Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold433
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: 252396
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.33
Warning! 11224 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:225372 original size:41 final size:41
Alignment explanation
Indices: 225184--225376 Score: 149
Period size: 41 Copynumber: 4.7 Consensus size: 41
225174 TTTACATAAT
** * * * * * *
225184 CGCCGCTAATGGTGCGGTCTTTCGCGGCGTTTTCTAATATG
1 CGCCGCTAATACTGCAGTCATTAGCGGCGTTTTTTAAAAAG
* * * *
225225 CACCGCTAATGCT-CAGGTCTTTAGCGGCGTTTTTTACAAAG
1 CGCCGCTAATACTGCA-GTCATTAGCGGCGTTTTTTAAAAAG
* * * **
225266 CGCCGCTAATGCTACAGTCTTTAGCGGCGTTTTTTACGAAG
1 CGCCGCTAATACTGCAGTCATTAGCGGCGTTTTTTAAAAAG
* * *
225307 CGCCGCTAATGCT-CAGGTCTTTAGCGGCGTTTCTTAAAAAG
1 CGCCGCTAATACTGCA-GTCATTAGCGGCGTTTTTTAAAAAG
*
225348 CGCCGCTAAAAACTGCAG-CATTAGCGGCG
1 CGCCGCT-AATACTGCAGTCATTAGCGGCG
225377 CATATTAGAA
Statistics
Matches: 131, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
40 3 0.02
41 119 0.91
42 7 0.05
43 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (41 bp):
CGCCGCTAATACTGCAGTCATTAGCGGCGTTTTTTAAAAAG
Found at i:225393 original size:82 final size:82
Alignment explanation
Indices: 225227--225397 Score: 220
Period size: 82 Copynumber: 2.1 Consensus size: 82
225217 CTAATATGCA
* * ** *
225227 CCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTACAGTCTTTAGCG
1 CCGCTAATGCTCAGGTCTTTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAACTACAGTCATTAGCG
** * *
225292 GCGTTTTTTACGAAGCG
66 GCGCATATTACGAAACG
*
225309 CCGCTAATGCTCAGGTCTTTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAAACTGCAG-CATTAGC
1 CCGCTAATGCTCAGGTCTTTAGCGGCGTTTCTTAAAAAGCGCCGCT-AAAACTACAGTCATTAGC
225373 GGCGCATATTA-GAAAACG
65 GGCGCATATTACG-AAACG
225391 CCGCTAA
1 CCGCTAA
225398 AGACCGGTGC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.01
82 69 0.90
83 7 0.09
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (82 bp):
CCGCTAATGCTCAGGTCTTTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAACTACAGTCATTAGCG
GCGCATATTACGAAACG
Found at i:226678 original size:73 final size:74
Alignment explanation
Indices: 226559--226731 Score: 267
Period size: 74 Copynumber: 2.4 Consensus size: 74
226549 GCACGAATTT
* * * * *
226559 GCGGCGTTTATTGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTTG-TTTTTATGCTGTTTA
1 GCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
226623 TTAGTATTA
66 TTAGTATTA
*
226632 GCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAATGACTTCGTTTTTTATACTGTTTA
1 GCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
*
226697 TTGGTATTA
66 TTAGTATTA
*
226706 GCGGTGTTTCTGGTACAAACGCCGCA
1 GCGGCGTTTCTGGTACAAACGCCGCA
226732 TATGATAGTT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
73 44 0.48
74 47 0.52
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (74 bp):
GCGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
TTAGTATTA
Found at i:227915 original size:16 final size:16
Alignment explanation
Indices: 227891--227921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
227881 ATTTTTCCTT
227891 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
227907 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
227922 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:229875 original size:16 final size:15
Alignment explanation
Indices: 229826--229867 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
229816 ATACATAACT
229826 TACATAACTTATTAA
1 TACATAACTTATTAA
*
229841 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
229857 TACATAACTTA
1 TACATAACTTA
229868 CATAATACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:235562 original size:87 final size:87
Alignment explanation
Indices: 235416--235598 Score: 321
Period size: 87 Copynumber: 2.1 Consensus size: 87
235406 GAGGAAACAT
235416 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
1 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
*
235481 GCGAGAGAAGTAGAGGCAGCAG
66 GCGAGAGAAGCAGAGGCAGCAG
*
235503 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGTA
1 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
* *
235568 GCGAGAGAAGCAGAGGCTGTAG
66 GCGAGAGAAGCAGAGGCAGCAG
*
235590 CGAGGGAAG
1 CGAGAGAAG
235599 TAGAGGCTGC
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.36, C:0.17, G:0.34, T:0.12
Consensus pattern (87 bp):
CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
GCGAGAGAAGCAGAGGCAGCAG
Found at i:235580 original size:21 final size:21
Alignment explanation
Indices: 235554--235644 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 21
235544 CAGCAGCTTA
*
235554 AAGCAGATGCGGTAGCGAGAG
1 AAGCAGAGGCGGTAGCGAGAG
* *
235575 AAGCAGAGGCTGTAGCGAGGG
1 AAGCAGAGGCGGTAGCGAGAG
* * * *
235596 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGTAGCGAGAG
* *** *
235617 AAGTAGAGGCTACAGCGAGGG
1 AAGCAGAGGCGGTAGCGAGAG
235638 AAGCAGA
1 AAGCAGA
235645 ACAGCTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.33, C:0.14, G:0.44, T:0.09
Consensus pattern (21 bp):
AAGCAGAGGCGGTAGCGAGAG
Found at i:236018 original size:43 final size:43
Alignment explanation
Indices: 235949--236341 Score: 624
Period size: 43 Copynumber: 9.1 Consensus size: 43
235939 CAAAATTAGC
* *
235949 GGCGTTTTTTGGGTAAGCCCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
235992 GGCGTTTTTTGGCTAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
236035 GGCGATTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
236078 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
236121 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
**
236164 GGCGTTTTTTGGCTAAGCATCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * ** *
236207 GACATTTTTTGGCTAAGAACCGCTAAAGACCATGGTCTATAGC
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * * *
236250 AGCGTTTGTTGGGTAAGCGCCACTAAAGACCATGGTCTATAGC
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
236293 GGCGTTTGTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
236336 GGCGTT
1 GGCGTT
236342 GTAAAGAAAA
Statistics
Matches: 326, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 326 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:237067 original size:18 final size:18
Alignment explanation
Indices: 237044--237091 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
237034 AAAATGTGAG
*
237044 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
237062 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
237080 AAATGATGTTCA
1 AAATGATGTTCA
237092 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:237616 original size:72 final size:71
Alignment explanation
Indices: 237521--237759 Score: 338
Period size: 72 Copynumber: 3.3 Consensus size: 71
237511 CAATGCTAAA
* *
237521 CTAGTTTTATCAATAGTTATTTATGTCTGGTTTTTGGATACTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGT-TGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
237586 GTGTAAT
65 GTGTAAT
** **
237593 CTAGTTTTATCAATAACTGTTTATGGTTGGTTTTTAAATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTAT-GTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
237658 GTGTAAT
65 GTGTAAT
* *
237665 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATG-TTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
237730 ACT-AAAT
65 -GTGTAAT
237737 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
237760 ATATCATTTT
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
71 23 0.15
72 123 0.83
73 3 0.02
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (71 bp):
CTAGTTTTATCAATAGTTGTTTATGTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
TGTAAT
Found at i:238894 original size:21 final size:21
Alignment explanation
Indices: 238868--238910 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
238858 AGAGGTAGAC
238868 TGGTATCTGGTAAATAAGAGA
1 TGGTATCTGGTAAATAAGAGA
238889 TGGTATCTGGTAAATAAGAGA
1 TGGTATCTGGTAAATAAGAGA
238910 T
1 T
238911 ATTCAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (21 bp):
TGGTATCTGGTAAATAAGAGA
Found at i:239823 original size:13 final size:13
Alignment explanation
Indices: 239786--239823 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
239776 ACACTCAAAT
239786 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
239799 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
239812 TTTTCAAAAGCA
1 TTTTCAAAAGCA
239824 TTGCCAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:242256 original size:23 final size:23
Alignment explanation
Indices: 242230--242274 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
242220 TTTCTTACTA
**
242230 TAGTAATTTTTGGGGTATTACAG
1 TAGTAATTTTCAGGGTATTACAG
242253 TAGTAATTTTCAGGGTATTACA
1 TAGTAATTTTCAGGGTATTACA
242275 TTTCTCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (23 bp):
TAGTAATTTTCAGGGTATTACAG
Found at i:243891 original size:50 final size:50
Alignment explanation
Indices: 243762--244048 Score: 224
Period size: 50 Copynumber: 5.6 Consensus size: 50
243752 GATAATAACA
* * * * *
243762 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATG-TTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATCT-CGG
* * * * * * *
243811 TGCCAATGCCATATCCCAGATATTGCCTTACATGGGAGTTCTCATTTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * * * *
243861 TGACC-ATGCCATGCCCCAAACATGGTCTTAC-GGGGGGCCTCTCATCCCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCTCGG
* * *
243911 TGCCAACGCCATGTCCCAGACATGGTCATACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * * *
243961 TGCCAATGCCATGTCTCAGACATAGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTC---ATCTC---GG
*
244017 TGCCAATGCCATGTCCCTGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
244049 CTGGCTCACA
Statistics
Matches: 187, Mismatches: 38, Indels: 19
0.77 0.16 0.08
Matches are distributed among these distances:
48 1 0.01
49 42 0.22
50 104 0.56
51 5 0.03
53 5 0.03
56 30 0.16
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
Found at i:246966 original size:23 final size:23
Alignment explanation
Indices: 246934--246977 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
246924 CTTTCTTACT
* *
246934 GTAGTTATTTTCGGGGTATTATA
1 GTAGTAATTTTCGGGATATTATA
246957 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
246978 CATTAGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTATA
Found at i:248027 original size:106 final size:108
Alignment explanation
Indices: 247903--248136 Score: 427
Period size: 108 Copynumber: 2.2 Consensus size: 108
247893 TCTTTATTTT
247903 ATTACTAATAAATTTTTAAAATTT-AAAACTA-ATTATAAATATTAAAACCTATATTTTTAATAT
1 ATTACTAATAAATTTTTAAAATTTAAAAACTATATTATAAATATTAAAACCTATATTTTTAATAT
247966 ATAACCTATATTAGTATGGATATATAACCTATATTTCAAATTC
66 ATAACCTATATTAGTATGGATATATAACCTATATTTCAAATTC
* * *
248009 ATTACTAATAAATTTTTAAATTTTAAAAATTATATTTTAAATATTAAAACCTATATTTTTAATAT
1 ATTACTAATAAATTTTTAAAATTTAAAAACTATATTATAAATATTAAAACCTATATTTTTAATAT
248074 ATAACCTATATTAGTATGGATATATAACCTATATTTCAAATTC
66 ATAACCTATATTAGTATGGATATATAACCTATATTTCAAATTC
248117 ATTACTAATAAATTTTTAAA
1 ATTACTAATAAATTTTTAAA
248137 TACAAATCTT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
106 23 0.19
107 6 0.05
108 94 0.76
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (108 bp):
ATTACTAATAAATTTTTAAAATTTAAAAACTATATTATAAATATTAAAACCTATATTTTTAATAT
ATAACCTATATTAGTATGGATATATAACCTATATTTCAAATTC
Found at i:248047 original size:21 final size:21
Alignment explanation
Indices: 248022--248073 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
248012 ACTAATAAAT
* *
248022 TTTTAAATTTTAAAAATTATA
1 TTTTAAATATTAAAAACTATA
*
248043 TTTTAAATATTAAAACCTATA
1 TTTTAAATATTAAAAACTATA
*
248064 TTTTTAATAT
1 TTTTAAATAT
248074 ATAACCTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAATATTAAAAACTATA
Found at i:248176 original size:9 final size:9
Alignment explanation
Indices: 248162--248233 Score: 65
Period size: 9 Copynumber: 8.0 Consensus size: 9
248152 TCTAATTTCC
*
248162 ACATAACAT
1 ACATAACTT
248171 ACATAACTT
1 ACATAACTT
*
248180 ACATAATTT
1 ACATAACTT
*
248189 ACATAA-AT
1 ACATAACTT
* * *
248197 ATATATCAT
1 ACATAACTT
*
248206 ATCAAAACTT
1 A-CATAACTT
248216 ACATAACTT
1 ACATAACTT
248225 ACATAACTT
1 ACATAACTT
248234 TAAAGAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
8 5 0.10
9 41 0.80
10 5 0.10
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (9 bp):
ACATAACTT
Found at i:248300 original size:9 final size:9
Alignment explanation
Indices: 248288--248458 Score: 120
Period size: 9 Copynumber: 18.8 Consensus size: 9
248278 ATATCATATA
248288 ATAACTTAC
1 ATAACTTAC
*
248297 ATAACTCAC
1 ATAACTTAC
*
248306 ATAACATAC
1 ATAACTTAC
248315 ATAACTTA-
1 ATAACTTAC
*
248323 ATAACTGATAT
1 ATAACT--TAC
* *
248334 ATATCATATC
1 ATAACTTA-C
248344 ATAACTTAC
1 ATAACTTAC
248353 ATAACTTA-
1 ATAACTTAC
*
248361 ATAACTTAT
1 ATAACTTAC
*
248370 ATATATCATATC
1 ATA-A-CTTA-C
248382 ATAACTTAC
1 ATAACTTAC
248391 ATAACTTAC
1 ATAACTTAC
248400 ATAA--TAC
1 ATAACTTAC
* *
248407 ATAA-ATAT
1 ATAACTTAC
*
248415 ATATCATGT-C
1 ATAAC-T-TAC
*
248425 AAAACTTAC
1 ATAACTTAC
248434 ATAACTTAC
1 ATAACTTAC
*
248443 ATAATTTAC
1 ATAACTTAC
248452 ATAACTT
1 ATAACTT
248459 TAAAGAATTA
Statistics
Matches: 128, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
7 7 0.05
8 20 0.16
9 74 0.58
10 15 0.12
11 9 0.07
12 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (9 bp):
ATAACTTAC
Found at i:248354 original size:38 final size:39
Alignment explanation
Indices: 248305--248446 Score: 189
Period size: 38 Copynumber: 3.6 Consensus size: 39
248295 ACATAACTCA
* *
248305 CATAACATACATAACTTA-ATAACTGATATATATCATAT
1 CATAACTTACATAACTTACATAACTAATATATATCATAT
*
248343 CATAACTTACATAACTTA-ATAACTTATATATATCATAT
1 CATAACTTACATAACTTACATAACTAATATATATCATAT
*
248381 CATAACTTACATAACTTACATAATACATAAATATATATCATGT
1 CATAACTTACATAACTTACAT-A-AC-T-AATATATATCATAT
*
248424 CAAAACTTACATAACTTACATAA
1 CATAACTTACATAACTTACATAA
248447 TTTACATAAC
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
38 54 0.57
39 2 0.02
40 1 0.01
41 3 0.03
42 2 0.02
43 32 0.34
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (39 bp):
CATAACTTACATAACTTACATAACTAATATATATCATAT
Found at i:248415 original size:43 final size:43
Alignment explanation
Indices: 248330--248584 Score: 184
Period size: 43 Copynumber: 5.9 Consensus size: 43
248320 TTAATAACTG
* *
248330 ATATATATCATATCATAACTTACATAACTTA-AT-A-AC-T-T
1 ATATATATCATATCAAAACTTACATAACTTACATAATACATAA
*
248368 ATATATATCATATCATAACTTACATAACTTACATAATACATAA
1 ATATATATCATATCAAAACTTACATAACTTACATAATACATAA
*
248411 ATATATATCATGTCAAAACTTACATAACTTACATAATTTACATAA
1 ATATATATCATATCAAAACTTACATAACTTACATAA--TACATAA
* * * ** * * * * *
248456 CTTTAAAGAAT-TAAAAAC-AAAAAAACTTTGGATCTTAACTTA-ATAA
1 ATATATATCATATCAAAACTTACATAAC-TT--A-CATAA--TACATAA
* * *
248502 CTTATATATATCATATCATAACTTACATAACTTAAATAATACAGAA
1 ---ATATATATCATATCAAAACTTACATAACTTACATAATACATAA
* *
248548 GTATATATAATATCAAAACTTACATAACTTACATAAT
1 ATATATATCATATCAAAACTTACATAACTTACATAAT
248585 TTACATAACT
Statistics
Matches: 169, Mismatches: 31, Indels: 29
0.74 0.14 0.13
Matches are distributed among these distances:
38 31 0.18
39 2 0.01
40 1 0.01
41 2 0.01
42 1 0.01
43 72 0.43
44 8 0.05
45 15 0.09
46 8 0.05
47 10 0.06
48 1 0.01
49 6 0.04
50 7 0.04
51 5 0.03
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (43 bp):
ATATATATCATATCAAAACTTACATAACTTACATAATACATAA
Found at i:248446 original size:137 final size:136
Alignment explanation
Indices: 248352--248670 Score: 523
Period size: 137 Copynumber: 2.3 Consensus size: 136
248342 TCATAACTTA
* *
248352 CATAACTTAATAACTTATATATATCATATCATAACTTACATAACTTACATAATACATAAATATAT
1 CATAACTTAATAACTTATATATATCATATCATAACTTACATAACTTAAATAATACAGAAATATAT
*
248417 ATCATGTCAAAACTTACATAACTTACATAATTTACATAACTTTAAAGAATTAAAAACAAAAAAAC
66 ATCATATCAAAACTTACATAACTTACATAATTTACATAACTTTAAAGAATTAAAAACAAAAAAAC
248482 TTTGGAT
131 TTT-GAT
* *
248489 CTTAACTTAATAACTTATATATATCATATCATAACTTACATAACTTAAATAATACAGAAGTATAT
1 CATAACTTAATAACTTATATATATCATATCATAACTTACATAACTTAAATAATACAGAAATATAT
*
248554 ATAATATCAAAACTTACATAACTTACATAATTTACATAACTTTAAAGAATTAAAAACAAAAAAAC
66 ATCATATCAAAACTTACATAACTTACATAATTTACATAACTTTAAAGAATTAAAAACAAAAAAAC
248619 TTTGGAT
131 TTT-GAT
* * *
248626 CTTAACTTAATAACTTATATATAT-ATAATCATAACGTACACAACT
1 CATAACTTAATAACTTATATATATCAT-ATCATAACTTACATAACT
248671 CACATAACTT
Statistics
Matches: 173, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
136 2 0.01
137 171 0.99
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (136 bp):
CATAACTTAATAACTTATATATATCATATCATAACTTACATAACTTAAATAATACAGAAATATAT
ATCATATCAAAACTTACATAACTTACATAATTTACATAACTTTAAAGAATTAAAAACAAAAAAAC
TTTGAT
Found at i:248530 original size:9 final size:9
Alignment explanation
Indices: 248491--248595 Score: 58
Period size: 9 Copynumber: 11.7 Consensus size: 9
248481 CTTTGGATCT
248491 TAACTTA-A
1 TAACTTACA
*
248499 TAACTTATA
1 TAACTTACA
*
248508 TATATCATATCA
1 TA-A-CTTA-CA
248520 TAACTTACA
1 TAACTTACA
*
248529 TAACTTAAA
1 TAACTTACA
248538 TAA--TACA
1 TAACTTACA
* * *
248545 GAAGTATATA
1 TAACT-TACA
248555 TAA--TATCA
1 TAACTTA-CA
*
248563 AAACTTACA
1 TAACTTACA
248572 TAACTTACA
1 TAACTTACA
*
248581 TAATTTACA
1 TAACTTACA
248590 TAACTT
1 TAACTT
248596 TAAAGAATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
7 7 0.09
8 10 0.14
9 39 0.53
10 11 0.15
11 4 0.05
12 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (9 bp):
TAACTTACA
Found at i:250446 original size:22 final size:21
Alignment explanation
Indices: 250405--250465 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 21
250395 AATTTTCAAG
250405 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTAAAGATAT
250424 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTA-AAGATAT
* *
250446 GATTTTGTAATCTTAAAGAT
1 GA-TATGCAATCTTAAAGAT
250466 TTAATTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 13 0.36
22 13 0.36
23 10 0.28
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (21 bp):
GATATGCAATCTTAAAGATAT
Found at i:250475 original size:21 final size:23
Alignment explanation
Indices: 250418--250475 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
250408 ATGCAATCTT
* *
250418 AGATATG-ATATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
250440 AGATATGATTTTGTAATCTTA-A
1 AGATATGAATTTGTAATCTTAGA
*
250462 AGAT-TTAATTTGTA
1 AGATATGAATTTGTA
250476 GATACCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.27
22 12 0.40
23 10 0.33
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:250706 original size:23 final size:23
Alignment explanation
Indices: 250662--250706 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
250652 TCTTATTTTG
* *
250662 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
250685 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
250707 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:250949 original size:3 final size:3
Alignment explanation
Indices: 250943--250974 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
250933 CATCATCATC
250943 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
250975 ATTCATGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:251242 original size:3 final size:3
Alignment explanation
Indices: 251236--251442 Score: 414
Period size: 3 Copynumber: 69.0 Consensus size: 3
251226 AAACAAAAGA
251236 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
251284 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
251332 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
251380 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
251428 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
251443 GTTTTTGTTT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 204 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.