTCATAG
*
58935 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
58957 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
58980 AAATGTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:60447 original size:103 final size:103
Alignment explanation
Indices: 60263--60480 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
60253 GTCGAGGGTC
*
60263 TATGTGGTTCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
60328 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
60366 TATGTGGTCCTTCGGGACATATATTTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
60431 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
60469 TATATGGTCCTT
1 TATGTGGTCCTT
60481 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:60530 original size:23 final size:23
Alignment explanation
Indices: 60499--60564 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
60489 TATTATATGG
* *
60499 CACTACGGTGCAATTCTACGCGG
1 CACTCCGGTGCAATTCTACGCGA
* *
60522 CAGTCCGGTGCAATTCTACGTGA
1 CACTCCGGTGCAATTCTACGCGA
* *
60545 CACTTCGGTGCAATTATACG
1 CACTCCGGTGCAATTCTACG
60565 AACTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (23 bp):
CACTCCGGTGCAATTCTACGCGA
Found at i:64633 original size:22 final size:22
Alignment explanation
Indices: 64608--64684 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
64598 ATCTACACTC
*
64608 TTCAAAGATGATAGATTTTCTT
1 TTCAAAGATGATAGATTCTCTT
64630 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
64652 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
64674 TTCAAAGATGA
1 TTCAAAGATGA
64685 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:65485 original size:76 final size:75
Alignment explanation
Indices: 65359--65553 Score: 300
Period size: 76 Copynumber: 2.6 Consensus size: 75
65349 CTATTTCCCA
* *
65359 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAA-CCTTCGAGAGCTTTTTGATGTTTTCAA
*
65424 AGCCTTAGGGT
65 AACCTTAGGGT
65435 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAA-CCTTCGAGAGCTTTTTGATGTTTTCAA
*
65500 AACCTTCGGGT
65 AACCTTAGGGT
* * * *
65511 CATCGGTAAGCCCTTCAGTACATGATGTTTTCAAAAACCTTCG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAACCTTCG
65554 GGTCATCTGT
Statistics
Matches: 110, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
75 6 0.05
76 104 0.95
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (75 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAACCTTCGAGAGCTTTTTGATGTTTTCAAA
ACCTTAGGGT
Found at i:65557 original size:46 final size:45
Alignment explanation
Indices: 65488--65637 Score: 219
Period size: 45 Copynumber: 3.3 Consensus size: 45
65478 GAGAGCTTTT
* *
65488 TGATGTTTTCAAAACCTTCGGGTCATCGGTAAGCCCTTCAGTACA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
65533 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCT
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
65579 TGATGTTTTCAAAACTTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
65624 TGATATTTCCAAAA
1 TGATGTTTTCAAAA
65638 AAGGCTTCGG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 53 0.56
46 42 0.44
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:65755 original size:76 final size:76
Alignment explanation
Indices: 65578--66156 Score: 480
Period size: 76 Copynumber: 7.4 Consensus size: 76
65568 CCTTCAGTGC
* * * * * *
65578 TTGATGTTTTCAAAACTTTCGGGTCATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAAGGC
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTC-AAAAAGCC
65643 TTCGGGAGCTTT
65 TTCGGGAGCTTT
65655 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
65720 TCGGGAGCTTT
66 TCGGGAGCTTT
* * * *
65731 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCT
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
* *
65795 TCGGG-TC-AT
66 TCGGGAGCTTT
* * ** * * ** * * *
65804 CTGTAAGCCCTTC-ATG-CTT-GATGT--T-T-TCAAAACCTTC-GGGTCATCTGTAAGTCCTAC
1 TTG-ATG-TTTTCAAAGCCTTAG-GGTCATCTGT-AAGTCCTACAGTG-CA--TG-ATGT--T--
* * * * *** *
65861 AGTGCATAATG-TTTCCAAAAAAGCCTTCGG
54 --TTCAAAAAGCCTT-C--GGGAG-CTT--T
**
65891 GAGATTTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAA
1 TTGA---T-G---TTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAA
65956 AAAGCCTTCGGGAGCTTT
59 AAAGCCTTCGGGAGCTTT
*
65974 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
66039 TCGGGAGCTTT
66 TCGGGAGCTTT
*
66050 TTGATGTTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
*
66115 TCGGGAGCTTA
66 TCGGGAGCTTT
* *
66126 TTGATGTTTTCAAAACCTTCGGGTCATCTGT
1 TTGATGTTTTCAAAGCCTTAGGGTCATCTGT
66157 GATGTTTTTA
Statistics
Matches: 401, Mismatches: 63, Indels: 77
0.74 0.12 0.14
Matches are distributed among these distances:
69 3 0.01
70 10 0.02
71 1 0.00
72 3 0.01
73 11 0.03
74 4 0.01
75 12 0.03
76 246 0.61
77 51 0.13
79 8 0.02
80 2 0.00
83 2 0.00
84 1 0.00
85 3 0.01
86 3 0.01
87 1 0.00
88 7 0.02
89 2 0.00
90 1 0.00
92 4 0.01
93 2 0.00
94 8 0.02
95 3 0.01
96 1 0.00
97 9 0.02
98 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCT
TCGGGAGCTTT
Found at i:65801 original size:46 final size:45
Alignment explanation
Indices: 65732--65880 Score: 237
Period size: 45 Copynumber: 3.3 Consensus size: 45
65722 GGGAGCTTTT
65732 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
65777 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCA-TGCT
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
65822 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
65867 TAATGTTTCCAAAA
1 TGATGTTTTCAAAA
65881 AAGCCTTCGG
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
44 28 0.29
45 38 0.40
46 30 0.31
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:65856 original size:243 final size:242
Alignment explanation
Indices: 65359--66156 Score: 1257
Period size: 243 Copynumber: 3.3 Consensus size: 242
65349 CTATTTCCCA
*
65359 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
65424 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
* *
65489 GATGTTTTCAAAACCTTCGGGTCATCGGTAAGCCCTTCAGTACATGATGTTTTCAAAAACCTTCG
131 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCG
*
65554 GGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACTTTCGGGT
196 GGTCATCTGTAAGCCCTTCA-TGCTTGATGTTTTCAAAACCTTCGGGT
* *
65602 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAAGGCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
65667 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
65732 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
130 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
65797 GGGTCATCTGTAAGCCCTTCATGCTTGATGTTTTCAAAACCTTCGGGT
195 GGGTCATCTGTAAGCCCTTCATGCTTGATGTTTTCAAAACCTTCGGGT
* * *
65845 CATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAAGCCTTCGGGAGATTTTTGATATTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
65910 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* * * * *
65975 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
130 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTT
* * *
66040 C-GG------G--AG--CTT--T--TTGATGTTTTTAAAGCCTTAGGGT
194 CGGGTCATCTGTAAGCCCTTCATGCTTGATGTTTTCAAAACCTTCGGGT
* *
66074 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
66139 AACCTTCGGGTCATCTGT
66 AGCCTTAGGGTCATCTGT
66157 GATGTTTTTA
Statistics
Matches: 526, Mismatches: 27, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
228 46 0.09
229 51 0.10
231 1 0.00
233 3 0.01
235 2 0.00
237 1 0.00
243 239 0.45
244 183 0.35
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (242 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCG
GGTCATCTGTAAGCCCTTCATGCTTGATGTTTTCAAAACCTTCGGGT
Found at i:66098 original size:152 final size:153
Alignment explanation
Indices: 65821--66156 Score: 602
Period size: 152 Copynumber: 2.2 Consensus size: 153
65811 CCCTTCATGC
65821 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAAGCC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAAGCC
65886 TTCGGGAGATTTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
66 TTCGGGAGATTTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
*
65951 TTCAAAAAGCCTTCGGGAGCTTT
131 TTCAAAAAGCCTTCGGGAGCTTA
* * *
65974 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCC
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAAGCC
* * *
66038 TTCGGGAGCTTTTTGATGTTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
66 TTCGGGAGATTTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
66103 TTCAAAAAGCCTTCGGGAGCTTA
131 TTCAAAAAGCCTTCGGGAGCTTA
66126 TTGATGTTTTCAAAACCTTCGGGTCATCTGT
1 TTGATGTTTTCAAAACCTTCGGGTCATCTGT
66157 GATGTTTTTA
Statistics
Matches: 174, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
152 121 0.70
153 53 0.30
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (153 bp):
TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAAGCC
TTCGGGAGATTTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
TTCAAAAAGCCTTCGGGAGCTTA
Found at i:66342 original size:18 final size:19
Alignment explanation
Indices: 66319--66399 Score: 89
Period size: 18 Copynumber: 4.3 Consensus size: 19
66309 TTTACTTAAT
66319 TTATTATTATTA-AAATTA
1 TTATTATTATTATAAATTA
66337 TTATTATTATTATAAA-TA
1 TTATTATTATTATAAATTA
*
66355 TTATTATTA-TATTATATATA
1 TTATTATTATTA-TAAAT-TA
*
66375 TTA-TATTATTATTAAATAA
1 TTATTATTATTA-TAAATTA
66394 TTATTA
1 TTATTA
66400 CAAGCCCATA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 26 0.48
19 12 0.22
20 14 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTATTATAAATTA
Found at i:66399 original size:3 final size:3
Alignment explanation
Indices: 66319--66388 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
66309 TTTACTTAAT
** * *
66319 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
66366 TTA -TA TATA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
66389 AATAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:67891 original size:13 final size:14
Alignment explanation
Indices: 67862--67892 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
67852 TAAAATCCTA
67862 TTTATAAATTTAAT
1 TTTATAAATTTAAT
67876 TTTATAAA-TTAAT
1 TTTATAAATTTAAT
67889 TTTA
1 TTTA
67893 AGAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:69195 original size:21 final size:21
Alignment explanation
Indices: 69171--69228 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
69161 CAACAGCAGA
* *
69171 AGCAGAGAGAGAAGTAGCGGT
1 AGCACAGAGAGAAGCAGCGGT
**
69192 AGCACAGAGAGAAGCAGCGAC
1 AGCACAGAGAGAAGCAGCGGT
*
69213 AACACAGAGAGAAGCA
1 AGCACAGAGAGAAGCA
69229 ACATATCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.17, G:0.34, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGGT
Found at i:69781 original size:43 final size:42
Alignment explanation
Indices: 69718--69905 Score: 200
Period size: 43 Copynumber: 4.4 Consensus size: 42
69708 ATATCAACAC
* * * **
69718 CTAAATCTCAAAACCAATTGCAGCATTTGTGTTAAAAACGCAG
1 CTAAATATCAACACCTATTGCAGCATTTGTGGGAAAAACGC-G
* * *
69761 CTAAATTTCAACACCTATTGC-GTCGTTTGTGAGAAAAACGTCG
1 CTAAATATCAACACCTATTGCAG-CATTTGTGGGAAAAACG-CG
*
69804 CTAAATATCAACACCTATTGCAGCATTT-TCGGGAAAAACGCT
1 CTAAATATCAACACCTATTGCAGCATTTGT-GGGAAAAACGCG
* ** *
69846 CTAAATCTCAACACCTATTGTGGCGTTTGTGGGAAAAACGCCG
1 CTAAATATCAACACCTATTGCAGCATTTGTGGGAAAAACG-CG
69889 CTAAATATCAACACCTA
1 CTAAATATCAACACCTA
69906 ACAAACGCCG
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
42 37 0.30
43 84 0.68
44 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (42 bp):
CTAAATATCAACACCTATTGCAGCATTTGTGGGAAAAACGCG
Found at i:69875 original size:85 final size:86
Alignment explanation
Indices: 69718--69905 Score: 254
Period size: 85 Copynumber: 2.2 Consensus size: 86
69708 ATATCAACAC
* * * ** *
69718 CTAAATCTCAAAACCAATTGCAGCATTTGTGTTAAAAACGCAGCTAAATTTCAACACCTATTGCG
1 CTAAATATCAACACCTATTGCAGCATTTGTGGGAAAAACGCAGCTAAATCTCAACACCTATTGCG
* *
69783 TCGTTTGTGAGAAAAACGTCG
66 GCGTTTGTGAGAAAAACGCCG
* *
69804 CTAAATATCAACACCTATTGCAGCATTT-TCGGGAAAAACGC-TCTAAATCTCAACACCTATTGT
1 CTAAATATCAACACCTATTGCAGCATTTGT-GGGAAAAACGCAGCTAAATCTCAACACCTATTGC
*
69867 GGCGTTTGTGGGAAAAACGCCG
65 GGCGTTTGTGAGAAAAACGCCG
69889 CTAAATATCAACACCTA
1 CTAAATATCAACACCTA
69906 ACAAACGCCG
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
85 56 0.62
86 34 0.38
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (86 bp):
CTAAATATCAACACCTATTGCAGCATTTGTGGGAAAAACGCAGCTAAATCTCAACACCTATTGCG
GCGTTTGTGAGAAAAACGCCG
Found at i:70753 original size:41 final size:43
Alignment explanation
Indices: 70667--70756 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 43
70657 GACTACAGTC
* * *
70667 ATTTTTTTCAATTTTAAATTATTATATATATATTTTTCTGTTA
1 ATTTTTTTCAATTTTAAAATATTATATATACATTTATCTGTTA
70710 ATTTATTTTC-ATTTTAAAATA-T-TATATACATTTATCT-TCTA
1 ATTT-TTTTCAATTTTAAAATATTATATATACATTTATCTGT-TA
70751 ATTTTT
1 ATTTTT
70757 GAAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 3 0.07
41 19 0.45
42 1 0.02
43 14 0.33
44 5 0.12
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (43 bp):
ATTTTTTTCAATTTTAAAATATTATATATACATTTATCTGTTA
Found at i:70802 original size:2 final size:2
Alignment explanation
Indices: 70797--70855 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
70787 GTCCCATCTA
70797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70839 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
70856 CATGATGGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72594 original size:60 final size:60
Alignment explanation
Indices: 72457--72594 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 60
72447 GAATACACGA
* * * *
72457 ATAGTCAGGT-GATCATTTTGTAACTTTTAGTAGTCGAGGGACTCAACAAAACAACACACT
1 ATAGTC-GGTAGATCATTTTGTAACTTTTACTAATCGAAGAACTCAACAAAACAACACACT
* * * * *
72517 ATAGTC-GAAGGACCATTTTGTAACTTTTACTAATCTAAGAACTCAATAAAACAACGTCA-T
1 ATAGTCGGTA-GATCATTTTGTAACTTTTACTAATCGAAGAACTCAACAAAACAAC-ACACT
72577 ATAGTCGGTAGATCATTT
1 ATAGTCGGTAGATCATTT
72595 ATATATTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
58 1 0.02
60 58 0.92
61 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (60 bp):
ATAGTCGGTAGATCATTTTGTAACTTTTACTAATCGAAGAACTCAACAAAACAACACACT
Found at i:80196 original size:39 final size:40
Alignment explanation
Indices: 80111--80199 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
80101 GCAAAGTTGA
* *
80111 CATCTTTGGTTGGTGGCTAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
* *
80151 CATCTTTGGTAGGTGGCCAACTTGTGCACA-TGGAAATTT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
80190 CATCTTTGGT
1 CATCTTTGGT
80200 CCCTAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 18 0.40
40 27 0.60
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
Found at i:84810 original size:15 final size:16
Alignment explanation
Indices: 84790--84819 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
84780 TATGTTTGAC
84790 TTGAAAGTT-GCAAAG
1 TTGAAAGTTGGCAAAG
84805 TTGAAAGTTGGCAAA
1 TTGAAAGTTGGCAAA
84820 TCTGACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
TTGAAAGTTGGCAAAG
Found at i:84887 original size:40 final size:39
Alignment explanation
Indices: 84825--84913 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 39
84815 GCAAATCTGA
* *
84825 CATCTTTGGTTGGTAGCTAACTTGTACACATTGGAAAATTT
1 CATCTTTGGTAGGTAGCCAACTTGTACACA-TGG-AAATTT
* * *
84866 -ATCTTTGGTAGGTGGCCAACTTGTGCACATGGGAATTT
1 CATCTTTGGTAGGTAGCCAACTTGTACACATGGAAATTT
84904 CATCTTTGGT
1 CATCTTTGGT
84914 CCCTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 5 0.12
39 12 0.29
40 25 0.60
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (39 bp):
CATCTTTGGTAGGTAGCCAACTTGTACACATGGAAATTT
Found at i:87264 original size:20 final size:19
Alignment explanation
Indices: 87197--87273 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
87187 GAATGCTCTA
87197 ATGGTATCGATACCCTCCCAT
1 ATGGTATCGATA-CC-CCCAT
*
87218 A-GGTTTCGATACCCCCAT
1 ATGGTATCGATACCCCCAT
87236 GCAATGGTATCGATACCCCTCAT
1 ---ATGGTATCGATACCCC-CAT
*
87259 ATGGTACCGATACCC
1 ATGGTATCGATACCC
87274 TAAGGCATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.10
19 2 0.04
20 23 0.48
21 2 0.04
22 13 0.27
23 3 0.06
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (19 bp):
ATGGTATCGATACCCCCAT
Done.