Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold208
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: 983439
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 37400 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:656657 original size:31 final size:31
Alignment explanation
Indices: 656619--656689 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
656609 ATAGTCTTAA
656619 TTTAGACTTTTCCTTCTCCGATATTTCAACC
1 TTTAGACTTTTCCTTCTCCGATATTTCAACC
656650 TTTAGACTTTTCCTTCTCCGATATTTCAACC
1 TTTAGACTTTTCCTTCTCCGATATTTCAACC
656681 TTTAGACTT
1 TTTAGACTT
656690 GGTGCATTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (31 bp):
TTTAGACTTTTCCTTCTCCGATATTTCAACC
Found at i:666990 original size:20 final size:20
Alignment explanation
Indices: 666965--667007 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
666955 TAGTCTGTTT
666965 TCAAACACTCCAAATCTCTC
1 TCAAACACTCCAAATCTCTC
666985 TCAAACACTCCAAATCTCTC
1 TCAAACACTCCAAATCTCTC
667005 TCA
1 TCA
667008 CCCTTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.26
Consensus pattern (20 bp):
TCAAACACTCCAAATCTCTC
Found at i:670250 original size:8 final size:7
Alignment explanation
Indices: 670214--670246 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
670204 TTATTATCTC
670214 TTTTTAT
1 TTTTTAT
670221 TTTTTAT
1 TTTTTAT
670228 TTTTTAT
1 TTTTTAT
670235 TTTTTAT
1 TTTTTAT
670242 TTTTT
1 TTTTT
670247 TATTACGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:677375 original size:15 final size:15
Alignment explanation
Indices: 677355--677386 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
677345 AACTAACCAA
677355 TTGAAAGTTTAAAAC
1 TTGAAAGTTTAAAAC
677370 TTGAAAGTTTAAAAC
1 TTGAAAGTTTAAAAC
677385 TT
1 TT
677387 CCAACCCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTGAAAGTTTAAAAC
Found at i:688449 original size:35 final size:35
Alignment explanation
Indices: 688383--688449 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
688373 ATAATTATAA
*
688383 TTATAATTTAAGTTACAATTATTAGTTAAAATTAT
1 TTATAATTTAAGTTACAATTATTAGTAAAAATTAT
*
688418 TTATAATTTAATTTTGAC-ATTATTA-TAAAAAT
1 TTATAATTTAA-GTT-ACAATTATTAGTAAAAAT
688450 GGTTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 17 0.61
36 9 0.32
37 2 0.07
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (35 bp):
TTATAATTTAAGTTACAATTATTAGTAAAAATTAT
Found at i:689633 original size:21 final size:22
Alignment explanation
Indices: 689607--689655 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
689597 TAAAAAAAAA
689607 TATTTTAGT-TCTCTATTTATT
1 TATTTTAGTCTCTCTATTTATT
* * *
689628 T-TTTTTGTCTTTTTATTTATT
1 TATTTTAGTCTCTCTATTTATT
689649 TATTTTA
1 TATTTTA
689656 AATTTGAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (22 bp):
TATTTTAGTCTCTCTATTTATT
Found at i:689839 original size:10 final size:9
Alignment explanation
Indices: 689793--689835 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
689783 ATTTATTTTT
689793 AAAAATTAA
1 AAAAATTAA
689802 AAAGAATTAA
1 AAA-AATTAA
*
689812 AATAATT-A
1 AAAAATTAA
689820 AAAAATATAA
1 AAAAAT-TAA
689830 AAAAAT
1 AAAAAT
689836 ATAATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 6 0.21
9 8 0.28
10 15 0.52
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:690672 original size:21 final size:21
Alignment explanation
Indices: 690646--690688 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
690636 ATAAGAGTCT
690646 AAAAAAATGTTAATAATGGAA
1 AAAAAAATGTTAATAATGGAA
690667 AAAAAAATGTTAATAATGGAA
1 AAAAAAATGTTAATAATGGAA
690688 A
1 A
690689 CCTTTCGCCT
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:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (21 bp):
AAAAAAATGTTAATAATGGAA
Found at i:705062 original size:4 final size:4
Alignment explanation
Indices: 705055--705125 Score: 70
Period size: 4 Copynumber: 16.8 Consensus size: 4
705045 TTCTTATTGG
** * *
705055 TTTA TTTA TTTA GTTCG TTTC TTTA TTTC TCATTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA T--TTA TTTA TTTA TTTA TTTA
705106 TTTA TGTTA TTTA TTTA TTT
1 TTTA T-TTA TTTA TTTA TTT
705126 TTATTCCTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 47 0.84
5 6 0.11
6 3 0.05
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:709681 original size:15 final size:15
Alignment explanation
Indices: 709657--709689 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
709647 GCTTGTTTCA
709657 TTTTTCTATTTTTGT
1 TTTTTCTATTTTTGT
*
709672 TTTTTTTATTTTTGT
1 TTTTTCTATTTTTGT
709687 TTT
1 TTT
709690 GTTGTACGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTCTATTTTTGT
Found at i:710785 original size:91 final size:91
Alignment explanation
Indices: 710685--710985 Score: 311
Period size: 91 Copynumber: 3.3 Consensus size: 91
710675 AGTTTACCAT
* * * * * * *
710685 TTTCAAACATCATTTTAAGCGCCTTTAAACATCATCAAAGCCTACAATCAGACACTATAATTTTC
1 TTTCGAACATCATTTAAATCACCTTTAAGCATCATCAAAGCATACAATCAGACACCATAATTTTC
*
710750 AGCAATTAAAATTTTCATTTAACAAC
66 AGCAATTAAAATTATCATTTAACAAC
* *
710776 TTTCGAACATCATTTAAATCACATTTAAGCATCATCAACA-CATACATTC-GAACACCATAATTT
1 TTTCGAACATCATTTAAATCACCTTTAAGCATCATCAA-AGCATACAATCAG-ACACCATAATTT
* * * * * *
710839 ACGGCAATTAAAATGACCAATTAACATC
64 TCAGCAATTAAAATTATCATTTAACAAC
* * * * * * *
710867 TTT-TAGACGTCATTTAAATCATCTTTGAGTATCATTAAAGCATACAATCAAACACCATAATTTT
1 TTTCGA-ACATCATTTAAATCACCTTTAAGCATCATCAAAGCATACAATCAGACACCATAATTTT
* * *
710931 CAGCAATTAAAATTGTAATTTAACCAC
65 CAGCAATTAAAATTATCATTTAACAAC
*
710958 TTTCGAACATCATTTAAATCACATTTAA
1 TTTCGAACATCATTTAAATCACCTTTAA
710986 ACAACACATT
Statistics
Matches: 165, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
90 3 0.02
91 160 0.97
92 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (91 bp):
TTTCGAACATCATTTAAATCACCTTTAAGCATCATCAAAGCATACAATCAGACACCATAATTTTC
AGCAATTAAAATTATCATTTAACAAC
Found at i:711019 original size:13 final size:13
Alignment explanation
Indices: 711001--711028 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
710991 ACATTTCGAA
711001 CAACATTAAAATT
1 CAACATTAAAATT
711014 CAACATTAAAATT
1 CAACATTAAAATT
711027 CA
1 CA
711029 TTTAAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (13 bp):
CAACATTAAAATT
Found at i:711833 original size:81 final size:81
Alignment explanation
Indices: 711698--711866 Score: 275
Period size: 81 Copynumber: 2.1 Consensus size: 81
711688 CCAATTCATT
* *
711698 AAATATATCAAATTATAATTTATCATATTCAATTTATAAATCATTTTATCGTTTCTTTATGATTT
1 AAATATCTCAAATTATAATTTATCATATTCAATTTATAAATCAATTTATCGTTTCTTTATGATTT
* * *
711763 ATTCCATGCCATAATC
66 AGTCCATACCATAAGC
*
711779 AAATATCTCAAATTATAATTTATCATATTCAATTTATAAATGAATTTATCGTTTCTTTATGATTT
1 AAATATCTCAAATTATAATTTATCATATTCAATTTATAAATCAATTTATCGTTTCTTTATGATTT
*
711844 AGTCCATATCATAAGC
66 AGTCCATACCATAAGC
711860 AAATATC
1 AAATATC
711867 AATTCGTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (81 bp):
AAATATCTCAAATTATAATTTATCATATTCAATTTATAAATCAATTTATCGTTTCTTTATGATTT
AGTCCATACCATAAGC
Found at i:715410 original size:414 final size:412
Alignment explanation
Indices: 714640--715858 Score: 2146
Period size: 414 Copynumber: 3.0 Consensus size: 412
714630 TTTGCCATTT
* *
714640 AATATTAACTAAAATTTCATAAATAACTACATCTTAACCGTCCACTATAAAGTAATAAGGTCTAA
1 AATATTAACTAAAATTTCATAAATAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
* * *
714705 TTAACTTTTAAAACCATCATTTCATGTTTACAAAACCATTAAGCACCTATAAACTAATAGTGATT
66 TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGATT
714770 AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATCCAAACTTTAAAATTACC
131 AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATCCAAACTTTAAAATTA-C
*
714835 AGACCAAATTTTAATACTACACTTCAACAACTTTATAAATATCAAATAAATAAAATTTTCTAACT
195 AGACCAAATTTTAATACTACACTTCAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACT
714900 CATTGGTCGGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATA
260 CATTGGTCGGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATA
*
714965 TTTCCTTAATATAATCCAGCCTTTCACTAAAAAAAAAAAACAAACTTAAAGTCAAGTCCTTCTCT
325 TTTCCTTAATATAATCCAGCCTTTCACT-AAAAAAAAAAACAAACTTAAAGTCAAGTCCCTCTCT
715030 ATGAAAAAAAAAACAAATCATAAC
389 ATGAAAAAAAAAACAAATCATAAC
715054 AATATTAACTAAAATTTCATAAATAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
1 AATATTAACTAAAATTTCATAAATAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
715119 TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGATT
66 TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGATT
* *
715184 AAATTTTGTAGCTTTTACGATTTAGTCATTTTTACTTAATTAACTATCCAAACTTTAAAATTACT
131 AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATCCAAACTTTAAAATTAC-
715249 AGACCAAATTTTAATACTACACTTCAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACT
195 AGACCAAATTTTAATACTACACTTCAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACT
*
715314 CATTGGTCAGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATA
260 CATTGGTCGGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATA
715379 TTTCCTTAATATAATCCAGCCTTTCACT---AAAAAAAACAAACTTAAAGTCAAGTCCCTCTCTA
325 TTTCCTTAATATAATCCAGCCTTTCACTAAAAAAAAAAACAAACTTAAAGTCAAGTCCCTCTCTA
*
715441 TG---AAAAAAAGAAATCATAAC
390 TGAAAAAAAAAACAAATCATAAC
*
715461 AATATTAACTAAAATTTCATAAAAAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
1 AATATTAACTAAAATTTCATAAATAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
*
715526 TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGGTT
66 TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGATT
* *
715591 AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATTCAAACTTTAAAGTTACA
131 AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATCCAAACTTTAAAATTACA
715656 GACCAAATTTTAATACTACA-TTCCAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACT
196 GACCAAATTTTAATACTACACTT-CAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACT
* * * * * *
715720 CATTGGTCGGAATTGTGGTGAAGTAATCATAGTGTTCAAAACCATTGAAAATAGGTTATTGCATA
260 CATTGGTCGGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATA
* *
715785 TTTCCTTAATATAATCTAGCCTTTCACTAAAAAAACAAACAAACTTAAAGTCAAGTCCCTCTCTA
325 TTTCCTTAATATAATCCAGCCTTTCACTAAAAAAAAAAACAAACTTAAAGTCAAGTCCCTCTCTA
715850 TGAAAAAAA
390 TGAAAAAAA
715859 GAAATTATCA
Statistics
Matches: 771, Mismatches: 26, Indels: 18
0.95 0.03 0.02
Matches are distributed among these distances:
405 2 0.00
406 147 0.19
407 205 0.27
409 35 0.05
410 35 0.05
412 4 0.01
413 1 0.00
414 342 0.44
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (412 bp):
AATATTAACTAAAATTTCATAAATAACTACATCTTAACCATCCATTATAAAGTAATAAGGTCTAA
TTACCTTTTAAAACCATCACTTCATGTTTATAAAACCATTAAGCACCTATAAACTAATAGTGATT
AACTTTTGTAGCTTTTACGATTTAGTCCTTTTTACTTAATTAACTATCCAAACTTTAAAATTACA
GACCAAATTTTAATACTACACTTCAACAACTTTATAAATATTAAATAAATAAAATTTTCTAACTC
ATTGGTCGGAATTGTGGTCAAGAAACCATAGTGTTCAACACCATTGAAAACAGGTTGTTGCATAT
TTCCTTAATATAATCCAGCCTTTCACTAAAAAAAAAAACAAACTTAAAGTCAAGTCCCTCTCTAT
GAAAAAAAAAACAAATCATAAC
Found at i:728277 original size:18 final size:18
Alignment explanation
Indices: 728256--728298 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
728246 TTTTCAGGTG
*
728256 TAATTAATTTAAAGTTTT
1 TAATTAATTGAAAGTTTT
**
728274 TAATTAATTGAATTTTTT
1 TAATTAATTGAAAGTTTT
728292 TAATTAA
1 TAATTAA
728299 AAATCTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAATTAATTGAAAGTTTT
Found at i:741217 original size:13 final size:13
Alignment explanation
Indices: 741197--741235 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
741187 TAATATAAAA
741197 AAATTATTTTATG
1 AAATTATTTTATG
*
741210 ACATTATTTTAATG
1 AAATTATTTT-ATG
*
741224 AAATAATTTTAT
1 AAATTATTTTAT
741236 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (13 bp):
AAATTATTTTATG
Found at i:741232 original size:14 final size:14
Alignment explanation
Indices: 741197--741234 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
741187 TAATATAAAA
741197 AAATTATTTT-ATG
1 AAATTATTTTAATG
*
741210 ACATTATTTTAATG
1 AAATTATTTTAATG
*
741224 AAATAATTTTA
1 AAATTATTTTA
741235 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
AAATTATTTTAATG
Found at i:745472 original size:33 final size:31
Alignment explanation
Indices: 745427--745548 Score: 118
Period size: 33 Copynumber: 3.7 Consensus size: 31
745417 TCCTGACGAA
* *
745427 CTCTATCTGTGTTTACTGTCCTAGCGCACTTT
1 CTCTATTTGTGTTTACTGTCCTAGCG-ACTAT
*
745459 CTCTATGTTGTGTTTACTGTCTTAGCAGACTAT
1 CTCTAT-TTGTGTTTACTGTCCTAGC-GACTAT
* * * *
745492 CTTTGTTTTGTGTTTACTGTCCCATCGGACTAT
1 CTCT-ATTTGTGTTTACTGTCCTAGC-GACTAT
*
745525 CTCTATTATGTGTTTACTATCCTA
1 CTCTATT-TGTGTTTACTGTCCTA
745549 ATGAATTATT
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
32 8 0.11
33 63 0.86
34 2 0.03
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (31 bp):
CTCTATTTGTGTTTACTGTCCTAGCGACTAT
Found at i:751274 original size:9 final size:10
Alignment explanation
Indices: 751191--751313 Score: 53
Period size: 10 Copynumber: 12.8 Consensus size: 10
751181 AGCATATATA
*
751191 ATTAATAATT
1 ATTAAAAATT
* *
751201 AGTAATAATT
1 ATTAAAAATT
*
751211 ATTAAAAATG
1 ATTAAAAATT
751221 A-TAAAAA-T
1 ATTAAAAATT
*
751229 ATTAATAATT
1 ATTAAAAATT
* ** *
751239 -CTAAGTAGT
1 ATTAAAAATT
*
751248 ATAAAAAATT
1 ATTAAAAATT
751258 ATTAAAAATT
1 ATTAAAAATT
*
751268 CTTAAAAA-T
1 ATTAAAAATT
*
751277 A--ATAAATGT
1 ATTAAAAAT-T
*
751286 ATT-TAAATT
1 ATTAAAAATT
*
751295 ATTTAAAAATC
1 A-TTAAAAATT
751306 ATTAAAAA
1 ATTAAAAA
751314 ATATAAATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
7 4 0.05
8 1 0.01
9 21 0.25
10 52 0.63
11 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.37
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:751749 original size:19 final size:19
Alignment explanation
Indices: 751727--751763 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
751717 AAATCAAATG
751727 AAAAAGAAGAAACAAAGAT
1 AAAAAGAAGAAACAAAGAT
*
751746 AAAATGAAGAAACAAAGA
1 AAAAAGAAGAAACAAAGA
751764 AGTTGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAGAAGAAACAAAGAT
Found at i:755944 original size:18 final size:18
Alignment explanation
Indices: 755906--755944 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
755896 CATTCTCATT
*
755906 TTCAACAACAACTTCCTC
1 TTCAACAACAACTTCCGC
* *
755924 TTCAGCAACAACTTTCGC
1 TTCAACAACAACTTCCGC
755942 TTC
1 TTC
755945 TGTAACATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (18 bp):
TTCAACAACAACTTCCGC
Found at i:783217 original size:22 final size:22
Alignment explanation
Indices: 783190--783232 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
783180 GACTAGAATG
783190 ATGTTGTTCATACAAGCCAATA
1 ATGTTGTTCATACAAGCCAATA
* *
783212 ATGTTGTTTATACAAGTCAAT
1 ATGTTGTTCATACAAGCCAAT
783233 GATCTCATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
ATGTTGTTCATACAAGCCAATA
Found at i:786171 original size:12 final size:12
Alignment explanation
Indices: 786156--786182 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
786146 ATTCTCTAAA
786156 AGAGCTTACAAT
1 AGAGCTTACAAT
786168 AGAGCTTACAAT
1 AGAGCTTACAAT
786180 AGA
1 AGA
786183 TGAGAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (12 bp):
AGAGCTTACAAT
Found at i:791259 original size:20 final size:20
Alignment explanation
Indices: 791221--791258 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
791211 CTTCAAAGTA
791221 AAAATGAATGTCAAATTTTG
1 AAAATGAATGTCAAATTTTG
*
791241 AAAATGTATGTC-AATTTT
1 AAAATGAATGTCAAATTTT
791259 TTATTTAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
AAAATGAATGTCAAATTTTG
Found at i:791642 original size:22 final size:22
Alignment explanation
Indices: 791616--791757 Score: 162
Period size: 22 Copynumber: 6.3 Consensus size: 22
791606 TCCAGGTCAA
* *
791616 AAGTATCAATACCTTTTTAGTC
1 AAGTATCGATACCTTTTTGGTC
*
791638 AAGTATCGATACCTTTTTGGTT
1 AAGTATCGATACCTTTTTGGTC
*
791660 AAGTATCGATA--TTTTTGATTTAGC
1 AAGTATCGATACCTTTTTG--GT--C
791684 TAAGTATCGATACCTTTTTGGTC
1 -AAGTATCGATACCTTTTTGGTC
*
791707 AAGTATTGATACCTTTTTGGTC
1 AAGTATCGATACCTTTTTGGTC
* *
791729 ATGTATCGATACCTTTTTGGTT
1 AAGTATCGATACCTTTTTGGTC
791751 AAGTATC
1 AAGTATC
791758 AATATTTTTG
Statistics
Matches: 102, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.06
22 77 0.75
23 1 0.01
25 12 0.12
27 6 0.06
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (22 bp):
AAGTATCGATACCTTTTTGGTC
Found at i:791689 original size:47 final size:43
Alignment explanation
Indices: 791629--791768 Score: 167
Period size: 47 Copynumber: 3.2 Consensus size: 43
791619 TATCAATACC
791629 TTTTT-AGTCAAGTATCGATACCTTTTTGGTTAAGTATCGATA
1 TTTTTGAGTCAAGTATCGATACCTTTTTGGTTAAGTATCGATA
* * *
791671 TTTTTGATTTAGCTAAGTATCGATACCTTTTTGGTCAAGTATTGATA
1 TTTTTGA-GT--C-AAGTATCGATACCTTTTTGGTTAAGTATCGATA
* *
791718 CCTTTTTG-GTCATGTATCGATACCTTTTTGGTTAAGTATCAATA
1 --TTTTTGAGTCAAGTATCGATACCTTTTTGGTTAAGTATCGATA
791762 TTTTTGA
1 TTTTTGA
791769 AATATCAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
42 11 0.13
43 1 0.01
44 30 0.37
45 1 0.01
46 1 0.01
47 32 0.39
49 6 0.07
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (43 bp):
TTTTTGAGTCAAGTATCGATACCTTTTTGGTTAAGTATCGATA
Found at i:809444 original size:11 final size:11
Alignment explanation
Indices: 809428--809455 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
809418 GTCGCCTCTT
809428 CCTTCGTTCTA
1 CCTTCGTTCTA
809439 CCTTCGTTCTA
1 CCTTCGTTCTA
809450 CCTTCG
1 CCTTCG
809456 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:810882 original size:106 final size:106
Alignment explanation
Indices: 810697--810907 Score: 395
Period size: 106 Copynumber: 2.0 Consensus size: 106
810687 AATTGTGCAG
*
810697 ATTTATGCATAGATACCTGCTGGTAATCATCCTTTATCTGAATGAGTTTAATCCAACAAATTTTG
1 ATTTATGCATAGATACCTGCTGGTAATCATCCTTTATCTAAATGAGTTTAATCCAACAAATTTTG
810762 ATAGGTAGAGGGATTACTGATCACATCGGCAATTACAGTTT
66 ATAGGTAGAGGGATTACTGATCACATCGGCAATTACAGTTT
* *
810803 ATTTATGCATAGATACCTGTTGGTAATCATCCTTTATCTAAATGAGTTTAATCCAGCAAATTTTG
1 ATTTATGCATAGATACCTGCTGGTAATCATCCTTTATCTAAATGAGTTTAATCCAACAAATTTTG
810868 ATAGGTAGAGGGATTACTGATCACATCGGCAATTACAGTT
66 ATAGGTAGAGGGATTACTGATCACATCGGCAATTACAGTT
810908 GGAATTACAT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (106 bp):
ATTTATGCATAGATACCTGCTGGTAATCATCCTTTATCTAAATGAGTTTAATCCAACAAATTTTG
ATAGGTAGAGGGATTACTGATCACATCGGCAATTACAGTTT
Found at i:811368 original size:47 final size:47
Alignment explanation
Indices: 811298--811392 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
811288 AAATAAGAGC
* *
811298 ATAAGCATAGAGAAGCTATCATGAACTCAAAACAGCATTACTCTTCA
1 ATAAGCATAGAGAAGCTACCATGAACTAAAAACAGCATTACTCTTCA
811345 ATAAGCATAGAGAAGCTACCATGAACTAAAAACAGCATTACTCTTCA
1 ATAAGCATAGAGAAGCTACCATGAACTAAAAACAGCATTACTCTTCA
811392 A
1 A
811393 CCTTACAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.22
Consensus pattern (47 bp):
ATAAGCATAGAGAAGCTACCATGAACTAAAAACAGCATTACTCTTCA
Found at i:816723 original size:16 final size:16
Alignment explanation
Indices: 816702--816737 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
816692 GATTTGCTAT
*
816702 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
816718 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
816734 TACA
1 TACA
816738 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:821181 original size:18 final size:17
Alignment explanation
Indices: 821153--821187 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
821143 NTTATTAAGA
*
821153 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
821170 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
821188 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:821444 original size:16 final size:16
Alignment explanation
Indices: 821423--821458 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
821413 GATTTGCTAT
821423 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
821439 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
821455 TACA
1 TACA
821459 GCAAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:821960 original size:55 final size:55
Alignment explanation
Indices: 821901--822031 Score: 174
Period size: 55 Copynumber: 2.4 Consensus size: 55
821891 GTGTTCAACA
* * *
821901 CCGTGTAACTCACTGACTTGGGTCACACGGCCACCCACATGC-CTGTGTGACTAGC
1 CCGTGTAACTCACTGACTTGGGTCACACGACCAACCACACGCTC-GTGTGACTAGC
* * *
821956 CCGTGTAACTGACTCACTTGGGTCACACGACTAACCACACGCTCGTGTGACTAGC
1 CCGTGTAACTCACTGACTTGGGTCACACGACCAACCACACGCTCGTGTGACTAGC
* *
822011 CCATATAACTCACTGACTTGG
1 CCGTGTAACTCACTGACTTGG
822032 CTTCATTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 64 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (55 bp):
CCGTGTAACTCACTGACTTGGGTCACACGACCAACCACACGCTCGTGTGACTAGC
Found at i:823324 original size:39 final size:39
Alignment explanation
Indices: 823281--823358 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
823271 ATATCTTGTC
823281 GAGAATTTTCGTAGTATCATATCAACTAATATATCAATT
1 GAGAATTTTCGTAGTATCATATCAACTAATATATCAATT
*
823320 GAGAATTTTCGTAGTATCATATCAACTAATATTTCAATT
1 GAGAATTTTCGTAGTATCATATCAACTAATATATCAATT
823359 AAGCATGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (39 bp):
GAGAATTTTCGTAGTATCATATCAACTAATATATCAATT
Found at i:830151 original size:16 final size:16
Alignment explanation
Indices: 830130--830181 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
830120 GAATTCTCTT
830130 TCATACTCAGCTATGG
1 TCATACTCAGCTATGG
* ** *
830146 TCATAC-GA-CCCTGT
1 TCATACTCAGCTATGG
830160 TCATACTCAGCTATGG
1 TCATACTCAGCTATGG
830176 TCATAC
1 TCATAC
830182 GACCCTGTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (16 bp):
TCATACTCAGCTATGG
Found at i:830165 original size:30 final size:30
Alignment explanation
Indices: 830129--830190 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
830119 CGAATTCTCT
830129 TTCATACTCAGCTATGGTCATACGACCCTG
1 TTCATACTCAGCTATGGTCATACGACCCTG
830159 TTCATACTCAGCTATGGTCATACGACCCTG
1 TTCATACTCAGCTATGGTCATACGACCCTG
830189 TT
1 TT
830191 TCAATTCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (30 bp):
TTCATACTCAGCTATGGTCATACGACCCTG
Found at i:839372 original size:3 final size:3
Alignment explanation
Indices: 839364--839419 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
839354 GTGCGTCTAT
839364 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
839412 TTC TTC TT
1 TTC TTC TT
839420 TATCGTTGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:846911 original size:40 final size:40
Alignment explanation
Indices: 846862--847032 Score: 306
Period size: 40 Copynumber: 4.3 Consensus size: 40
846852 TTAGGACACC
* *
846862 GGCATTAAGCCTGTTAGACATTAAGTCTGAAAATTTCACT
1 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
*
846902 AGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
1 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
846942 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
1 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
846982 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
1 GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
*
847022 GACAATAAGCC
1 GGCAATAAGCC
847033 CACTAGAAAC
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 126 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (40 bp):
GGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACT
Found at i:847052 original size:80 final size:80
Alignment explanation
Indices: 846888--847052 Score: 249
Period size: 80 Copynumber: 2.1 Consensus size: 80
846878 GACATTAAGT
*
846888 CTGAAAATTTCACTAGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACTGGCAATAAGCC
1 CTGAAAATTTCACTAGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACTGACAATAAGCC
** * ** **
846953 TGCTAGACATTAAGT
66 CACTAGAAACAAAAC
*
846968 CTGAAAATTTCACTGGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACTGACAATAAGCC
1 CTGAAAATTTCACTAGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACTGACAATAAGCC
847033 CACTAGAAACAAAAC
66 CACTAGAAACAAAAC
847048 CTGAA
1 CTGAA
847053 TATCACAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (80 bp):
CTGAAAATTTCACTAGCAATAAGCCTGCTAGACATTAAGTCTGAAAATTTCACTGACAATAAGCC
CACTAGAAACAAAAC
Found at i:872057 original size:276 final size:276
Alignment explanation
Indices: 871564--872122 Score: 1082
Period size: 276 Copynumber: 2.0 Consensus size: 276
871554 GTCTCAAGAA
871564 TTGAACCATAATGTCTCGAGACCTTTACCCATAAATGCATGAAACAATCATTTTTGTTCTTAAGG
1 TTGAACCATAATGTCTCGAGACCTTTACCCATAAATGCATGAAACAATCATTTTTGTTCTTAAGG
*
871629 TCTCAAGACATATGTAAAATAACCTAAATTGAACATTTCAAAGCATCCAAATTATAATCATTCCA
66 TCTCAAGACATATGTAAAATAACCTAAATTGAACATTTCAAAGCATACAAATTATAATCATTCCA
871694 TACCTAAATTACGTAACACCTTATTCCAAACCTGATCGCCAAGTCCAGGTACCGGATGCTACACC
131 TACCTAAATTACGTAACACCTTATTCCAAACCTGATCGCCAAGTCCAGGTACCGGATGCTACACC
*
871759 AACCCAAATCCCTTAATGATACTTCTGTGTCTATTTTAATTACATGCTTGAACAACTTAAATTAA
196 AACCCAAATACCTTAATGATACTTCTGTGTCTATTTTAATTACATGCTTGAACAACTTAAATTAA
871824 AAAATCTAACTGTTAT
261 AAAATCTAACTGTTAT
871840 TTGAACCATAATGTCTCGAGACCTTTACCCATAAATGCATGAAACAATCATTTTTGTTCTTAAGG
1 TTGAACCATAATGTCTCGAGACCTTTACCCATAAATGCATGAAACAATCATTTTTGTTCTTAAGG
871905 TCTCAAGACATATGTAAAATAACCTAAATTGAACATTTCAAAGCATACAAATTATAATCATTCCA
66 TCTCAAGACATATGTAAAATAACCTAAATTGAACATTTCAAAGCATACAAATTATAATCATTCCA
*
871970 TACCTAAATTACGTAACACCTTATTCCAAACCTGATCGCCAAGTCCAGGTACCGGATGCTACACT
131 TACCTAAATTACGTAACACCTTATTCCAAACCTGATCGCCAAGTCCAGGTACCGGATGCTACACC
872035 AACCCAAATACCTTAATGATACTTCTGTGTCTATTTTAATTACATGCTTGAACAACTTAAATTAA
196 AACCCAAATACCTTAATGATACTTCTGTGTCTATTTTAATTACATGCTTGAACAACTTAAATTAA
872100 AAAATCTAACTGTTAT
261 AAAATCTAACTGTTAT
*
872116 TTAAACC
1 TTGAACC
872123 TATACAAAAT
Statistics
Matches: 279, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
276 279 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (276 bp):
TTGAACCATAATGTCTCGAGACCTTTACCCATAAATGCATGAAACAATCATTTTTGTTCTTAAGG
TCTCAAGACATATGTAAAATAACCTAAATTGAACATTTCAAAGCATACAAATTATAATCATTCCA
TACCTAAATTACGTAACACCTTATTCCAAACCTGATCGCCAAGTCCAGGTACCGGATGCTACACC
AACCCAAATACCTTAATGATACTTCTGTGTCTATTTTAATTACATGCTTGAACAACTTAAATTAA
AAAATCTAACTGTTAT
Found at i:876788 original size:35 final size:35
Alignment explanation
Indices: 876749--876818 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
876739 ATACGAAAAG
*
876749 AAAGCTTATATTAGTAGATGAATGTAACATGTCCA
1 AAAGCTTATATTAGTAGATGAACGTAACATGTCCA
876784 AAAGCTTATATTAGTAGATGAACGTAACATGTCCA
1 AAAGCTTATATTAGTAGATGAACGTAACATGTCCA
876819 TAGTTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (35 bp):
AAAGCTTATATTAGTAGATGAACGTAACATGTCCA
Found at i:879327 original size:16 final size:16
Alignment explanation
Indices: 879308--879344 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
879298 AATAAATATC
879308 ACCATAAATATCCATA
1 ACCATAAATATCCATA
*
879324 ACCACAAATATCCATA
1 ACCATAAATATCCATA
879340 ACCAT
1 ACCAT
879345 TATTGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.22
Consensus pattern (16 bp):
ACCATAAATATCCATA
Found at i:881421 original size:54 final size:54
Alignment explanation
Indices: 881308--881427 Score: 123
Period size: 54 Copynumber: 2.2 Consensus size: 54
881298 GTATAGTTTG
* ** * *
881308 AAAATAGGGTCACACGGTCATGTCGCAAACTGTGTGCCCGCCCCTGTGCAAATC
1 AAAATAGGGTCAAACGGTCATGTCGCAAACCATGTGCCAGACCCTGTGCAAATC
* * * * ** *
881362 GAAATAGGGTCAAACGGTCATGTCGTAAACCATGTGTCAGACCTTGTGTGATTC
1 AAAATAGGGTCAAACGGTCATGTCGCAAACCATGTGCCAGACCCTGTGCAAATC
*
881416 AAAATAAGGTCA
1 AAAATAGGGTCA
881428 CACAGTCGTG
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (54 bp):
AAAATAGGGTCAAACGGTCATGTCGCAAACCATGTGCCAGACCCTGTGCAAATC
Found at i:882392 original size:45 final size:45
Alignment explanation
Indices: 882321--882522 Score: 239
Period size: 45 Copynumber: 4.5 Consensus size: 45
882311 TGTTCAAGGA
* * * *
882321 TGCCATAGTGTTTTTCAGCTACGGTCTTATTCATTTCCGTCATGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGTCATGT
* *
882366 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGTCCTGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGTCATGT
* * * * *
882411 T-CCATAGTGTCTTTCAATTGTAGTCTTATTCATTT-TTTACATGA
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGT-CATGT
* * *
882455 TGCCATAATTTCTTTCAACTATGGTCTTATTCATTTCTGAT-ATAT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTG-TCATGT
882500 TGCCATAGTGTCTTTCAACTATG
1 TGCCATAGTGTCTTTCAACTATG
882523 TTTTTATTTG
Statistics
Matches: 131, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.02
44 35 0.27
45 92 0.70
46 1 0.01
47 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGTCATGT
Found at i:882474 original size:89 final size:90
Alignment explanation
Indices: 882344--882517 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 90
882334 TTCAGCTACG
* * * *
882344 GTCTTATTCATTTCCGTCATGTTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTG-TCC
1 GTCTTATTCATTTCCGTCATGATGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTGAT-A
*
882408 TGTT-CCATAGTGTCTTTCAATTGTA
65 TATTGCCATAGTGTCTTTCAATTGTA
** *
882433 GTCTTATTCATTT-TTTACATGATGCCATAATTTCTTTCAACTATGGTCTTATTCATTTCTGATA
1 GTCTTATTCATTTCCGT-CATGATGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTGATA
882497 TATTGCCATAGTGTCTTTCAA
65 TATTGCCATAGTGTCTTTCAA
882518 CTATGTTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
88 1 0.01
89 56 0.76
90 17 0.23
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (90 bp):
GTCTTATTCATTTCCGTCATGATGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTGATAT
ATTGCCATAGTGTCTTTCAATTGTA
Found at i:888264 original size:845 final size:845
Alignment explanation
Indices: 886635--888324 Score: 3380
Period size: 845 Copynumber: 2.0 Consensus size: 845
886625 GCAAAAATTT
886635 AGTAGCCATAGACCCCCTTGCCGGCCACACATGTGGAAAGTTTGAACATTTTAAACTTGTTAAAT
1 AGTAGCCATAGACCCCCTTGCCGGCCACACATGTGGAAAGTTTGAACATTTTAAACTTGTTAAAT
886700 TTAGCTTAGGGTGGATCTTTGAAAGCACACAAAGTGAAGGGGTTTGAATGTAATTTCAAGAAAAC
66 TTAGCTTAGGGTGGATCTTTGAAAGCACACAAAGTGAAGGGGTTTGAATGTAATTTCAAGAAAAC
886765 TTTAAGGGCTGATTTGTAAGTCAAATAATCAACTAATTTTAGCTGATTAGGTCAACATGTTGGAC
131 TTTAAGGGCTGATTTGTAAGTCAAATAATCAACTAATTTTAGCTGATTAGGTCAACATGTTGGAC
886830 TGTTCTGGGCAGCCCATTTGCTCGGTTGGATCAGTCTTTCGGTTTAGCACAACTGGGCCTTATTT
196 TGTTCTGGGCAGCCCATTTGCTCGGTTGGATCAGTCTTTCGGTTTAGCACAACTGGGCCTTATTT
886895 CATAATATAATTAATAATAAATTTTTTAACCCAAAATAAATTGGATATAATTAAAATTAACTATA
261 CATAATATAATTAATAATAAATTTTTTAACCCAAAATAAATTGGATATAATTAAAATTAACTATA
886960 TTATGAATTAATATTCATAATTTGGACCGTCTTAGGCCGAAAAATTAATTCGCCTTGATGCTTCA
326 TTATGAATTAATATTCATAATTTGGACCGTCTTAGGCCGAAAAATTAATTCGCCTTGATGCTTCA
887025 AAAATCGTTTCCCAGTTTTGTGCTTCTAGTAGAGTCTGTCGAGCCAATTTTTACCTTTCGTGCGA
391 AAAATCGTTTCCCAGTTTTGTGCTTCTAGTAGAGTCTGTCGAGCCAATTTTTACCTTTCGTGCGA
887090 ATCTATCGAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATTTAA
456 ATCTATCGAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATTTAA
887155 GTATAATTTAATTATTTTATAATTATATTCTATTTTTCAACAAGAATTACTACGAAATTTCATGA
521 GTATAATTTAATTATTTTATAATTATATTCTATTTTTCAACAAGAATTACTACGAAATTTCATGA
887220 ATTTGAGTTAAAAGGGGCATAAAAAGTCAATATTTCGTGTTTCCACACGCTCCCAAAGTTTATTA
586 ATTTGAGTTAAAAGGGGCATAAAAAGTCAATATTTCGTGTTTCCACACGCTCCCAAAGTTTATTA
887285 GCTCACCTTTAGGCCTCCTTCGGCCCTTAAGGTCAATAAAAGACTAAAATTACACACTTTATTGA
651 GCTCACCTTTAGGCCTCCTTCGGCCCTTAAGGTCAATAAAAGACTAAAATTACACACTTTATTGA
887350 ATTTGACTAAACTTGCAAAAATGTAATTAAAACTTAACCAAAATTCTTGTGTTCAAGCTCCTCAA
716 ATTTGACTAAACTTGCAAAAATGTAATTAAAACTTAACCAAAATTCTTGTGTTCAAGCTCCTCAA
887415 GTGAGAAAACTAGTTTAATCTGCTACACCAAATTACGGCAGATCAATAAGCTAATTTTTATTCCA
781 GTGAGAAAACTAGTTTAATCTGCTACACCAAATTACGGCAGATCAATAAGCTAATTTTTATTCCA
887480 AGTAGCCATAGACCCCCTTGCCGGCCACACATGTGGAAAGTTTGAACATTTTAAACTTGTTAAAT
1 AGTAGCCATAGACCCCCTTGCCGGCCACACATGTGGAAAGTTTGAACATTTTAAACTTGTTAAAT
887545 TTAGCTTAGGGTGGATCTTTGAAAGCACACAAAGTGAAGGGGTTTGAATGTAATTTCAAGAAAAC
66 TTAGCTTAGGGTGGATCTTTGAAAGCACACAAAGTGAAGGGGTTTGAATGTAATTTCAAGAAAAC
887610 TTTAAGGGCTGATTTGTAAGTCAAATAATCAACTAATTTTAGCTGATTAGGTCAACATGTTGGAC
131 TTTAAGGGCTGATTTGTAAGTCAAATAATCAACTAATTTTAGCTGATTAGGTCAACATGTTGGAC
887675 TGTTCTGGGCAGCCCATTTGCTCGGTTGGATCAGTCTTTCGGTTTAGCACAACTGGGCCTTATTT
196 TGTTCTGGGCAGCCCATTTGCTCGGTTGGATCAGTCTTTCGGTTTAGCACAACTGGGCCTTATTT
887740 CATAATATAATTAATAATAAATTTTTTAACCCAAAATAAATTGGATATAATTAAAATTAACTATA
261 CATAATATAATTAATAATAAATTTTTTAACCCAAAATAAATTGGATATAATTAAAATTAACTATA
887805 TTATGAATTAATATTCATAATTTGGACCGTCTTAGGCCGAAAAATTAATTCGCCTTGATGCTTCA
326 TTATGAATTAATATTCATAATTTGGACCGTCTTAGGCCGAAAAATTAATTCGCCTTGATGCTTCA
887870 AAAATCGTTTCCCAGTTTTGTGCTTCTAGTAGAGTCTGTCGAGCCAATTTTTACCTTTCGTGCGA
391 AAAATCGTTTCCCAGTTTTGTGCTTCTAGTAGAGTCTGTCGAGCCAATTTTTACCTTTCGTGCGA
887935 ATCTATCGAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATTTAA
456 ATCTATCGAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATTTAA
888000 GTATAATTTAATTATTTTATAATTATATTCTATTTTTCAACAAGAATTACTACGAAATTTCATGA
521 GTATAATTTAATTATTTTATAATTATATTCTATTTTTCAACAAGAATTACTACGAAATTTCATGA
888065 ATTTGAGTTAAAAGGGGCATAAAAAGTCAATATTTCGTGTTTCCACACGCTCCCAAAGTTTATTA
586 ATTTGAGTTAAAAGGGGCATAAAAAGTCAATATTTCGTGTTTCCACACGCTCCCAAAGTTTATTA
888130 GCTCACCTTTAGGCCTCCTTCGGCCCTTAAGGTCAATAAAAGACTAAAATTACACACTTTATTGA
651 GCTCACCTTTAGGCCTCCTTCGGCCCTTAAGGTCAATAAAAGACTAAAATTACACACTTTATTGA
888195 ATTTGACTAAACTTGCAAAAATGTAATTAAAACTTAACCAAAATTCTTGTGTTCAAGCTCCTCAA
716 ATTTGACTAAACTTGCAAAAATGTAATTAAAACTTAACCAAAATTCTTGTGTTCAAGCTCCTCAA
888260 GTGAGAAAACTAGTTTAATCTGCTACACCAAATTACGGCAGATCAATAAGCTAATTTTTATTCCA
781 GTGAGAAAACTAGTTTAATCTGCTACACCAAATTACGGCAGATCAATAAGCTAATTTTTATTCCA
888325 TCCCACCAAA
Statistics
Matches: 845, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
845 845 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (845 bp):
AGTAGCCATAGACCCCCTTGCCGGCCACACATGTGGAAAGTTTGAACATTTTAAACTTGTTAAAT
TTAGCTTAGGGTGGATCTTTGAAAGCACACAAAGTGAAGGGGTTTGAATGTAATTTCAAGAAAAC
TTTAAGGGCTGATTTGTAAGTCAAATAATCAACTAATTTTAGCTGATTAGGTCAACATGTTGGAC
TGTTCTGGGCAGCCCATTTGCTCGGTTGGATCAGTCTTTCGGTTTAGCACAACTGGGCCTTATTT
CATAATATAATTAATAATAAATTTTTTAACCCAAAATAAATTGGATATAATTAAAATTAACTATA
TTATGAATTAATATTCATAATTTGGACCGTCTTAGGCCGAAAAATTAATTCGCCTTGATGCTTCA
AAAATCGTTTCCCAGTTTTGTGCTTCTAGTAGAGTCTGTCGAGCCAATTTTTACCTTTCGTGCGA
ATCTATCGAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTAAATATGTTAATAATTTAA
GTATAATTTAATTATTTTATAATTATATTCTATTTTTCAACAAGAATTACTACGAAATTTCATGA
ATTTGAGTTAAAAGGGGCATAAAAAGTCAATATTTCGTGTTTCCACACGCTCCCAAAGTTTATTA
GCTCACCTTTAGGCCTCCTTCGGCCCTTAAGGTCAATAAAAGACTAAAATTACACACTTTATTGA
ATTTGACTAAACTTGCAAAAATGTAATTAAAACTTAACCAAAATTCTTGTGTTCAAGCTCCTCAA
GTGAGAAAACTAGTTTAATCTGCTACACCAAATTACGGCAGATCAATAAGCTAATTTTTATTCCA
Found at i:889980 original size:74 final size:75
Alignment explanation
Indices: 889859--890007 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
889849 ACCTTTTGAG
889859 CTCTAATTCAAGTAGTTCCGTAGTAAATTTTGTCAAAATTCACACTTTAATTATAAAATAATT-A
1 CTCTAATTCAAGTAGTTCCGTAGTAAATTTTGTCAAAATTCACACTTTAATTATAAAATAATTAA
889923 TTTTCACTTA
66 TTTTCACTTA
889933 CTCTAATTCAAGTAGTTCCGTAGTAAATTTTGTCAAAATTCACACTTTAATTATAAAATAATTAA
1 CTCTAATTCAAGTAGTTCCGTAGTAAATTTTGTCAAAATTCACACTTTAATTATAAAATAATTAA
889998 TTTTCACTTA
66 TTTTCACTTA
890008 AATTATTAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 63 0.85
75 11 0.15
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (75 bp):
CTCTAATTCAAGTAGTTCCGTAGTAAATTTTGTCAAAATTCACACTTTAATTATAAAATAATTAA
TTTTCACTTA
Found at i:899058 original size:16 final size:16
Alignment explanation
Indices: 899037--899069 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
899027 TAACTCAAGA
899037 TAGGGTGATACACTAG
1 TAGGGTGATACACTAG
899053 TAGGGTGATACACTAG
1 TAGGGTGATACACTAG
899069 T
1 T
899070 GAGATGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (16 bp):
TAGGGTGATACACTAG
Found at i:899841 original size:126 final size:126
Alignment explanation
Indices: 899449--900098 Score: 845
Period size: 126 Copynumber: 5.2 Consensus size: 126
899439 AAGGCCAAGT
* * *
899449 AGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTACTGACAGTGCA
1 AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCA
* * ** *
899514 TCCTGCTCGAAGCGTTTTCTACACTATTTTTTCAGAATTGTCTTCTCAAAATTATTTGTTC
66 TCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * *
899575 AGGAACTACTATAGAAAAAAAGCGTCCACTTGGGAGCTTTTTTCAGTAATTTTGCTGACACTGCA
1 AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * **
899640 TCCTGCTTGAAGC-ATTTTTACACTTTTTTTTCAAAACTATCTTCTCAAAATTATTTTTTC
66 TCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * * * * *
899700 AGAAACTACTGTAGAAAAATAGCGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTAATAGTACA
1 AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * *
899765 TCTTTCTTGAAGTGTTTTTTATACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
66 TCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * * *
899826 AGGAACTATTATAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAGTGCA
1 AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCA
* *
899891 TCCTGCTTGAAGCATTTTTTACACTATTTTTTCAGAACCGTCTTCTTAAAATTATTTTTTTC
66 TCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTA-TTTTTTC
* * * *
899953 AGGAACTACTATAGAAAAAAAACATCCACGTGGGGGTCTTTTTT-AGTAATTTTGCTGACATTGT
1 AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGT-TTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
900017 ATCCTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTC
65 ATCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * *
900079 TGAAACTAGTGTAGAAAAAA
1 AGGAACTACTATAGAAAAAA
900099 CACAAAACCT
Statistics
Matches: 452, Mismatches: 69, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
125 106 0.23
126 235 0.52
127 105 0.23
128 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (126 bp):
AGGAACTACTATAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
Found at i:899895 original size:251 final size:252
Alignment explanation
Indices: 899452--900098 Score: 861
Period size: 251 Copynumber: 2.6 Consensus size: 252
899442 GCCAAGTAGG
* * * *
899452 AACTACTGTAGAAAAAGAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTACTGACAGTGCATCC
1 AACTACTGTAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTAATAGT-CATCC
* * ** *
899517 TGCTCGAAGCGTTTTCTACACTATTTTTTCAGAATTGTCTTCTCAAAATTATTTGTTCAGGAACT
65 TGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAACT
* * *
899582 ACTATAGAAAAAAAGCGTCCACTTGGGAGCTTTTTTCAGTAATTTTGCTGACACTGCATCCTGCT
130 ACTATAGAAAAAAAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACACTGCATCCTGCT
* *
899647 TGAAGCA-TTTTTACACTTTTTTTTCAAAACTATCTTCTCAAAATTA-TTTTTTCAGA
195 TGAAGCATTTTTTACACTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTTTCAGA
* * *
899703 AACTACTGTAGAAAAATAGCGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTAATAGTACATCT
1 AACTACTGTAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTAATAGT-CATCC
* * *
899768 TTCTTGAAGTGTTTTTTATACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAACT
65 TGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAACT
* * * *
899833 ATTATAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAGTGCATCCTGCT
130 ACTATAGAAAAAAAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACACTGCATCCTGCT
* * * *
899898 TGAAGCATTTTTTACACTATTTTTTCAGAACCGTCTTCTTAAAATTATTTTTTTCAGG
195 TGAAGCATTTTTTACACTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTTTCAGA
* * * *
899956 AACTACTATAGAAAAAAAACATCCACGTGGGGGTCTTTTTT-AGTAATTTTGCTGACATTGT-AT
1 AACTACTGTAGAAAAAAAGCATCCACGTGGGAGT-TTTTTTCAGTAATTTTGCT-A-ATAGTCAT
* * * * * *
900019 CCTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTGAAA
63 CCTGCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAA
* *
900084 CTAGTGTAGAAAAAA
128 CTACTATAGAAAAAA
900099 CACAAAACCT
Statistics
Matches: 344, Mismatches: 47, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
251 180 0.52
252 34 0.10
253 119 0.35
254 7 0.02
255 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (252 bp):
AACTACTGTAGAAAAAAAGCATCCACGTGGGAGTTTTTTTCAGTAATTTTGCTAATAGTCATCCT
GCTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAACTA
CTATAGAAAAAAAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACACTGCATCCTGCTT
GAAGCATTTTTTACACTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTTTCAGA
Found at i:900246 original size:34 final size:34
Alignment explanation
Indices: 900208--900291 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
900198 AAAATCATTT
900208 TTAAAAAAACTAAACCCTAATTTAAATAATTTTC
1 TTAAAAAAACTAAACCCTAATTTAAATAATTTTC
** * * *
900242 TTAAAAACTCTTAAACTCTAATTTAATTAATTTTT
1 TTAAAAAAAC-TAAACCCTAATTTAAATAATTTTC
900277 TTAAAAAAATCTAAA
1 TTAAAAAAA-CTAAA
900292 TCTTGATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 8 0.20
35 32 0.78
36 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAAAAAAACTAAACCCTAATTTAAATAATTTTC
Found at i:900301 original size:35 final size:34
Alignment explanation
Indices: 900205--900301 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 34
900195 ACAAAAATCA
*
900205 TTTTTAAAAAAA-CTAAACCCTAATTTAAATAATT
1 TTTTTAAAAAAATCTAAA-CTTAATTTAAATAATT
* * *
900239 TTCTT-AAAAACTCTTAAACTCTAATTTAATTAATT
1 TTTTTAAAAAAATC-TAAACT-TAATTTAAATAATT
*
900274 TTTTTAAAAAAATCTAAATCTTGATTTA
1 TTTTTAAAAAAATCTAAA-CTTAATTTA
900302 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
33 5 0.10
34 6 0.12
35 31 0.61
36 9 0.18
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTTTAAAAAAATCTAAACTTAATTTAAATAATT
Found at i:901827 original size:21 final size:24
Alignment explanation
Indices: 901785--901835 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
901775 TCCTCTCTCG
901785 CTTTCGCTCTCTGTTAGATCTTTC
1 CTTTCGCTCTCTGTTAGATCTTTC
*
901809 CTTTC-CTCTCT-TTCG-TCTTTC
1 CTTTCGCTCTCTGTTAGATCTTTC
*
901830 TTTTCG
1 CTTTCG
901836 TTATAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 6 0.25
24 5 0.21
ACGTcount: A:0.04, C:0.31, G:0.10, T:0.55
Consensus pattern (24 bp):
CTTTCGCTCTCTGTTAGATCTTTC
Found at i:906503 original size:2 final size:2
Alignment explanation
Indices: 906496--906521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
906486 TTGTTTCTAA
906496 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
906522 GGTGTGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:906630 original size:2 final size:2
Alignment explanation
Indices: 906623--906654 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
906613 TTGTTTCTAA
906623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
906655 GGTGTGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:906704 original size:133 final size:127
Alignment explanation
Indices: 906467--906730 Score: 465
Period size: 133 Copynumber: 2.0 Consensus size: 127
906457 TTGAGGCCGA
906467 TTTTGAAATTTGATCATAGTTGTTTCTAAATATATATATATATATATATATATATGGTGTGATGG
1 TTTTGAAATTTGATCATAGTTGTTTCTAAATATATATATATATATATATATATATGGTGTGATGG
906532 GTAATTATGGTAATTACTGTATTTTATTGAATATAGTATAATTGGAACACTTCAATTACGTT
66 GTAATTATGGTAATTACTGTATTTTATTGAATATAGTATAATTGGAACACTTCAATTACGTT
*
906594 TTTTTAAATTTGATCATAGTTGTTTCTAAATATATATATATATATATATATATATATATATGGTG
1 TTTTGAAATTTGATCATAGTTGTTTC----TA-A-ATATATATATATATATATATATATATGGTG
906659 TGATGGGTAATTATGGTAATTACTGTATTTTATTGAATATAGTATAATTGGAACACTTCAATTAC
60 TGATGGGTAATTATGGTAATTACTGTATTTTATTGAATATAGTATAATTGGAACACTTCAATTAC
906724 GTT
125 GTT
906727 TTTT
1 TTTT
906731 AATTGTTAGA
Statistics
Matches: 130, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
127 25 0.19
131 2 0.02
132 1 0.01
133 102 0.78
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (127 bp):
TTTTGAAATTTGATCATAGTTGTTTCTAAATATATATATATATATATATATATATGGTGTGATGG
GTAATTATGGTAATTACTGTATTTTATTGAATATAGTATAATTGGAACACTTCAATTACGTT
Found at i:907304 original size:34 final size:35
Alignment explanation
Indices: 907261--907351 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 35
907251 TAGAGTTTTT
* * *
907261 TAAATTAATTAAATTATGTTTTAGGGGTTTTAA-A
1 TAAATTAATTAAATTAGGGTTTAGAGGTTTTAAGA
* *
907295 TAAATTAATTAAAATAGGGTTTAGAGTTTTTAAGA
1 TAAATTAATTAAATTAGGGTTTAGAGGTTTTAAGA
907330 -AAATTAATTAAATTAGGGTTTA
1 TAAATTAATTAAATTAGGGTTTA
907352 TTTTAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
34 49 0.98
35 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (35 bp):
TAAATTAATTAAATTAGGGTTTAGAGGTTTTAAGA
Found at i:907368 original size:30 final size:32
Alignment explanation
Indices: 907287--907368 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 32
907277 TGTTTTAGGG
*
907287 GTTTTAAATAAATTAATTAAAATAGGGTTTAGA
1 GTTTTAAAAAAATTAATTAAAATAGGGTTTA-A
* *
907320 GTTTTTAAGAAAATTAATTAAATTAGGGTTT-A
1 G-TTTTAAAAAAATTAATTAAAATAGGGTTTAA
*
907352 -TTTTAAAAAAAATAATT
1 GTTTTAAAAAAATTAATT
907369 TTTGTGTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 15 0.35
32 1 0.02
33 1 0.02
34 26 0.60
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (32 bp):
GTTTTAAAAAAATTAATTAAAATAGGGTTTAA
Found at i:907614 original size:125 final size:128
Alignment explanation
Indices: 907455--907723 Score: 384
Period size: 126 Copynumber: 2.1 Consensus size: 128
907445 TTTGTTTTTT
* * * *
907455 TTTTTCTATAGTAGTT-TAAGAAAAATTAATTTTGAGAAGATGGTTCTGAAAAGATAATGT-CAA
1 TTTTTCTACAGTAGTTCTAAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATGTAAAA
* * * * * *
907518 AAACGCTTCAAGCAGGATGCATTGTCAGCAAAATTACTAAAAAAAGCTCTCACGTGGATGCTC
66 AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACATGAACGCTC
* * *
907581 TTTTTCTACAGTAGTTCTTA-AAAAA-TAATTTTGATAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCTAAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATGTAAAA
*
907644 AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATGAACGCTC
66 AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACATGAACGCTC
907707 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
907724 CTGCTTGACC
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
125 30 0.24
126 95 0.75
127 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (128 bp):
TTTTTCTACAGTAGTTCTAAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATGTAAAA
AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACATGAACGCTC
Found at i:913874 original size:23 final size:23
Alignment explanation
Indices: 913844--913889 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
913834 TGTTTATATA
913844 TATATATATATATGTTATTTGAT
1 TATATATATATATGTTATTTGAT
913867 TATATATATATATGTTATTTGAT
1 TATATATATATATGTTATTTGAT
913890 GGATATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (23 bp):
TATATATATATATGTTATTTGAT
Found at i:921778 original size:23 final size:23
Alignment explanation
Indices: 921748--921793 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
921738 TGTTTATATA
921748 TATATATATATATGTTATTTGAT
1 TATATATATATATGTTATTTGAT
921771 TATATATATATATGTTATTTGAT
1 TATATATATATATGTTATTTGAT
921794 GGATATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (23 bp):
TATATATATATATGTTATTTGAT
Found at i:928301 original size:43 final size:44
Alignment explanation
Indices: 928253--928340 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
928243 ATAGAGCGTT
928253 AGTTTTTAGTTGTTTTATTTAAATATTTTATAT-ATGATAATAA
1 AGTTTTTAGTTGTTTTATTTAAATATTTTATATAATGATAATAA
928296 AGTTTTTAGTTGTTTTATTTAAATATTTTATATAATGATAATAA
1 AGTTTTTAGTTGTTTTATTTAAATATTTTATATAATGATAATAA
928340 A
1 A
928341 AAAGAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 33 0.75
44 11 0.25
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (44 bp):
AGTTTTTAGTTGTTTTATTTAAATATTTTATATAATGATAATAA
Found at i:929997 original size:227 final size:227
Alignment explanation
Indices: 929600--930049 Score: 792
Period size: 227 Copynumber: 2.0 Consensus size: 227
929590 AAATTGATTG
*
929600 GAATCAGATATTGTCCATATATAACCAGATTATATCTGCTGAGGAAAAATAAATTCGTGTTGGGC
1 GAATCAGATACTGTCCATATATAACCAGATTATATCTGCTGAGGAAAAATAAATTCGTGTTGGGC
* * *
929665 TATCCGCAGGCCCATTTGGGCCCGCCCGGTCCAAACATTTCGCGTCTCCCACGTCGTGCGGGTGT
66 TATCCGCAGGCCCATTTGGGCCCGACCGATCCAAACATTTCACGTCTCCCACGTCGTGCGGGTGT
* *
929730 GCCCCAACCCCGTCGGGGCTGGACTTGCACCCGCCCCCTGCGCGAGGCAAGGTTACAAGCTTAGT
131 GCCCCAACCCCATCGGGGCTGGACCTGCACCCGCCCCCTGCGCGAGGCAAGGTTACAAGCTTAGT
929795 CATTCAATTACCCTTCAAGAGAGTTCACATTA
196 CATTCAATTACCCTTCAAGAGAGTTCACATTA
*
929827 GAATCAGATACTGTCCATATATAAGCAGATTATATCTGCTGAGGAAAAATAAATTCGTGTTGGGC
1 GAATCAGATACTGTCCATATATAACCAGATTATATCTGCTGAGGAAAAATAAATTCGTGTTGGGC
** * *
929892 TATCCGTGGGCCCATTTGGGCCCGACCGATCCTAACATTTCACGTCTCCCAGGTCGTGCGGGTGT
66 TATCCGCAGGCCCATTTGGGCCCGACCGATCCAAACATTTCACGTCTCCCACGTCGTGCGGGTGT
*
929957 GCCCCAACCCCATCGGGGCTGGACCTGCACCCGTCCCCTGCGCGAGGCAAGGTTACAAGCTTAGT
131 GCCCCAACCCCATCGGGGCTGGACCTGCACCCGCCCCCTGCGCGAGGCAAGGTTACAAGCTTAGT
930022 CATTCAATTACCCTTCAAGAGAGTTCAC
196 CATTCAATTACCCTTCAAGAGAGTTCAC
930050 TTATATAAAC
Statistics
Matches: 211, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
227 211 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (227 bp):
GAATCAGATACTGTCCATATATAACCAGATTATATCTGCTGAGGAAAAATAAATTCGTGTTGGGC
TATCCGCAGGCCCATTTGGGCCCGACCGATCCAAACATTTCACGTCTCCCACGTCGTGCGGGTGT
GCCCCAACCCCATCGGGGCTGGACCTGCACCCGCCCCCTGCGCGAGGCAAGGTTACAAGCTTAGT
CATTCAATTACCCTTCAAGAGAGTTCACATTA
Found at i:936341 original size:17 final size:18
Alignment explanation
Indices: 936304--936341 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
936294 ATGTTCATGC
*
936304 TTTCTTAAACTCATGTTT
1 TTTCTTAAACTCATATTT
*
936322 TTTCTTGAACTCA-ATTT
1 TTTCTTAAACTCATATTT
936339 TTT
1 TTT
936342 AAATTCTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTCTTAAACTCATATTT
Found at i:937216 original size:111 final size:108
Alignment explanation
Indices: 937040--937257 Score: 298
Period size: 111 Copynumber: 2.0 Consensus size: 108
937030 AAATGGCCGG
**
937040 TACCAGAGTACGAGAAAAAGTAAAAAAAAAATTTTTTTTGGTGGTGGCCTGGCAATGGCCAGCAC
1 TACCAGAGTACGAGAAAAAGTAAAAAAAAAATAATTTTTGGTGGTGGCCTGGCAATGGCCAGCAC
*
937105 CACCTTTTAAAAAAACAATTTTTTTTACTTTTTTCGTGTCAGATAAGA
66 CACATTTT----AAA-AATTTTTTTTACTTTTTTCGTGTCAGATAAGA
*
937153 TACCAGTA-TACG-GAAAAAGTAAAAAAAAAA-AATTTTTGGTGGTGGCCTGGCAATGGCCGGCA
1 TACCAG-AGTACGAGAAAAAGTAAAAAAAAAATAATTTTTGGTGGTGGCCTGGCAATGGCCAGCA
** *
937215 CCACATTTTAAATTTTTTTTTTACTTTTTTCGTTTCAGATAAG
65 CCACATTTTAAAAATTTTTTTTACTTTTTTCGTGTCAGATAAG
937258 CCACCACAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
106 28 0.29
107 3 0.03
111 37 0.38
112 18 0.19
113 10 0.10
114 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (108 bp):
TACCAGAGTACGAGAAAAAGTAAAAAAAAAATAATTTTTGGTGGTGGCCTGGCAATGGCCAGCAC
CACATTTTAAAAATTTTTTTTACTTTTTTCGTGTCAGATAAGA
Found at i:949063 original size:16 final size:16
Alignment explanation
Indices: 949044--949079 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
949034 TAATTTAGCA
*
949044 ATTTTTTTATTTTAAT
1 ATTTTTTTAATTTAAT
949060 ATTTTTTTAATTTAAT
1 ATTTTTTTAATTTAAT
949076 -TTTT
1 ATTTT
949080 ACATTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTTAATTTAAT
Found at i:954626 original size:5 final size:5
Alignment explanation
Indices: 954616--954669 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
954606 AAATTGTATT
*
954616 TTTTA TTTTA TTTTA TTTT- TGTTTA TTTT- TGTTT- TTTGTT TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA T-TTTA TTT-TA TTTTA
954661 TTTTA TTTT
1 TTTTA TTTT
954670 TATTGGTGCG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
4 4 0.09
5 35 0.81
6 4 0.09
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:954631 original size:35 final size:35
Alignment explanation
Indices: 954588--954673 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
954578 GTTTTTCTGC
954588 TTTA-TTTATTTTTATTTCA-AATTGTATTTTT-TAT
1 TTTATTTTATTTTTATTT-ATAATTGT-TTTTTGTAT
* ** *
954622 TTTATTTTATTTTTGTTTATTTTTGTTTTTTGTTT
1 TTTATTTTATTTTTATTTATAATTGTTTTTTGTAT
954657 TTTATTTTATTTTTATT
1 TTTATTTTATTTTTATT
954674 GGTGCGACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 10 0.23
35 34 0.77
ACGTcount: A:0.16, C:0.01, G:0.05, T:0.78
Consensus pattern (35 bp):
TTTATTTTATTTTTATTTATAATTGTTTTTTGTAT
Found at i:955663 original size:16 final size:17
Alignment explanation
Indices: 955644--955676 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
955634 AAACAAAATC
955644 GAAAAAAAT-GAAAAAA
1 GAAAAAAATAGAAAAAA
*
955660 GAAAATAATAGAAAAAA
1 GAAAAAAATAGAAAAAA
955677 AAGAGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
GAAAAAAATAGAAAAAA
Found at i:964150 original size:19 final size:19
Alignment explanation
Indices: 964128--964184 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
964118 AAGCTCATTT
964128 CTCACTTTTTCAATCATCC
1 CTCACTTTTTCAATCATCC
* * *
964147 CTCA----TCCTATCATCT
1 CTCACTTTTTCAATCATCC
964162 CTCACTTTTTCAATCATCC
1 CTCACTTTTTCAATCATCC
964181 CTCA
1 CTCA
964185 TCTCATAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 12 0.43
19 16 0.57
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCACTTTTTCAATCATCC
Found at i:964170 original size:34 final size:34
Alignment explanation
Indices: 964122--964200 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 34
964112 AAATAAAAGC
*
964122 TCATTTCTCACTTTTTCAATCATCCCTCATC-CTA
1 TCATCTCTCACTTTTTCAATCATCCCTCATCTC-A
964156 TCATCTCTCACTTTTTCAATCATCCCTCATCTCA
1 TCATCTCTCACTTTTTCAATCATCCCTCATCTCA
*
964190 TAATCTCTCAC
1 TCATCTCTCAC
964201 CCATTCATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 41 0.98
35 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.42
Consensus pattern (34 bp):
TCATCTCTCACTTTTTCAATCATCCCTCATCTCA
Found at i:975201 original size:7 final size:7
Alignment explanation
Indices: 975189--975215 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
975179 TAATTAGAAT
975189 TAAATTA
1 TAAATTA
975196 TAAATTA
1 TAAATTA
975203 TAAATTA
1 TAAATTA
975210 TAAATT
1 TAAATT
975216 GTTTGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATTA
Done.