Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011104.1 Kokia drynarioides strain JFW-HI SEQ_126077, 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: 126970
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:97 original size:15 final size:16
Alignment explanation
Indices: 68--98 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58 AAAACATATC
68 AATAATAGTCATTATT
1 AATAATAGTCATTATT
84 AATAATAG-CATTATT
1 AATAATAGTCATTATT
99 GGCGTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
AATAATAGTCATTATT
Found at i:1326 original size:59 final size:58
Alignment explanation
Indices: 1182--1542 Score: 304
Period size: 59 Copynumber: 6.2 Consensus size: 58
1172 CCCAAGACTG
* ** * *
1182 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCATTTTTGACCCCGAAACT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
* ** * *
1240 TC-CAAAATTTTCATTTTTACCCCCGAACTTTCAAAAATCTCA-TTTTGACCCATAGATT
1 TCTAAAAATTACCA-TTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCA-AAATT
* ** * * *
1298 ATCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCA-TTTTAATCTCAAAACT
1 -TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
* * * *
1357 TCCAAAAATT-TCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGAACTT
1 TCTAAAAATTACCA-TTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCC-AAAATT
* * * * *
1416 TCCAAAAATTATCATTTTA-CCCCTAAATTTCTAAAAATCCCATTTTTAACCCCAAAACTT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTC-AAAAATCCCATTTTTGA-CCCAAAA-TT
* ** * *
1476 T-TAAAAATTACCATTTTACCCCCAAACTCACAAAAATCCTATTTTTGACCCCAAAACT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
1534 TCTAAAAAT
1 TCTAAAAAT
1543 CCTATTTTTA
Statistics
Matches: 243, Mismatches: 45, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
57 13 0.05
58 80 0.33
59 122 0.50
60 28 0.12
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCAAAATT
Found at i:1388 original size:117 final size:117
Alignment explanation
Indices: 1182--1526 Score: 416
Period size: 117 Copynumber: 2.9 Consensus size: 117
1172 CCCAAGACTG
* *
1182 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCATTTTTGACCCCGAAACTTCCAAA
1 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
*
1246 ATTTTCATTTTTACCCCCGAACTTTCAAAAATCTCA-TTTTGACCCAT-AGA-TT
66 AATTTCATTTTTACCCCCGAACTTTCAAAAATC-CATTTTTGACCC-TGA-ACTT
* *
1298 ATCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCA-TTTTAATCTCAAAACTTCCAA
1 -TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAA
1362 AAATTTCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGAACTT
65 AAATTTCATTTTTACCCCCGAACTTTCAAAAAT-CCATTTTTGACCCTGAACTT
* * * * * * **
1416 TCCAAAAATTATCATTTTACCC-CTAAATTTCTAAAAATCCCATTTTTAACCCCAAAACTTTTAA
1 TCTAAAAATTACCATTTTACCCTC-GAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAA
* * **
1480 AAATTACCA-TTTTACCCCCAAACTCACAAAAATCCTATTTTTGACCC
65 AAATT-TCATTTTTACCCCCGAACTTTCAAAAATCC-ATTTTTGACCC
1527 CAAAACTTCT
Statistics
Matches: 200, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
116 1 0.00
117 127 0.63
118 70 0.35
119 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (117 bp):
TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
AATTTCATTTTTACCCCCGAACTTTCAAAAATCCATTTTTGACCCTGAACTT
Found at i:1481 original size:30 final size:29
Alignment explanation
Indices: 1213--1552 Score: 178
Period size: 29 Copynumber: 11.6 Consensus size: 29
1203 CTCGAACTCC
* *
1213 CAAAAAT-CCATTTTTGACCCCGAAACTTC
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
* ** **
1242 CAAAATTTTCATTTTTACCCCCGAACTTT
1 CAAAAATCCCATTTTTACCCCAAAACTTT
* * *
1271 CAAAAATCTCATTTTGA-CCCATAGA-TTAT
1 CAAAAATCCCATTTTTACCCCA-AAACTT-T
* * **
1300 CTAAAAATTACCA-TTTTACCCTC-GAACTCC
1 C-AAAAA-TCCCATTTTTACCC-CAAAACTTT
* * * *
1330 CAAAAATCCCATTTTAATCTCAAAACTTC
1 CAAAAATCCCATTTTTACCCCAAAACTTT
** **
1359 CAAAAATTTCATTTTTACCCCCGAACTTT
1 CAAAAATCCCATTTTTACCCCAAAACTTT
**
1388 CAAAAATCCCATTTTTGA-CCCTGAACTTT
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
** *
1417 CCAAAAATTATCA-TTTTACCCCTAAA-TTT
1 -CAAAAA-TCCCATTTTTACCCCAAAACTTT
1446 CTAAAAATCCCATTTTTAACCCCAAAACTTT
1 C-AAAAATCCCATTTTT-ACCCCAAAACTTT
* * * **
1477 TAAAAATTACCA-TTTTACCCCCAAACTCA
1 CAAAAA-TCCCATTTTTACCCCAAAACTTT
*
1506 CAAAAATCCTATTTTTGACCCCAAAAC-TT
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
*
1535 CTAAAAATCCTATTTTTA
1 C-AAAAATCCCATTTTTA
1553 ACCTCGAATT
Statistics
Matches: 237, Mismatches: 52, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
28 17 0.07
29 127 0.54
30 76 0.32
31 16 0.07
32 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATCCCATTTTTACCCCAAAACTTT
Found at i:14529 original size:59 final size:58
Alignment explanation
Indices: 14385--14745 Score: 304
Period size: 59 Copynumber: 6.2 Consensus size: 58
14375 CCCAAGACTG
* ** * *
14385 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCATTTTTGACCCCGAAACT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
* ** * *
14443 TC-CAAAATTTTCATTTTTACCCCCGAACTTTCAAAAATCTCA-TTTTGACCCATAGATT
1 TCTAAAAATTACCA-TTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCA-AAATT
* ** * * *
14501 ATCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCA-TTTTAATCTCAAAACT
1 -TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
* * * *
14560 TCCAAAAATT-TCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGAACTT
1 TCTAAAAATTACCA-TTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCC-AAAATT
* * * * *
14619 TCCAAAAATTATCATTTTA-CCCCTAAATTTCTAAAAATCCCATTTTTAACCCCAAAACTT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTC-AAAAATCCCATTTTTGA-CCCAAAA-TT
* ** * *
14679 T-TAAAAATTACCATTTTACCCCCAAACTCACAAAAATCCTATTTTTGACCCCAAAACT
1 TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CCCAAAATT
14737 TCTAAAAAT
1 TCTAAAAAT
14746 CCTATTTTTA
Statistics
Matches: 243, Mismatches: 45, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
57 13 0.05
58 80 0.33
59 122 0.50
60 28 0.12
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
TCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCAAAATT
Found at i:14591 original size:117 final size:117
Alignment explanation
Indices: 14385--14729 Score: 416
Period size: 117 Copynumber: 2.9 Consensus size: 117
14375 CCCAAGACTG
* *
14385 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT-CCATTTTTGACCCCGAAACTTCCAAA
1 TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
*
14449 ATTTTCATTTTTACCCCCGAACTTTCAAAAATCTCA-TTTTGACCCAT-AGA-TT
66 AATTTCATTTTTACCCCCGAACTTTCAAAAATC-CATTTTTGACCC-TGA-ACTT
* *
14501 ATCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCA-TTTTAATCTCAAAACTTCCAA
1 -TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAA
14565 AAATTTCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGAACTT
65 AAATTTCATTTTTACCCCCGAACTTTCAAAAAT-CCATTTTTGACCCTGAACTT
* * * * * * **
14619 TCCAAAAATTATCATTTTACCC-CTAAATTTCTAAAAATCCCATTTTTAACCCCAAAACTTTTAA
1 TCTAAAAATTACCATTTTACCCTC-GAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAA
* * **
14683 AAATTACCA-TTTTACCCCCAAACTCACAAAAATCCTATTTTTGACCC
65 AAATT-TCATTTTTACCCCCGAACTTTCAAAAATCC-ATTTTTGACCC
14730 CAAAACTTCT
Statistics
Matches: 200, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
116 1 0.00
117 127 0.63
118 70 0.35
119 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (117 bp):
TCTAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
AATTTCATTTTTACCCCCGAACTTTCAAAAATCCATTTTTGACCCTGAACTT
Found at i:14684 original size:30 final size:29
Alignment explanation
Indices: 14416--14755 Score: 178
Period size: 29 Copynumber: 11.6 Consensus size: 29
14406 CTCGAACTCC
* *
14416 CAAAAAT-CCATTTTTGACCCCGAAACTTC
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
* ** **
14445 CAAAATTTTCATTTTTACCCCCGAACTTT
1 CAAAAATCCCATTTTTACCCCAAAACTTT
* * *
14474 CAAAAATCTCATTTTGA-CCCATAGA-TTAT
1 CAAAAATCCCATTTTTACCCCA-AAACTT-T
* * **
14503 CTAAAAATTACCA-TTTTACCCTC-GAACTCC
1 C-AAAAA-TCCCATTTTTACCC-CAAAACTTT
* * * *
14533 CAAAAATCCCATTTTAATCTCAAAACTTC
1 CAAAAATCCCATTTTTACCCCAAAACTTT
** **
14562 CAAAAATTTCATTTTTACCCCCGAACTTT
1 CAAAAATCCCATTTTTACCCCAAAACTTT
**
14591 CAAAAATCCCATTTTTGA-CCCTGAACTTT
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
** *
14620 CCAAAAATTATCA-TTTTACCCCTAAA-TTT
1 -CAAAAA-TCCCATTTTTACCCCAAAACTTT
14649 CTAAAAATCCCATTTTTAACCCCAAAACTTT
1 C-AAAAATCCCATTTTT-ACCCCAAAACTTT
* * * **
14680 TAAAAATTACCA-TTTTACCCCCAAACTCA
1 CAAAAA-TCCCATTTTTACCCCAAAACTTT
*
14709 CAAAAATCCTATTTTTGACCCCAAAAC-TT
1 CAAAAATCCCATTTTT-ACCCCAAAACTTT
*
14738 CTAAAAATCCTATTTTTA
1 C-AAAAATCCCATTTTTA
14756 ACCTCGAATT
Statistics
Matches: 237, Mismatches: 52, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
28 17 0.07
29 127 0.54
30 76 0.32
31 16 0.07
32 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATCCCATTTTTACCCCAAAACTTT
Found at i:36360 original size:206 final size:193
Alignment explanation
Indices: 36019--36574 Score: 853
Period size: 193 Copynumber: 2.8 Consensus size: 193
36009 AACGATGAGG
* *
36019 TCATCTTCCCAATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACATAAGCAAATCT
1 TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAGCAAATCT
*
36084 TCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
36149 GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGGGATACAGAGAAGCGAATTGAAAC
131 GATGAGATACTGAGAAGTGGACCAAATTCGTCTT-CT--T--GAT--------GCGAATTGAAAC
36214 AAACGACGCGC
183 AAACGACGCGC
36225 TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAGCAAATCT
1 TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAGCAAATCT
36290 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
* * *
36355 GATGAGATACTGAGAAATGGATCAAATTCGTCTTCTTGATGCGAATTGAAACAAACGACGCGG
131 GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGCGAATTGAAACAAACGACGCGC
* * * * *
36418 TCATCTTCTCGATGAGATTCTGAGAAGAAGACCGAATCAAATTCATGCTCGACGTAAGCAAATCT
1 TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAGCAAATCT
*
36483 TCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
**
36548 GATGAGAT-CTCGAGAAGAAGACCAAAT
131 GATGAGATACT-GAGAAGTGGACCAAAT
36575 CAAGTCTACG
Statistics
Matches: 333, Mismatches: 16, Indels: 15
0.91 0.04 0.04
Matches are distributed among these distances:
192 2 0.01
193 166 0.50
201 3 0.01
203 1 0.00
205 2 0.01
206 159 0.48
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (193 bp):
TCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAGCAAATCT
TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGCGAATTGAAACAAACGACGCGC
Found at i:36531 original size:193 final size:197
Alignment explanation
Indices: 36006--36563 Score: 865
Period size: 206 Copynumber: 2.8 Consensus size: 197
35996 ATGATTATCC
* * *
36006 ACAAACGATGAGGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
* *
36071 CATAAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 CGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
*
36136 CGGTTGGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGGGATACAGAGA
131 CGGTTGGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCT-AT-GGAT-------
36201 AGCGAATTGAA
187 AGCGAATTGAA
*
36212 ACAAACGACGCGCTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
36277 CGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 CGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
*
36342 CGGTTGGCTTCCTGATGAGATACTGAGAAATGGATCAAATTCGTCTT-CT-T-GAT-GCGAATTG
131 CGGTTGGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTATGGATAGCGAATTG
36403 AA
196 AA
* * * * *
36405 ACAAACGACGCGGTCATCTTCTCGATGAGATTCTGAGAAGAAGACCGAATCAAATTCATGCTCGA
1 ACAAACGACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
*
36470 CGTAAGCAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 CGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
36535 CGGTTGGCTTCCTGATGAGAT-CTCGAGAA
131 CGGTTGGCTTCCTGATGAGATACT-GAGAA
36564 GAAGACCAAA
Statistics
Matches: 336, Mismatches: 15, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
192 2 0.01
193 159 0.47
201 3 0.01
203 1 0.00
205 2 0.01
206 169 0.50
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (197 bp):
ACAAACGACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGA
CGTAAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
CGGTTGGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTATGGATAGCGAATTG
AA
Found at i:36644 original size:120 final size:120
Alignment explanation
Indices: 36428--36691 Score: 322
Period size: 120 Copynumber: 2.2 Consensus size: 120
36418 TCATCTTCTC
* * * *
36428 GATGAGATTCTGAGAAGAAGACCGAATCAAATTCATGCTCGACGTAAGCAAATCTTCGAACCCCA
1 GATGAGATTCTGAGAAGAAGACCAAATCAAATTCACGCTCGACATAAGCAAATCTTCGAACACCA
* *
36493 GCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
66 GCTTCCTGATGAGACACGGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
* * *
36548 GATGAGA-TCTCGAGAAGAAGACCAAATC-AAGTCTACGCTCGATATAAGCAAATCTTCGAATAC
1 GATGAGATTCT-GAGAAGAAGACCAAATCAAATTC-ACGCTCGACATAAGCAAATCTTCGAACAC
* * * *
36611 CAGCTTCCTGATGAGACACGGAGAAGC-GAGTCGAAGCAAT-GAACGATTAG-TGTCTT
64 CAGCTTCCTGATGAGACACGGAGAAGCAG-GTCGAAGCAATAAAACGGTTGGCT-TCCT
* *
36667 GATGAGATACTGAGAAGAAGGCCAA
1 GATGAGATTCTGAGAAGAAGACCAA
36692 GACTCAAAGA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
118 1 0.01
119 38 0.31
120 85 0.69
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (120 bp):
GATGAGATTCTGAGAAGAAGACCAAATCAAATTCACGCTCGACATAAGCAAATCTTCGAACACCA
GCTTCCTGATGAGACACGGAGAAGCAGGTCGAAGCAATAAAACGGTTGGCTTCCT
Found at i:36949 original size:17 final size:17
Alignment explanation
Indices: 36924--36969 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
36914 CCCAACAAAT
36924 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* * *
36941 TTAAGTTTATCTTAAAT
1 TTAAATTTATTTTAAAA
36958 TTAAATTTATTT
1 TTAAATTTATTT
36970 AAATTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:37003 original size:17 final size:17
Alignment explanation
Indices: 36920--37005 Score: 59
Period size: 17 Copynumber: 5.1 Consensus size: 17
36910 TGGGCCCAAC
* *
36920 AAATTTAAATTTATTTT
1 AAATTTAAAATTAATTT
* * *
36937 AAAATT-AAGTTTATCTT
1 AAATTTAAAATTAAT-TT
*
36954 AAATTT-AAATTTATTT
1 AAATTTAAAATTAATTT
** *
36970 AAATTTATTATGAATTT
1 AAATTTAAAATTAATTT
*
36987 AAATTTAAAATTCATTT
1 AAATTTAAAATTAATTT
37004 AA
1 AA
37006 TATATATATA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
16 13 0.25
17 40 0.75
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATTTAAAATTAATTT
Found at i:41503 original size:22 final size:21
Alignment explanation
Indices: 41478--41537 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
41468 AAATAGTGAG
*
41478 AAAACAACAAGAAAATAACAGC
1 AAAACAACAA-AAAATAAAAGC
* *
41500 AAAACAATAAAAAAAAAAAGC
1 AAAACAACAAAAAATAAAAGC
*
41521 AAGAAAAACAACAAAAT
1 AA-AACAACAA-AAAAT
41538 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 11 0.37
22 15 0.50
23 4 0.13
ACGTcount: A:0.75, C:0.13, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAACAACAAAAAATAAAAGC
Found at i:42552 original size:5 final size:5
Alignment explanation
Indices: 42542--42566 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42532 TTCAAACACT
42542 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
42567 AGACTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:42609 original size:54 final size:54
Alignment explanation
Indices: 42551--42660 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
42541 TTATAATATA
42551 ATATAATATAATATA-AAGACTAATTGCAACTAAATGAAAGTGACTGCTAGTTTG
1 ATATAATATAATATATAA-ACTAATTGCAACTAAATGAAAGTGACTGCTAGTTTG
* * * *
42605 ATATAATATTATATATAAACTAATTGCCACTAAATTAAAGTGATTGCTAGTTTG
1 ATATAATATAATATATAAACTAATTGCAACTAAATGAAAGTGACTGCTAGTTTG
42659 AT
1 AT
42661 CATATGCATG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 49 0.96
55 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (54 bp):
ATATAATATAATATATAAACTAATTGCAACTAAATGAAAGTGACTGCTAGTTTG
Found at i:44051 original size:8 final size:9
Alignment explanation
Indices: 44028--44064 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
44018 TTTTAGGGAC
*
44028 TAAATTGAA
1 TAAATTGTA
44037 TAAATTGTA
1 TAAATTGTA
44046 -AAATTGTA
1 TAAATTGTA
44054 TAAATTG-A
1 TAAATTGTA
44062 TAA
1 TAA
44065 TTGAGTGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 12 0.46
9 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (9 bp):
TAAATTGTA
Found at i:56822 original size:17 final size:17
Alignment explanation
Indices: 56800--56832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56790 ATTAAAATTT
56800 ATAAAAAAATTATAAAA
1 ATAAAAAAATTATAAAA
*
56817 ATAAAATAATTATAAA
1 ATAAAAAAATTATAAA
56833 TTTTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATTATAAAA
Found at i:64252 original size:30 final size:31
Alignment explanation
Indices: 64218--64280 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
64208 TTACAAAATG
64218 GTCACTAAACTATTCGAAAGTTTTCA-TTAA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
* *
64248 GTCACTAAACTATTCGGAAGTTTTTATTTAA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
64279 GT
1 GT
64281 TGGGTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (31 bp):
GTCACTAAACTATTCGAAAGTTTTCATTTAA
Found at i:65041 original size:24 final size:24
Alignment explanation
Indices: 65009--65055 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
64999 CAAAAATTAA
65009 TAATTCAATATAAATTTATTTTAG
1 TAATTCAATATAAATTTATTTTAG
*
65033 TAATTCAATGTAAATTTATTTTA
1 TAATTCAATATAAATTTATTTTA
65056 ACTCTTCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
TAATTCAATATAAATTTATTTTAG
Found at i:65422 original size:25 final size:24
Alignment explanation
Indices: 65386--65453 Score: 104
Period size: 25 Copynumber: 2.9 Consensus size: 24
65376 CAGGGTTAAG
65386 TTTTTTTTTAGATTAGATTTTCCC
1 TTTTTTTTTAGATTAGATTTTCCC
65410 TTTTCTTTTTAGATTAGATTTTCCC
1 TTTT-TTTTTAGATTAGATTTTCCC
*
65435 --TTTTTTTAGATTAAATTTT
1 TTTTTTTTTAGATTAGATTTT
65454 ATTTTTGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 16 0.38
23 2 0.05
24 4 0.10
25 20 0.48
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.63
Consensus pattern (24 bp):
TTTTTTTTTAGATTAGATTTTCCC
Found at i:66996 original size:31 final size:29
Alignment explanation
Indices: 66939--66997 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
66929 TTTCTTAAAA
* *
66939 TTTTTAAAATTTTAATTAAACTCTCAAAT
1 TTTTTAAAAATTTAATTAAACCCTCAAAT
*
66968 TTTTTGAAAAATTTAATTAGACCCCTCAAA
1 TTTTT-AAAAATTTAATTA-AACCCTCAAA
66998 ACTTAATGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
30 12 0.48
31 8 0.32
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTTTAAAAATTTAATTAAACCCTCAAAT
Found at i:69280 original size:3 final size:3
Alignment explanation
Indices: 69272--69297 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
69262 GACTCAATTT
69272 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
69298 TTTGCCATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:69949 original size:2 final size:2
Alignment explanation
Indices: 69942--69966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
69932 GAAGGGTATC
69942 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
69967 TTTTTTTTTT
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:82831 original size:137 final size:137
Alignment explanation
Indices: 82575--82897 Score: 463
Period size: 137 Copynumber: 2.4 Consensus size: 137
82565 ATTTATTTAA
*
82575 ACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTTTCTAAAAAAATATTAAT
1 ACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATA-TTTTTCCAAAAAAATATTAAT
* * ** * *
82640 TTTTATGCTTTTTATATTTTGATTGAAATTAATTAATATAACTGTTTATTTTAATAAATTCAATA
65 TTTTATGCTTTTTATATTCTAACCGAAATTAATTAATACAACTGTTTATATTAATAAATTCAATA
82705 AAATATAT
130 AAATATAT
* * *
82713 ACAATTAATACTTTGTATGAATAAAATTCATATATTAATTATATTTTTCCAAAAGAATATTAATT
1 ACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTTCCAAAAAAATATTAATT
* **
82778 TTCATAT-C-TTTTATATTCTAACCGAAATTAATTAATACAATTGTTTATATTAATAAATTCGGT
66 TT--TATGCTTTTTATATTCTAACCGAAATTAATTAATACAACTGTTTATATTAATAAATTCAAT
82841 AAAATATAT
129 AAAATATAT
*
82850 ATC-ATTAATATTTTGTATGAATCAAATTTATATATTAATTATATTTTT
1 A-CAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTT
82898 AAAAATATAT
Statistics
Matches: 166, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
137 120 0.72
138 43 0.26
139 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (137 bp):
ACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTTCCAAAAAAATATTAATT
TTTATGCTTTTTATATTCTAACCGAAATTAATTAATACAACTGTTTATATTAATAAATTCAATAA
AATATAT
Found at i:82906 original size:23 final size:24
Alignment explanation
Indices: 82879--82938 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
82869 AATCAAATTT
82879 ATATATTAATTATATTTT-TAAA-A
1 ATATATT-ATTATATTTTATAAATA
* *
82902 ATATATTTTTTTATTTTATAAATA
1 ATATATTATTATATTTTATAAATA
*
82926 ATAAATTATTATA
1 ATATATTATTATA
82939 CGGAGTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 8 0.27
23 11 0.37
24 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATTATTATATTTTATAAATA
Found at i:83035 original size:21 final size:22
Alignment explanation
Indices: 82993--83040 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
82983 TAATTTTTTT
* *
82993 TTATTTTTTATGTTGCTTTAAA
1 TTATTTTATATGTTGCTCTAAA
*
83015 TTATTTTATATTTTG-TCTAAA
1 TTATTTTATATGTTGCTCTAAA
83036 TTATT
1 TTATT
83041 AGGATGGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (22 bp):
TTATTTTATATGTTGCTCTAAA
Found at i:84623 original size:2 final size:2
Alignment explanation
Indices: 84616--84642 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
84606 AATTTACTCG
84616 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 T
84643 GCCTAAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102929 original size:51 final size:51
Alignment explanation
Indices: 102836--102935 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
102826 ATTATATTAG
*
102836 AATTTACGTAAAAATCTCTTGACAAAATAATATATTTGTCAATCACATTGA
1 AATTTACATAAAAATCTCTTGACAAAATAATATATTTGTCAATCACATTGA
* * *
102887 AATTTACATGAAAA-CTCGTTGATAAAATACTATACTTT-TCAATCACATT
1 AATTTACATAAAAATCTC-TTGACAAAATAATATA-TTTGTCAATCACATT
102936 TTAAAAACAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 3 0.07
51 37 0.86
52 3 0.07
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (51 bp):
AATTTACATAAAAATCTCTTGACAAAATAATATATTTGTCAATCACATTGA
Found at i:108889 original size:21 final size:22
Alignment explanation
Indices: 108852--108894 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
108842 ACTTCAAGGG
108852 TTAAATTTATCATTATATATTT
1 TTAAATTTATCATTATATATTT
108874 TTAAATTATAT-ATATATATAT
1 TTAAATT-TATCAT-TATATAT
108895 ATATTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAATTTATCATTATATATTT
Found at i:111849 original size:6 final size:6
Alignment explanation
Indices: 111840--111872 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
111830 TTTTAATTCG
*
111840 ATTGAT ATTGAT ATTGAT ATTGAT ATTGTT ATT
1 ATTGAT ATTGAT ATTGAT ATTGAT ATTGAT ATT
111873 AGTGCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
ATTGAT
Found at i:113389 original size:17 final size:18
Alignment explanation
Indices: 113353--113391 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
113343 ATTTTACCTT
*
113353 ATTTATTTTATTATTATA
1 ATTTATTTTATGATTATA
*
113371 ATTTATTTTCTGA-TATA
1 ATTTATTTTATGATTATA
113388 ATTT
1 ATTT
113392 TAAATTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTATTTTATGATTATA
Found at i:125138 original size:222 final size:221
Alignment explanation
Indices: 124736--125148 Score: 691
Period size: 222 Copynumber: 1.9 Consensus size: 221
124726 ATGTATGTCA
* * * *
124736 GCATGTTTAGATCTTGTGTTGAAGATAAAAGCCATGAACATCCTTTCCGTTTGTTTCCAAGAGGA
1 GCATCTTTAGATCTTGTGTTGAAGATAAAAGCCATGAACATCCTTTCAGTTTGTTTACAAGACGA
* * *
124801 TCATCATTCATTTGTGATGCATGTGGTATTGAAGGAGGTTATGCTTCCTACATATGTTGTACATG
66 TCATCATTCATTTGTGATGCATGTGGTATTGAAGGAAGTTATGCTGCCTACATATGTTGTAAATG
* *
124866 CAACATTATGGTCCATAAAAAATGCACTTCATTGCCACGCATTATCAAAAGCAGGTGGCATCACC
131 CAACATTATGGTCCATAAAAAATGCACTTCATTGCCACGCATCATCAAAAGCAAGTGGCATCACC
124931 ATCCTGTTTCATTGAAGATAAAAAAT
196 ATCCTGTTTCATTGAAGATAAAAAAT
*
124957 GCATCTTTAGATCTTGTTGTTGAAGATAAAAGGCATGAACATCCTTTCAGTTTGTTTACAAGACG
1 GCATCTTTAGATCTTG-TGTTGAAGATAAAAGCCATGAACATCCTTTCAGTTTGTTTACAAGACG
**
125022 ATGGTCATTCATTTGTGATGCATGTGGTATTGAAGGAAGTTATGCTGCCTACATATGTTGTAAAT
65 ATCATCATTCATTTGTGATGCATGTGGTATTGAAGGAAGTTATGCTGCCTACATATGTTGTAAAT
* *
125087 GCAACATTATGGTCCATACAAAGTGCACTTCATTGCCACGCATCATCAAAAGCAAGTGGCAT
130 GCAACATTATGGTCCATAAAAAATGCACTTCATTGCCACGCATCATCAAAAGCAAGTGGCAT
125149 GATCATTGCC
Statistics
Matches: 177, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
221 15 0.08
222 162 0.92
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (221 bp):
GCATCTTTAGATCTTGTGTTGAAGATAAAAGCCATGAACATCCTTTCAGTTTGTTTACAAGACGA
TCATCATTCATTTGTGATGCATGTGGTATTGAAGGAAGTTATGCTGCCTACATATGTTGTAAATG
CAACATTATGGTCCATAAAAAATGCACTTCATTGCCACGCATCATCAAAAGCAAGTGGCATCACC
ATCCTGTTTCATTGAAGATAAAAAAT
Done.