Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014705.1 Kokia drynarioides strain JFW-HI SEQ_129744, 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: 370394
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:224232 original size:91 final size:91
Alignment explanation
Indices: 224077--224258 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
224067 CATGTCATAA
224077 TCTAATTAAAATAGATCTGTTATGAAGTACGGTAATCCATTAGTTAAAATGTTTTTTTAGCTGGT
1 TCTAATTAAAATAGATCTGTTATGAAGTACGGTAATCCATTAGTTAAAATGTTTTTTTAGCTGGT
224142 AAAAGTACCACAAAATCTTTTGTACT
66 AAAAGTACCACAAAATCTTTTGTACT
*
224168 TCTAATTAAAATAGATCTGTTATGAAGTACGGTAGTCCATTAGTTAAAATGTTTTTTTAGCTGGT
1 TCTAATTAAAATAGATCTGTTATGAAGTACGGTAATCCATTAGTTAAAATGTTTTTTTAGCTGGT
224233 AAAAGTACCACAAAATCTTTTGTACT
66 AAAAGTACCACAAAATCTTTTGTACT
224259 AAACCCTAGA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (91 bp):
TCTAATTAAAATAGATCTGTTATGAAGTACGGTAATCCATTAGTTAAAATGTTTTTTTAGCTGGT
AAAAGTACCACAAAATCTTTTGTACT
Found at i:225155 original size:31 final size:30
Alignment explanation
Indices: 225103--225169 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
225093 TAATTTATAT
* * *
225103 TTTTATAATTTTTAAACGATTAAATTACAA
1 TTTTATAATTTTTAAAAGATTAAAATAAAA
225133 TTTTATAA-TTTTAAGAGAGATTAAAATAAAA
1 TTTTATAATTTTTAA-A-AGATTAAAATAAAA
225164 TTTTAT
1 TTTTAT
225170 CTTTATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 9 0.28
31 17 0.53
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAGATTAAAATAAAA
Found at i:227514 original size:18 final size:17
Alignment explanation
Indices: 227491--227525 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
227481 ATTAGGTTCC
*
227491 AAAATTATTATTTTTAAA
1 AAAATTAAT-TTTTTAAA
227509 AAAATTAATTTTTTAAA
1 AAAATTAATTTTTTAAA
227526 TTTTAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTAATTTTTTAAA
Found at i:227567 original size:40 final size:41
Alignment explanation
Indices: 227522--227616 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
227512 ATTAATTTTT
* *
227522 TAAATTTT-AAACTTTTT-TAGAT-TTTTTATATTTTAAAATA
1 TAAATTTTGAAA-TTTTTATAAATCTTTTTA-ATTTAAAAATA
227562 TAAATTTTGAAATTTTTATAAATCTTTTTAATTTAAAAAT-
1 TAAATTTTGAAATTTTTATAAATCTTTTTAATTTAAAAATA
*
227602 T--ATTTTGAATTTTTT
1 TAAATTTTGAAATTTTT
227617 TTTTGTAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 13 0.27
40 14 0.29
41 16 0.33
42 6 0.12
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (41 bp):
TAAATTTTGAAATTTTTATAAATCTTTTTAATTTAAAAATA
Found at i:227963 original size:21 final size:22
Alignment explanation
Indices: 227939--227980 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
227929 ATATATTTAA
* *
227939 AATTATAAAAATTA-TAAAAGT
1 AATTACAAAAAGTATTAAAAGT
227960 AATTACAAAAAGTATTAAAAG
1 AATTACAAAAAGTATTAAAAG
227981 CACTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (22 bp):
AATTACAAAAAGTATTAAAAGT
Found at i:230310 original size:29 final size:29
Alignment explanation
Indices: 230268--230430 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 29
230258 AGTTTTCGTA
* *
230268 AAAGTAAAGTCTTTGTGGCTGAATTTGTT
1 AAAGTGAAGCCTTTGTGGCTGAATTTGTT
*
230297 AAAGTGAAACCTTTGTGGCTGAATTTGTT
1 AAAGTGAAGCCTTTGTGGCTGAATTTGTT
* *
230326 AATA-TG-AGCCTTTGTGGTTGAATCTGTT
1 AA-AGTGAAGCCTTTGTGGCTGAATTTGTT
* * * *
230354 AAAGTTAAGCATTTATGGATGAATTTGTT
1 AAAGTGAAGCCTTTGTGGCTGAATTTGTT
* * * *
230383 ATAGTGAAGCCTTTGTAGTTAAATTTGTT
1 AAAGTGAAGCCTTTGTGGCTGAATTTGTT
*
230412 AACGTG-AGCCTTTGTGGCT
1 AAAGTGAAGCCTTTGTGGCT
230431 AGATCTGTTA
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
27 1 0.01
28 33 0.30
29 74 0.68
30 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.40
Consensus pattern (29 bp):
AAAGTGAAGCCTTTGTGGCTGAATTTGTT
Found at i:230377 original size:57 final size:58
Alignment explanation
Indices: 230278--230418 Score: 169
Period size: 57 Copynumber: 2.4 Consensus size: 58
230268 AAAGTAAAGT
* * * *
230278 CTTTGTGGCTGAATTTGTTAAAGTGAAACCTTTGTGGCTGAATTTGTTAATA-TG-AGC
1 CTTTGTGGTTGAATTTGTTAAAGTGAAACATTTATGGATGAATTTGTT-ATAGTGAAGC
* * *
230335 CTTTGTGGTTGAATCTGTTAAAGTTAAGCATTTATGGATGAATTTGTTATAGTGAAGC
1 CTTTGTGGTTGAATTTGTTAAAGTGAAACATTTATGGATGAATTTGTTATAGTGAAGC
* * *
230393 CTTTGTAGTTAAATTTGTTAACGTGA
1 CTTTGTGGTTGAATTTGTTAAAGTGA
230419 GCCTTTGTGG
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 3 0.04
57 43 0.61
58 24 0.34
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (58 bp):
CTTTGTGGTTGAATTTGTTAAAGTGAAACATTTATGGATGAATTTGTTATAGTGAAGC
Found at i:230457 original size:86 final size:86
Alignment explanation
Indices: 230287--230457 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 86
230277 TCTTTGTGGC
* * * *
230287 TGAATTTGTTAAAGTGAAACCTTTGTGGCTGAATTTGTTAATATGAGCCTTTGTGGTTGAATCTG
1 TGAATTTGTTAAAGTGAAACCTTTGTAGCTAAATTTGTTAACATGAGCCTTTGTGGTAGAATCTG
* * *
230352 TTAAAGTTAAGCATTTATGGA
66 TTAAAGTGAACCATCTATGGA
* * * *
230373 TGAATTTGTTATAGTGAAGCCTTTGTAGTTAAATTTGTTAACGTGAGCCTTTGTGGCTAG-ATCT
1 TGAATTTGTTAAAGTGAAACCTTTGTAGCTAAATTTGTTAACATGAGCCTTTGTGG-TAGAATCT
* * *
230437 GTTAATGTGATCCCTCTATGG
65 GTTAAAGTGAACCATCTATGG
230458 CTAACTCTGT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
86 68 0.97
87 2 0.03
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (86 bp):
TGAATTTGTTAAAGTGAAACCTTTGTAGCTAAATTTGTTAACATGAGCCTTTGTGGTAGAATCTG
TTAAAGTGAACCATCTATGGA
Found at i:232421 original size:34 final size:34
Alignment explanation
Indices: 232357--232421 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
232347 TAGGCAATAT
* * *
232357 TGTTCTTCAGGCAATACTATCCGTCGGGCGATGC
1 TGTTCATCAGGCAATACTACCCGTCAGGCGATGC
*
232391 TGTTCATCGGGCAATACTACCCG-CTAGGCGA
1 TGTTCATCAGGCAATACTACCCGTC-AGGCGA
232422 AACTGTCCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 1 0.04
34 25 0.96
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (34 bp):
TGTTCATCAGGCAATACTACCCGTCAGGCGATGC
Found at i:239830 original size:24 final size:24
Alignment explanation
Indices: 239802--239900 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
239792 AGAAATAATC
* *
239802 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTG
*
239826 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
239850 TTTAAATTAAACTCCGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* * *
239874 TTTCAATTAAACTTTATTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
239898 TTT
1 TTT
239901 GAGTCAAATT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:239863 original size:48 final size:48
Alignment explanation
Indices: 239808--239900 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
239798 AATCTTTCAG
* * *
239808 TTAAACTCTGTTTATTTATTTCAATTAAACTATGTTTATTTGTTTAAA
1 TTAAACTCCGTTTATTTATTTCAATTAAACTATATTTAGTTGTTTAAA
* *
239856 TTAAACTCCGTTTATTTGTTTCAATTAAACTTTATTTAGTTGTTT
1 TTAAACTCCGTTTATTTATTTCAATTAAACTATATTTAGTTGTTT
239901 GAGTCAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.55
Consensus pattern (48 bp):
TTAAACTCCGTTTATTTATTTCAATTAAACTATATTTAGTTGTTTAAA
Found at i:241845 original size:24 final size:24
Alignment explanation
Indices: 241817--241867 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
241807 AGAAATAATC
* * *
241817 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
241841 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
241865 TTT
1 TTT
241868 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:242864 original size:5 final size:6
Alignment explanation
Indices: 242848--242874 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
242838 CTTTATAATT
242848 TAAAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAA
242875 GGTGACTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:245213 original size:563 final size:551
Alignment explanation
Indices: 243955--245450 Score: 1821
Period size: 562 Copynumber: 2.7 Consensus size: 551
243945 CAGAACACCG
* * * * * * * *
243955 AACAGTTTAAAAAAAATCCAACCAAACTACACTCAGTCTAGACCTATTCATTGATCGGGCTATCC
1 AACAATTTAAAAAAATTCCAACCAAACTGCAATCAGCCTAGACCTGTTCATAGGTCGGGCTATCC
* ** * *
244020 GTTCAGGCCTGAAGGTC-CATCCGAAATTTGAGAAGGTTTGGAAAAAAATTAGACCCGTTTAAAA
66 G-TCAAGCCCAAAGGTCGC-T-CGAAATTTGAGAGGGTTTGGGAAAAAATTAGA-CCGTTTAAAA
* *
244084 TATGGG-TCGGGATTTAACATTCAAGGCCTGAGCTCGGCCCGACCTAATCCAACCCGTTTTAAGT
127 TATGGGTTC-GGCTTTAACATTCAAGGCC-GAGCCCGGCCCGA--T--T-CAACCCGTTTTAAGT
*
244148 TTATAATATTTTATATTATGTTATTTTTATCTATTATTTAATTTAAAACACATAAAAAA-ATTAT
185 TTATAATATTTTATATTATGTTATTTTTATCTATTATTTAATTTAAAACACTTAAAAAATA-TAT
* * *
244212 ACTAAATATATAATATTACTCTAATGTAAACATTAAAATAATGTTAAAATGATTATATAAAAAAC
249 ACTAAATATATAATACTACTCTAATGTAAACATTAAAATAATGTTAAAATGACTATATAAAAAAA
* * *
244277 TTCAATAAATAAAAA-ATATAAAAATATTAAATATT-AAATAAAATAAAATGAATATTTTTTTAA
314 TTCAATAAATAAAAATGTAT-AAAATTTTAAATATTAAAATAAAATAAAATAAATATTTTTTTAA
* * *
244340 AAATAATATGGGCAGATTTAAAATAGGCTTGGATTAATCTTTTGCAAATATGAGCGTGTTAGGAC
378 AAATAATATGGACAGACTTAAAATAGGCTTGGATTAATCTTTTGCAAATATGAGCATGTTAGGAC
* * *
244405 AAAATTTTAAGCCAAGAGTTCAGGTCAAGCCAGGCTTGAACAAGCATAAAATATGTTAATACCAT
443 AAAACTTTAAGCCAAGAGTTCAGGTCAAGCCAGGCTTGAAAAAGCATAAAATATGTCAATACCAT
* **
244470 ACTTAGACCCGATGGAAAATTTGAAACAGAACACCATTATTGTG
508 ACTTAGACCCGATGGAAAATTCGAAACAGAACACCATTATTGCA
* * * * * **
244514 AACAATTTAAAAAAATTCCAACCAAACTGCAGTCAACTTAGACTTGTTCATAGGTCGAGCTATTT
1 AACAATTTAAAAAAATTCCAACCAAACTGCAATCAGCCTAGACCTGTTCATAGGTCGGGCTATCC
* * * * * *
244579 GTCTAGCCCAAAGGTTCGCTTGAAATTTTAGAGGGTTTGAGAGAAAAATTAGATCCATTTAAAAA
66 GTCAAGCCCAAAGG-TCGCTCGAAATTTGAGAGGGTTTGGGA-AAAAATTAGA-CCGTTTAAAAT
* * * *
244644 ATGGGTTCGGCTTTAACATTCAATGCTCGAGCCCGGTCCGATTCGACCCATTTTAAGTTTATAAT
128 ATGGGTTCGGCTTTAACATTCAAGGC-CGAGCCCGGCCCGATTCAACCCGTTTTAAGTTTATAAT
244709 ATTTTATATTATGTTATTTTTATCTATTATTTAATTTAAAACACTTAAAAAATATATACTAAAAT
192 ATTTTATATTATGTTATTTTTATCTATTATTTAATTTAAAACACTTAAAAAATATATACT-AAAT
* *
244774 ATATAATACTACTCTAATGTAAACATTAAAATAATGTTAACATGACTATATAAAAAAAATTCAGT
256 ATATAATACTACTCTAATGTAAACATTAAAATAATGTTAAAATGACTATAT-AAAAAAATTCAAT
244839 AAATAAAAATGTATAAAATTTTTAAATATTAAAATAAAATAAAATAAAATAAATATTTTTTAAAA
320 AAATAAAAATGTATAAAA-TTTTAAATATTAAAATAAAATAAAAT-AAAT--AT-TTTTTT-AAA
** * * * * *
244904 AATAATATGGATGGGCTTAAAATGGGCTTGCG-TTAGTCTTTTTCAAATATGCGCATGTTAGGAC
379 AATAATATGGACAGACTTAAAATAGGCTTG-GATTAATCTTTTGCAAATATGAGCATGTTAGGAC
* * * *
244968 AAAACTTT-AGACCTAGA-TTCTAGGTC-GGCTAGGCTTGAAAAAGCATAAAATATGTCAATATC
443 AAAACTTTAAG-CCAAGAGTTC-AGGTCAAGCCAGGCTTGAAAAAGCATAAAATATGTCAATACC
* *
245030 ATACTTAGACCTGATGGAAAATTCGAAATAGAACACCATTATTGCA
506 ATACTTAGACCCGATGGAAAATTCGAAACAGAACACCATTATTGCA
* * *
245076 AACAATTTAAAAAAATTCCAACCAAAGTGCAATCAGCCTAGACCTGTTCATGGGTCGGGTTATCC
1 AACAATTTAAAAAAATTCCAACCAAACTGCAATCAGCCTAGACCTGTTCATAGGTCGGGCTATCC
245141 GTCCAAGCCCAAAGGCTCGCTCGAAATTTGAGAGGGTTTGGGAAAAATATTAGACCTGTTTAAAA
66 GT-CAAGCCCAAAGG-TCGCTCGAAATTTGAGAGGGTTTGGGAAAAA-ATTAGACC-GTTTAAAA
* *
245206 TATGGGTTGGGCTTTAACATTCAAGGCCCGAGCCCGGCCCAAGCCGACCCGATCCAACCCGTTTT
127 TATGGGTTCGGCTTTAACATTCAAGG-CCGA-----GCCC--G--G-CCCGATTCAACCCGTTTT
*
245271 AAGTTTATAATATTTT-T-TTATGTTATTTTTATCTATTATGTAATTTAAAACACTTAAAAAAAT
181 AAGTTTATAATATTTTATATTATGTTATTTTTATCTATTATTTAATTTAAAACACTT-AAAAAAT
* * * *
245334 TTATACTAAATATATAATACTACTCTAATGTAAATATTAAAATAATATTAAGATGACTATATAAA
245 ATATACTAAATATATAATACTACTCTAATGTAAACATTAAAATAATGTTAAAATGACTATATAAA
*
245399 AAATTTCAATAAAATAAAAAATGTATAAAATTTTAAA-A-TAAAATAAAATAAA
310 AAAATTCAAT-AAAT-AAAAATGTATAAAATTTTAAATATTAAAATAAAATAAA
245451 TATGTTTTTA
Statistics
Matches: 808, Mismatches: 93, Indels: 62
0.84 0.10 0.06
Matches are distributed among these distances:
554 77 0.10
555 54 0.07
556 24 0.03
557 14 0.02
558 40 0.05
559 109 0.13
560 4 0.00
561 2 0.00
562 146 0.18
563 146 0.18
564 2 0.00
568 4 0.00
569 14 0.02
570 13 0.02
571 100 0.12
572 29 0.04
573 30 0.04
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (551 bp):
AACAATTTAAAAAAATTCCAACCAAACTGCAATCAGCCTAGACCTGTTCATAGGTCGGGCTATCC
GTCAAGCCCAAAGGTCGCTCGAAATTTGAGAGGGTTTGGGAAAAAATTAGACCGTTTAAAATATG
GGTTCGGCTTTAACATTCAAGGCCGAGCCCGGCCCGATTCAACCCGTTTTAAGTTTATAATATTT
TATATTATGTTATTTTTATCTATTATTTAATTTAAAACACTTAAAAAATATATACTAAATATATA
ATACTACTCTAATGTAAACATTAAAATAATGTTAAAATGACTATATAAAAAAATTCAATAAATAA
AAATGTATAAAATTTTAAATATTAAAATAAAATAAAATAAATATTTTTTTAAAAATAATATGGAC
AGACTTAAAATAGGCTTGGATTAATCTTTTGCAAATATGAGCATGTTAGGACAAAACTTTAAGCC
AAGAGTTCAGGTCAAGCCAGGCTTGAAAAAGCATAAAATATGTCAATACCATACTTAGACCCGAT
GGAAAATTCGAAACAGAACACCATTATTGCA
Found at i:246185 original size:40 final size:40
Alignment explanation
Indices: 246141--246343 Score: 208
Period size: 40 Copynumber: 5.1 Consensus size: 40
246131 ACCTAACAGC
* ** **
246141 GTTTACAGTGTCATTGTTGGTTCAGTTGTAGGGTTGTAGT
1 GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
* * * * * * ** *
246181 GTTTATAATGTCATTGCCGATTCAATCATAATATCGTAGT
1 GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
* *
246221 GTTTACAGTGTCACTGCCGGTTCAGTAATAGCATTGTAGT
1 GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
* * *
246261 GTTTATAGTGTCACTATCGGTTCAGTAATAGCATTGTAGT
1 GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
* * *
246301 GTTTACAGTGTCATTGTCAGTTCACTAATAGCTTTGTAGT
1 GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
246341 GTT
1 GTT
246344 ATATTGTCAC
Statistics
Matches: 133, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 133 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (40 bp):
GTTTACAGTGTCATTGTCGGTTCAGTAATAGCATTGTAGT
Found at i:246258 original size:80 final size:79
Alignment explanation
Indices: 246141--246407 Score: 257
Period size: 80 Copynumber: 3.4 Consensus size: 79
246131 ACCTAACAGC
*** ** ** *
246141 GTTTACAGTGTCATTGTTGGTTCAGTTGTAGGGTTGTAGTGTTTATAATGTCATTGCCGATTCAA
1 GTTTACAGTGTCATTGCCAGTTCAGTAATAGCATTGTAGTGTTTATAATGTCACTG-CGATTCAA
* *
246206 TCATAATATCGTAGT
65 TAATAATATTGTAGT
* * * * * *
246221 GTTTACAGTGTCACTGCCGGTTCAGTAATAGCATTGTAGTGTTTATAGTGTCACTATCGGTTCAG
1 GTTTACAGTGTCATTGCCAGTTCAGTAATAGCATTGTAGTGTTTATAATGTCACT-GCGATTCAA
**
246286 TAATAGCATTGTAGT
65 TAATAATATTGTAGT
* * * * *
246301 GTTTACAGTGTCATTGTCAGTTCACTAATAGCTTTGTAGTG-TTATATTGTCACTGCTAGTTCAA
1 GTTTACAGTGTCATTGCCAGTTCAGTAATAGCATTGTAGTGTTTATAATGTCACTGCGA-TTCAA
*
246365 TAATAATATTGTAAT
65 TAATAATATTGTAGT
* * *
246380 GTTTATAGTGCCATTGCCAATTCAGTAA
1 GTTTACAGTGTCATTGCCAGTTCAGTAA
246408 CAATATTTCC
Statistics
Matches: 151, Mismatches: 34, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
78 1 0.01
79 51 0.34
80 99 0.66
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (79 bp):
GTTTACAGTGTCATTGCCAGTTCAGTAATAGCATTGTAGTGTTTATAATGTCACTGCGATTCAAT
AATAATATTGTAGT
Found at i:258314 original size:37 final size:37
Alignment explanation
Indices: 258265--258339 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
258255 TTCAAATTGG
*
258265 AAGAAAGAATGTTGTGTGAAATGAGGGTTGAGAATAA
1 AAGAAAGAATGTTGTGTGAAATGAGGGCTGAGAATAA
258302 AAGAAAGAATGTTGTGTGAAATGAGGGCTGAGAATAA
1 AAGAAAGAATGTTGTGTGAAATGAGGGCTGAGAATAA
258339 A
1 A
258340 GAGGGAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.44, C:0.01, G:0.32, T:0.23
Consensus pattern (37 bp):
AAGAAAGAATGTTGTGTGAAATGAGGGCTGAGAATAA
Found at i:259926 original size:52 final size:51
Alignment explanation
Indices: 259767--259938 Score: 170
Period size: 50 Copynumber: 3.4 Consensus size: 51
259757 TTAATAAAGT
* * * ** * * *
259767 CATGCATTATGTAAGTTTCAAG-TTAATTAAGTATGCATCATAAATAACGA
1 CATGCATTATGTAACTCTCATGATTTGTTAAGTTTGCATCATAAATAATGG
**
259817 CATGCATTGCGTAACTCTCATGATTTGTTAAGTTTGCATCATAAATAATGG
1 CATGCATTATGTAACTCTCATGATTTGTTAAGTTTGCATCATAAATAATGG
* * *
259868 CGTGCATTATATGTAACTCTCATG-TTTGTTAAGATTT-CATCATAAATTATGT
1 CATGCA-T-TATGTAACTCTCATGATTTGTTAAG-TTTGCATCATAAATAATGG
*
259920 TATGCATTATGTAACTCTC
1 CATGCATTATGTAACTCTC
259939 TCGTTAAAGT
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
50 29 0.29
51 29 0.29
52 27 0.27
53 16 0.16
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (51 bp):
CATGCATTATGTAACTCTCATGATTTGTTAAGTTTGCATCATAAATAATGG
Found at i:259940 original size:52 final size:53
Alignment explanation
Indices: 259793--259938 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 53
259783 TTCAAGTTAA
* * * **
259793 TTAAGTATGCATCATAAATAACGACATGCA-T-TGCGTAACTCTCATGATTTG
1 TTAAGTTTGCATCATAAATAATGGCATGCATTATATGTAACTCTCATGATTTG
*
259844 TTAAGTTTGCATCATAAATAATGGCGTGCATTATATGTAACTCTCATG-TTTG
1 TTAAGTTTGCATCATAAATAATGGCATGCATTATATGTAACTCTCATGATTTG
* **
259896 TTAAGATTT-CATCATAAATTATGTTATGCA-T-TATGTAACTCTC
1 TTAAG-TTTGCATCATAAATAATGGCATGCATTATATGTAACTCTC
259939 TCGTTAAAGT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
50 12 0.15
51 27 0.33
52 27 0.33
53 16 0.20
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (53 bp):
TTAAGTTTGCATCATAAATAATGGCATGCATTATATGTAACTCTCATGATTTG
Found at i:260655 original size:36 final size:36
Alignment explanation
Indices: 260615--260694 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
260605 AAGATGGAGA
260615 CCTTTAAGCTA-TCCAAGGACAAATAAAAAGACATGC
1 CCTTTAAGCTACTCCAA-GACAAATAAAAAGACATGC
* ** * *
260651 CCTTTCATTTACTCCAAGACAAATGAAGAGACATGC
1 CCTTTAAGCTACTCCAAGACAAATAAAAAGACATGC
*
260687 CTTTTAAG
1 CCTTTAAG
260695 TTAAAACTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
36 30 0.86
37 5 0.14
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (36 bp):
CCTTTAAGCTACTCCAAGACAAATAAAAAGACATGC
Found at i:276881 original size:8 final size:8
Alignment explanation
Indices: 276860--276893 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
276850 ACAATTTTTT
276860 TTAAAA-A
1 TTAAAATA
276867 TTAAAAATA
1 TT-AAAATA
276876 TTAAAATA
1 TTAAAATA
276884 TTAAAATA
1 TTAAAATA
276892 TT
1 TT
276894 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 2 0.08
8 20 0.80
9 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAATA
Found at i:277786 original size:15 final size:15
Alignment explanation
Indices: 277766--277800 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
277756 ATTATTCGAG
277766 AATAATTACATTCAA
1 AATAATTACATTCAA
* *
277781 AATAATTATATTTAA
1 AATAATTACATTCAA
277796 AATAA
1 AATAA
277801 AATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATTACATTCAA
Found at i:277850 original size:17 final size:16
Alignment explanation
Indices: 277752--277872 Score: 52
Period size: 16 Copynumber: 7.4 Consensus size: 16
277742 TGTTCAAAAC
277752 AATTATTATTCGAGAAT
1 AATTATTATT-GAGAAT
* * *
277769 AATTA-CATTCAAAAT
1 AATTATTATTGAGAAT
* *
277784 AATTA-TATTTAAAAT
1 AATTATTATTGAGAAT
277799 AAAATT-TTAATTGAGAAT
1 --AATTATT-ATTGAGAAT
* * *
277817 AACTGTTGTAT-AGAAT
1 AATTATTAT-TGAGAAT
277833 AATTATTATTCGAGAAT
1 AATTATTATT-GAGAAT
* * * *
277850 AGTTTTTATTTAAAAT
1 AATTATTATTGAGAAT
277866 AATTATT
1 AATTATT
277873 GCTCAAAACA
Statistics
Matches: 78, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
15 18 0.23
16 27 0.35
17 26 0.33
18 7 0.09
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (16 bp):
AATTATTATTGAGAAT
Found at i:284343 original size:87 final size:86
Alignment explanation
Indices: 284186--284344 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 86
284176 TGCATAAGAA
* *
284186 TGAGTTTTTAATCTTAATGAATCCATAGCCCAGATTTTGGGTGGTCCTATTTAGACGGACTTGAT
1 TGAGTTTTTAATCTTAATGAATCCATAGCCCAGATTTTGGGTGGTCCTATTGAGACAGACTTGAT
284251 GAATTCATCGACTTGAGAGGT
66 GAATTCATCGACTTGAGAGGT
* * * * *
284272 TGAGTTTATTACTCTTAATGAGTTCATATCCCA-ATGTTTGGGTGGTCCTATTGATACAGACTTG
1 TGAGTTT-TTAATCTTAATGAATCCATAGCCCAGAT-TTTGGGTGGTCCTATTGAGACAGACTTG
284336 ATGAATTCA
64 ATGAATTCA
284345 CCGAACATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
86 9 0.14
87 55 0.86
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (86 bp):
TGAGTTTTTAATCTTAATGAATCCATAGCCCAGATTTTGGGTGGTCCTATTGAGACAGACTTGAT
GAATTCATCGACTTGAGAGGT
Found at i:288884 original size:70 final size:67
Alignment explanation
Indices: 288753--288885 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
288743 ATAAACAATA
* * * * *
288753 TAATGGTTTTGTCTTTTAATTTAATAGGTAAACATTTATCAAAATGACATAATTTTTCCTTTTAA
1 TAATAGTTTTGACTTTTAATTTAAAAGGTAAACATTTATCAAAATGACATAATCTTGCCTTTTAA
288818 CT
66 CT
** *
288820 TAATAGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAATGATGTAGTCTTGCCTTT
1 TAATAGTTTTGACTTTTAA-TTTA-AAA-GGTAAACATTTATCAAAATGACATAATCTTGCCTTT
288885 T
63 T
288886 CTTATTCGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 17 0.31
68 4 0.07
69 2 0.04
70 32 0.58
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (67 bp):
TAATAGTTTTGACTTTTAATTTAAAAGGTAAACATTTATCAAAATGACATAATCTTGCCTTTTAA
CT
Found at i:290325 original size:18 final size:18
Alignment explanation
Indices: 290304--290356 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 18
290294 TATCATATAA
290304 AATAATGTTTTTATACAT
1 AATAATGTTTTTATACAT
*
290322 AATAATAGAATTTTTATACCT
1 AATAAT-G--TTTTTATACAT
* *
290343 AAAAATATTTTTAT
1 AATAATGTTTTTAT
290357 TATAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 13 0.45
19 1 0.03
21 15 0.52
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (18 bp):
AATAATGTTTTTATACAT
Found at i:300309 original size:10 final size:10
Alignment explanation
Indices: 300265--300326 Score: 56
Period size: 10 Copynumber: 6.0 Consensus size: 10
300255 AAGTACAAAC
300265 AAATTAAAGAT
1 AAATTAAA-AT
300276 ACGAATTAAAA-
1 A--AATTAAAAT
300287 AAA-TAAAATT
1 AAATTAAAA-T
*
300297 AAATTAAACT
1 AAATTAAAAT
300307 AAATTAAAAT
1 AAATTAAAAT
*
300317 AAAATAAAAT
1 AAATTAAAAT
300327 TACTAGGATC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 22 0.51
11 6 0.14
12 1 0.02
13 7 0.16
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:300312 original size:15 final size:15
Alignment explanation
Indices: 300286--300324 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
300276 ACGAATTAAA
*
300286 AAAATAAAATTAAATT
1 AAAAT-AAATTAAAAT
*
300302 AAACTAAATTAAAAT
1 AAAATAAATTAAAAT
300317 AAAATAAA
1 AAAATAAA
300325 ATTACTAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAAATTAAAAT
Found at i:302885 original size:43 final size:42
Alignment explanation
Indices: 302816--302938 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
302806 ATGCTCTCAC
* * ** *
302816 TCAATCACTTA-TTATCAATATTAGGAAATAGTGTTTCATTCAT
1 TCAATCACATACTT-TCAATA-TAGGAAATAGTGTTCCACACAA
* * *
302859 TCGATCACATACTTTTAATGCTAGGAAATAGTGTTCCACACAA
1 TCAATCACATACTTTCAAT-ATAGGAAATAGTGTTCCACACAA
302902 TCAATCACATACTTTCAATATAAGGAAATAGTGTTCC
1 TCAATCACATACTTTCAATAT-AGGAAATAGTGTTCC
302939 TCTCACTATC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.02
43 63 0.95
44 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (42 bp):
TCAATCACATACTTTCAATATAGGAAATAGTGTTCCACACAA
Found at i:310893 original size:43 final size:43
Alignment explanation
Indices: 310843--310944 Score: 159
Period size: 43 Copynumber: 2.4 Consensus size: 43
310833 TCACATATTA
** * **
310843 TCAATATTAGGAAACAGTGTTCCATTCATTCGATCACGTACTT
1 TCAATATTAGGAAACAGTGTTCCACACAATCGATCACAAACTT
310886 TCAATATTAGGAAACAGTGTTCCACACAATCGATCACAAACTT
1 TCAATATTAGGAAACAGTGTTCCACACAATCGATCACAAACTT
310929 TCAATATTAGGAAACA
1 TCAATATTAGGAAACA
310945 ATGCTCCTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (43 bp):
TCAATATTAGGAAACAGTGTTCCACACAATCGATCACAAACTT
Found at i:314525 original size:22 final size:21
Alignment explanation
Indices: 314500--314543 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
314490 TAGTGACCGT
*
314500 TGGACCACAATTATCGATACCA
1 TGGACCA-AAGTATCGATACCA
*
314522 TGGAGCAAAGTATCGATACCA
1 TGGACCAAAGTATCGATACCA
314543 T
1 T
314544 ATGAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
TGGACCAAAGTATCGATACCA
Found at i:317656 original size:22 final size:21
Alignment explanation
Indices: 317631--317674 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
317621 TAGTGACCGT
317631 TGGACCAAAATTATCGATACCA
1 TGGACC-AAATTATCGATACCA
*
317653 TGGAGCAAATTATCGATACCA
1 TGGACCAAATTATCGATACCA
317674 T
1 T
317675 ATGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
TGGACCAAATTATCGATACCA
Found at i:324393 original size:16 final size:17
Alignment explanation
Indices: 324361--324394 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
324351 AAATTAAAAA
324361 AAAAATCAGTAAAATAT
1 AAAAATCAGTAAAATAT
*
324378 AAAAATCA-TAATATAT
1 AAAAATCAGTAAAATAT
324394 A
1 A
324395 CTTAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATCAGTAAAATAT
Found at i:328825 original size:117 final size:118
Alignment explanation
Indices: 328704--328978 Score: 419
Period size: 117 Copynumber: 2.3 Consensus size: 118
328694 GGTTGAACAG
* * *
328704 GGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATT
1 GGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATT
* *
328768 TTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTGAGGTAAAAAAT
66 TTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGGTTCGAGGTAAAAAAT
*
328821 GGGATTTTTGGAAGTTCGGGAGTAAAATTGTAA-TTTTGGAAGGTTCGGGGTCAAAAATGAGATT
1 GGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATT
* * * *
328885 TTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
66 TTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGGTTCGAGGTAAAAAAT
* * *
328938 GAGATTTTTGGAAGTTCAGGAGTAAAATGATAATTTTTGGA
1 GGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGA
328979 CAGTCTGGGG
Statistics
Matches: 142, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
116 19 0.13
117 116 0.82
118 7 0.05
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (118 bp):
GGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATT
TTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGGTTCGAGGTAAAAAAT
Found at i:328926 original size:59 final size:59
Alignment explanation
Indices: 328706--328978 Score: 406
Period size: 58 Copynumber: 4.7 Consensus size: 59
328696 TTGAACAGGG
* *
328706 GATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGG
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
* * * * * *
328764 GATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTGAGGTAAAAAATGG
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
* *
328823 GATTTTTGGAAGTTCGGGAGTAAAATTGTAA-TTTTGGAAGGTTCGGGGTCAAAAATGA
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
*
328881 GATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
* * *
328940 GATTTTTGGAAGTTCAGGAGTAAAATGATAATTTTTGGA
1 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGA
328979 CAGTCTGGGG
Statistics
Matches: 193, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
58 97 0.50
59 96 0.50
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGA
Found at i:329540 original size:12 final size:12
Alignment explanation
Indices: 329523--329547 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
329513 AAATAAAAAC
329523 CCAAAATCCTCT
1 CCAAAATCCTCT
329535 CCAAAATCCTCT
1 CCAAAATCCTCT
329547 C
1 C
329548 ACCCCCTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (12 bp):
CCAAAATCCTCT
Found at i:329997 original size:4 final size:4
Alignment explanation
Indices: 329988--330017 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
329978 GACTTTTCGT
329988 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
330018 AATTATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:332395 original size:30 final size:32
Alignment explanation
Indices: 332331--332397 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
332321 CATTATACAT
*
332331 TAATATTTGATTATTATTATTATTATTTGAATA
1 TAATATTTGATTATTATTATTATAATTT-AATA
332364 TAATATTTGATTATTATTATTA-AATTT-ATA
1 TAATATTTGATTATTATTATTATAATTTAATA
332394 TAAT
1 TAAT
332398 TAAAAACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 7 0.21
32 4 0.12
33 22 0.67
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (32 bp):
TAATATTTGATTATTATTATTATAATTTAATA
Found at i:342428 original size:118 final size:118
Alignment explanation
Indices: 342221--342441 Score: 327
Period size: 118 Copynumber: 1.9 Consensus size: 118
342211 GAAGAACCAA
* * * * *
342221 AATAAGCTGTGATGGCAAGCCTACATATGGTTGTTTGATACACAAAGGAAATTTGGGACATTTTG
1 AATAAGCTGTAATGACAAGCCTACATATGGTTATTTGATACAAAAAGGAAATTTGGGACATTTTA
* * *
342286 TCTAGGAGTCCTTTTGTAGTTCTCATACACTAGTTGCTCCCTGGAAGAGCAAC
66 TCTAGGAGTCCTTTTATAGCTCTCAAACACTAGTTGCTCCCTGGAAGAGCAAC
* *
342339 AATAAGCTGTAATTACAAGCCTACATATGGTTATTTGATACAAAAAGGAAATTTGGGATATTTTA
1 AATAAGCTGTAATGACAAGCCTACATATGGTTATTTGATACAAAAAGGAAATTTGGGACATTTTA
*
342404 TCTAGGAGGT-TTTTTATAGCTCTCAAACACTAGTTGCT
66 TCTAGGA-GTCCTTTTATAGCTCTCAAACACTAGTTGCT
342442 GCCTTTGTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
118 89 0.98
119 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (118 bp):
AATAAGCTGTAATGACAAGCCTACATATGGTTATTTGATACAAAAAGGAAATTTGGGACATTTTA
TCTAGGAGTCCTTTTATAGCTCTCAAACACTAGTTGCTCCCTGGAAGAGCAAC
Found at i:344608 original size:70 final size:70
Alignment explanation
Indices: 344514--344654 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
344504 ATGATCTGCA
344514 TTCTTTGATATTATGAAGAAAGGCTGAAGCCAATAGGTATTAAAGATGACAAAATATGATCAAGC
1 TTCTTTGATATTATGAAGAAAGGCTGAAGCCAATAGGTATTAAAGATGACAAAATATGATCAAGC
344579 ATGGT
66 ATGGT
344584 TTCTTTGATATTATGAAGAAAGGCTGAAGCCAATAGGTATTAAAGATGACAAAATATGATCAAGC
1 TTCTTTGATATTATGAAGAAAGGCTGAAGCCAATAGGTATTAAAGATGACAAAATATGATCAAGC
344649 ATGGT
66 ATGGT
344654 T
1 T
344655 GTTGGTATCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (70 bp):
TTCTTTGATATTATGAAGAAAGGCTGAAGCCAATAGGTATTAAAGATGACAAAATATGATCAAGC
ATGGT
Found at i:347039 original size:17 final size:17
Alignment explanation
Indices: 347016--347060 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
347006 ATTGAACCAA
*
347016 AATTTTTTAATTTTTAT
1 AATTTTTTAATTTTAAT
* *
347033 CATTTTTGAATTTTAAT
1 AATTTTTTAATTTTAAT
*
347050 AAGTTTTTAAT
1 AATTTTTTAAT
347061 CGGACTAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
AATTTTTTAATTTTAAT
Found at i:347560 original size:12 final size:12
Alignment explanation
Indices: 347543--347579 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
347533 TTTGCATGAA
347543 AAATAAATAATT
1 AAATAAATAATT
347555 AAATAAATAATT
1 AAATAAATAATT
347567 AAATAAAT-ATT
1 AAATAAATAATT
347578 AA
1 AA
347580 CTCACAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAATAATT
Found at i:349815 original size:6 final size:6
Alignment explanation
Indices: 349804--349869 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
349794 TCAAATTTAT
** **
349804 TTTAAA TTTAAA TTTATC TTTGAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
*
349852 TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
349870 GGATTTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:349818 original size:17 final size:17
Alignment explanation
Indices: 349796--349869 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
349786 AAATTGATTC
349796 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
349813 AAATTTATCTTTGAAATTT
1 AAATTTAT-TTT-AAATTT
**
349832 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
349849 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
349866 AAAT
1 AAAT
349870 GGATTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 32 0.64
18 6 0.12
19 12 0.24
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:350615 original size:3 final size:3
Alignment explanation
Indices: 350609--350648 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
350599 TAATTATTTT
350609 TAA TAA TAA TAA TAA TAA -AA -AA TTAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TA
350649 TTAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:351772 original size:30 final size:29
Alignment explanation
Indices: 351736--352106 Score: 289
Period size: 29 Copynumber: 12.6 Consensus size: 29
351726 TCCCTAAAAT
* *
351736 TTCCAAAAATTCCATTTTTGATCTTGAAAC
1 TTCCAAAAATTCCATTTTT-ACCTCGAAAC
*
351766 TTCCAAAAATCCCATTTTTACCCTCG-AAC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAAC
*
351795 TTCAAAAAATTCCATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCTCGAAAC
* * *
351825 TTTCGAAAATTTCATTTTTACTCTCG-AAC
1 TTCCAAAAATTCCATTTTTAC-CTCGAAAC
351854 TTCCAAAAATTCCATTTTTGATCC-CGAAAC
1 TTCCAAAAATTCCATTTTT-A-CCTCGAAAC
*
351884 TTCC-AAAATTCCATTTTTACCCTC-AATC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAAC
* * *
351912 TTCTAAAAATTCCATTTTCAACTCTGAAAC
1 TTCCAAAAATTCCATTTTTACCTC-GAAAC
* *
351942 TTCCAAAAATTACATTTTTACCCTTG-AAC
1 TTCCAAAAATTCCATTTTTA-CCTCGAAAC
* * * *
351971 CTCCAAAATTTCCATTTTTGACCCCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCTCGAAAC
* *
352001 TTTCAAAAATTCCATTTTTACCCCTG-AA-
1 TTCCAAAAATTCCATTTTTACCTC-GAAAC
*
352029 TGTCTAAAAATTCCATCTTTTAACCTCG-AAC
1 T-TCCAAAAATTCCAT-TTTT-ACCTCGAAAC
* * *
352060 TTCCCCAAAATTACCA-TCTTGCCTCGAAA-
1 TT-CCAAAAATT-CCATTTTTACCTCGAAAC
*
352089 GTCC-AAAATTACCATTTT
1 TTCCAAAAATT-CCATTTT
352107 GCCCTGAGTA
Statistics
Matches: 276, Mismatches: 42, Indels: 48
0.75 0.11 0.13
Matches are distributed among these distances:
27 10 0.04
28 17 0.06
29 124 0.45
30 107 0.39
31 15 0.05
32 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCTCGAAAC
Found at i:351795 original size:29 final size:29
Alignment explanation
Indices: 351736--352063 Score: 294
Period size: 29 Copynumber: 11.1 Consensus size: 29
351726 TCCCTAAAAT
* *
351736 TTCCAAAAATTCCATTTTTGA-TCTTGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
*
351766 TTCCAAAAATCCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* *
351795 TTCAAAAAATTCCATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTTACCCTCG-AAC
* * * *
351825 TTTCGAAAATTTCATTTTTACTCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
*
351854 TTCCAAAAATTCCATTTTTGATCC-CGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCG-AAC
351884 TTCC-AAAATTCCATTTTTACCCTC-AATC
1 TTCCAAAAATTCCATTTTTACCCTCGAA-C
* * *
351912 TTCTAAAAATTCCATTTTCA-ACTCTGAAAC
1 TTCCAAAAATTCCATTTTTACCCTC-G-AAC
* *
351942 TTCCAAAAATTACATTTTTACCCTTGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* * *
351971 CTCCAAAATTTCCATTTTTGACCC-CAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTC-GAAC
*
352001 TTTCAAAAATTCCATTTTTACCC-CTGAA-
1 TTCCAAAAATTCCATTTTTACCCTC-GAAC
* *
352029 TGTCTAAAAATTCCATCTTTTAACCTCGAAC
1 T-TCCAAAAATTCCAT-TTTTACCCTCGAAC
352060 TTCC
1 TTCC
352064 CCAAAATTAC
Statistics
Matches: 241, Mismatches: 40, Indels: 34
0.77 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 11 0.05
29 115 0.48
30 107 0.44
31 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAC
Found at i:351834 original size:59 final size:59
Alignment explanation
Indices: 351736--352058 Score: 352
Period size: 59 Copynumber: 5.5 Consensus size: 59
351726 TCCCTAAAAT
* * * * *
351736 TTCCAAAAATTCCATTTTTGATCTTGAAACTTCCAAAAATCCCATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTACCCTCGAAC
* * * *
351795 TTCAAAAAATTCCATTTTTAACCTCGAAACTTTCGAAAATTTCATTTTTACTCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTACCCTCGAAC
* *
351854 TTCCAAAAATTCCATTTTTGATCC-CGAAAC-TTCCAAAATTCCATTTTTACCCTC-AATC
1 TTCCAAAAATTCCATTTTT-AACCTCGAAACTTTCAAAAATTCCATTTTTACCCTCGAA-C
* * * * *
351912 TTCTAAAAATTCCATTTTCAA-CTCTGAAACTTCCAAAAATTACATTTTTACCCTTGAAC
1 TTCCAAAAATTCCATTTTTAACCTC-GAAACTTTCAAAAATTCCATTTTTACCCTCGAAC
* * * * *
351971 CTCCAAAATTTCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTTACCC-CTGAA-
1 TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTACCCTC-GAAC
*
352029 TGTCTAAAAATTCCATCTTTTAACCTCGAA
1 T-TCCAAAAATTCCAT-TTTTAACCTCGAA
352059 CTTCCCCAAA
Statistics
Matches: 217, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
56 1 0.00
57 4 0.02
58 44 0.20
59 151 0.70
60 17 0.08
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCATTTTTACCCTCGAAC
Found at i:355254 original size:30 final size:29
Alignment explanation
Indices: 355200--355258 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
355190 TCAAAAAATT
* * *
355200 ATTAATTGATCTTTGATTGAATTAATTTG
1 ATTAATTGATCGTTAATAGAATTAATTTG
355229 ATTAATTGATCGGTTAATAGAATTAATTTG
1 ATTAATTGATC-GTTAATAGAATTAATTTG
355259 GTTTTACTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.47
Consensus pattern (29 bp):
ATTAATTGATCGTTAATAGAATTAATTTG
Found at i:362490 original size:22 final size:20
Alignment explanation
Indices: 362465--362516 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
362455 AAAATTATTT
362465 AATAATTTTATTATTTCAAAAA
1 AATAATTTTA-TATTT-AAAAA
**
362487 AATAATTTTATATTTTTAAA
1 AATAATTTTATATTTAAAAA
362507 AATAATTTTA
1 AATAATTTTA
362517 ATAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.46
21 5 0.18
22 10 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTTTATATTTAAAAA
Found at i:362507 original size:21 final size:21
Alignment explanation
Indices: 362465--362528 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
362455 AAAATTATTT
**
362465 AATAATTTTATTATTTCAAAAA
1 AATAATTTTA-TATTTTTAAAA
362487 AATAATTTTATATTTTT-AAA
1 AATAATTTTATATTTTTAAAA
*
362507 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATATTTTTAAAA
362529 TCATTTGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 12 0.32
21 12 0.32
22 13 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATTTTATATTTTTAAAA
Found at i:362509 original size:20 final size:20
Alignment explanation
Indices: 362465--362528 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
362455 AAAATTATTT
**
362465 AATAATTTTATTATTTCAAAAA
1 AATAATTTTA-TATTT-TTAAA
362487 AATAATTTTATATTTTTAAA
1 AATAATTTTATATTTTTAAA
*
362507 AATAATTTTAATAATTTTAAA
1 AATAATTTT-ATATTTTTAAA
362528 A
1 A
362529 TCATTTGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.32
21 16 0.42
22 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTATATTTTTAAA
Found at i:364941 original size:38 final size:38
Alignment explanation
Indices: 364890--365067 Score: 214
Period size: 38 Copynumber: 4.7 Consensus size: 38
364880 AAATGGCAAG
* *
364890 TATACTTAATGCTTGCTCAAGTGAG-AGAATCCACTAAT
1 TATACTGAATGCTTGCTCAAGCGAGCA-AATCCACTAAT
*
364928 TATACTGAATGCTTGCTCAAGCGAGCAAATCCACTGAT
1 TATACTGAATGCTTGCTCAAGCGAGCAAATCCACTAAT
* *
364966 TATACTGAATGCTTGCTCAAGCAAGCAAATCCACTGAT
1 TATACTGAATGCTTGCTCAAGCGAGCAAATCCACTAAT
* * * * *
365004 TATACCGAATGATTGTTCAAACGAGCGAATCCACTAAT
1 TATACTGAATGCTTGCTCAAGCGAGCAAATCCACTAAT
* * * *
365042 TTTACTGAATGTTTGTTCAAACGAGC
1 TATACTGAATGCTTGCTCAAGCGAGC
365068 GATAACTATT
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 124 0.99
39 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (38 bp):
TATACTGAATGCTTGCTCAAGCGAGCAAATCCACTAAT
Found at i:368473 original size:46 final size:47
Alignment explanation
Indices: 368401--368493 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 47
368391 AGGTGATGGA
*
368401 TCATCGTTATCGGGCAACCCGAGATGACTTAATTGGTGTGTT-TTGG
1 TCATCGTTATCGGGCAACCCGAGATGACATAATTGGTGTGTTATTGG
* * *
368447 TCATCGTTTTTGGGCAACCCGGGATGACATAATTGGTGTGTTATTGG
1 TCATCGTTATCGGGCAACCCGAGATGACATAATTGGTGTGTTATTGG
368494 ATGGATGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 38 0.90
47 4 0.10
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.35
Consensus pattern (47 bp):
TCATCGTTATCGGGCAACCCGAGATGACATAATTGGTGTGTTATTGG
Done.