Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold989.1
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: 623950
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 10082 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:428680 original size:19 final size:19
Alignment explanation
Indices: 428656--428692 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
428646 AAGGGTATTG
428656 AGGGCTAGAAATGAGTAGA
1 AGGGCTAGAAATGAGTAGA
428675 AGGGCTAGAAATGAGTAG
1 AGGGCTAGAAATGAGTAG
428693 GACCTACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.38, T:0.16
Consensus pattern (19 bp):
AGGGCTAGAAATGAGTAGA
Found at i:429469 original size:48 final size:48
Alignment explanation
Indices: 429398--429495 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
429388 TTTTAGGCCG
* *
429398 AACACCCCTACTAATCAACGAGAGCTTCAATTGTCTATAAAATAGGGA
1 AACACCCCTACTAATCAACGAGAGCTGCAATTGTCTATAAAAGAGGGA
429446 AACACCCCTACTAATCAACGAGAGCTGCAATTGTCTATAAAAGAGGGA
1 AACACCCCTACTAATCAACGAGAGCTGCAATTGTCTATAAAAGAGGGA
429494 AA
1 AA
429496 GAACACACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (48 bp):
AACACCCCTACTAATCAACGAGAGCTGCAATTGTCTATAAAAGAGGGA
Found at i:435995 original size:45 final size:46
Alignment explanation
Indices: 435933--436059 Score: 184
Period size: 45 Copynumber: 2.8 Consensus size: 46
435923 GACGGTTGAG
435933 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA
* * *
435979 TATCCAAACT-GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA
** * *
436024 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTTACTTA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
436060 GGGGCGGGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 39 0.55
46 32 0.45
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA
Found at i:443227 original size:46 final size:46
Alignment explanation
Indices: 443174--443299 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
443164 CGGTTGAGCA
*
443174 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
443220 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
443266 CCCGAGCTCGTTGAGTTGAGTCAGAGTTTACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
443300 GGGGCGGGTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:445845 original size:41 final size:44
Alignment explanation
Indices: 445795--445927 Score: 125
Period size: 45 Copynumber: 3.0 Consensus size: 44
445785 ATGCTATCTC
*
445795 ATATTGATGCCACTGTCCTAGACAGGGTCTTACACGAATCA-A-
1 ATATCGATGCCACTGTCCTAGACAGGGTCTTACACGAATCACAT
* * * *
445837 ATA-CGATGCTGA-TGTCCTAGACATGGTCTTACGCGTAACCACAT
1 ATATCGATGC-CACTGTCCTAGACAGGGTCTTACACG-AATCACAT
*
445881 ATATCGATGCCAAC-ATCCTAGAC-GTGGTCTTACACGAGATCACAT
1 ATATCGATGCC-ACTGTCCTAGACAG-GGTCTTACACGA-ATCACAT
445926 AT
1 AT
445928 CAAAAATCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
41 26 0.36
42 8 0.11
43 1 0.01
44 4 0.06
45 33 0.46
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (44 bp):
ATATCGATGCCACTGTCCTAGACAGGGTCTTACACGAATCACAT
Found at i:447071 original size:14 final size:15
Alignment explanation
Indices: 447054--447082 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
447044 GCACGAAAAT
447054 TTCACACAT-ATAAA
1 TTCACACATAATAAA
447068 TTCACACATAATAAA
1 TTCACACATAATAAA
447083 CACAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:454659 original size:26 final size:26
Alignment explanation
Indices: 454630--454679 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
454620 ACCAATATCA
*
454630 GTATCGCAGCAAAGATACTAGTAACG
1 GTATCGCAGCAAAGATACCAGTAACG
*
454656 GTATCGCAGCAAAGCTACCAGTAA
1 GTATCGCAGCAAAGATACCAGTAA
454680 TCAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
GTATCGCAGCAAAGATACCAGTAACG
Found at i:456354 original size:24 final size:24
Alignment explanation
Indices: 456327--456382 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
456317 TCTTAAAATC
*
456327 TCTCCATAATCCTCTCCTTGATTT
1 TCTCCACAATCCTCTCCTTGATTT
* *
456351 TCTCCCCCATCCTCTCCTTGATTT
1 TCTCCACAATCCTCTCCTTGATTT
*
456375 CCTCCACA
1 TCTCCACA
456383 TACTCCCTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (24 bp):
TCTCCACAATCCTCTCCTTGATTT
Found at i:459988 original size:13 final size:13
Alignment explanation
Indices: 459970--459994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459960 TATAAACACC
459970 AAAAATATTTTTA
1 AAAAATATTTTTA
459983 AAAAATATTTTT
1 AAAAATATTTTT
459995 CTAACTTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATATTTTTA
Found at i:461569 original size:27 final size:26
Alignment explanation
Indices: 461534--461645 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
461524 AGCATGGCTG
* *
461534 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
461560 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
461588 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
461615 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
461642 CCAG
1 CCAG
461646 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:461626 original size:54 final size:54
Alignment explanation
Indices: 461534--461645 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
461524 AGCATGGCTG
* *
461534 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
461588 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
461642 CCAG
1 CCAG
461646 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:469296 original size:27 final size:27
Alignment explanation
Indices: 469261--469372 Score: 122
Period size: 27 Copynumber: 4.1 Consensus size: 27
469251 AGCATGGCTG
* *
469261 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
469287 CCACATACAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
469315 CCAGA-ACAGAAATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
469342 CCAGAT-CAGATAATTTTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
469369 CCAG
1 CCAG
469373 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
26 5 0.07
27 52 0.71
28 16 0.22
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:469319 original size:54 final size:54
Alignment explanation
Indices: 469261--469372 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
469251 AGCATGGCTG
* *
469261 CCAGAACAGATA-ATGTGACAGAGTCACCACATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCACAT-CAGATAATCGTGGCAGAGCCA
* * ** *
469315 CCAGAACAGAAATATGTGGCAGAGCCACCAGATCAGATAATTTTGGCATAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCACATCAGATAATCGTGGCAGAGCCA
469369 CCAG
1 CCAG
469373 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAATATGTGACAGAGCCACCACATCAGATAATCGTGGCAGAGCCA
Found at i:469811 original size:16 final size:15
Alignment explanation
Indices: 469790--469819 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
469780 AAAATACCAA
469790 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
469806 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
469820 CCGATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:477552 original size:42 final size:42
Alignment explanation
Indices: 477462--477586 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
477452 ATATCATACA
* * *
477462 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACATG-AATCACACATTG
477505 ATGCC-ACTGTCCCAGATAG-GGTCTTACATGAATCACACATTG
1 ATGCCAAC-GTCCCAGA-AGTGGTCTTACATGAATCACACATTG
*
477547 ATGCCAACGTCCCAGAAGTGGTCTTACATG-ATAACACATT
1 ATGCCAACGTCCCAGAAGTGGTCTTACATGAATCACACATT
477587 TTGGAAATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
41 11 0.15
42 36 0.49
43 26 0.35
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACATGAATCACACATTG
Found at i:477829 original size:79 final size:79
Alignment explanation
Indices: 477725--477878 Score: 290
Period size: 79 Copynumber: 1.9 Consensus size: 79
477715 TACTTATAAA
* *
477725 AATCTCATATAATTAAATCAGCATATAAAGTTCTTATACATTCAAAATTAATAACATTTATTTGC
1 AATCTCATACAATTAAATCAGCATATAAAGTTCTTATACATTCAAAATTAATAACATTCATTTGC
477790 TTATAAACCTACCT
66 TTATAAACCTACCT
477804 AATCTCATACAATTAAATCAGCATATAAAGTTCTTATACATTCAAAATTAATAACATTCATTTGC
1 AATCTCATACAATTAAATCAGCATATAAAGTTCTTATACATTCAAAATTAATAACATTCATTTGC
477869 TTATAAACCT
66 TTATAAACCT
477879 GCCTCAGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (79 bp):
AATCTCATACAATTAAATCAGCATATAAAGTTCTTATACATTCAAAATTAATAACATTCATTTGC
TTATAAACCTACCT
Found at i:478840 original size:13 final size:13
Alignment explanation
Indices: 478824--478848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
478814 TATAAACACA
478824 AAAAATATTTTTT
1 AAAAATATTTTTT
478837 AAAAATATTTTT
1 AAAAATATTTTT
478849 CTAACTCGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:481604 original size:43 final size:43
Alignment explanation
Indices: 481542--481659 Score: 184
Period size: 43 Copynumber: 2.7 Consensus size: 43
481532 ACTGTACTAT
*
481542 TCGGGCCTTCGAGCCTAGCAGGCTATAATGCTGATGAGTTAATA
1 TCGGG-CTTCGAGCCTAGCAGGCTATAATGCCGATGAGTTAATA
*
481586 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGATGAGTTAATA
* *
481629 TTGGGCTTCGAGCCTAGCAGGC-CTAATGCCG
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCG
481660 GTGAATGAGT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 8 0.11
43 57 0.81
44 5 0.07
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (43 bp):
TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGATGAGTTAATA
Found at i:485124 original size:49 final size:49
Alignment explanation
Indices: 484942--485116 Score: 215
Period size: 49 Copynumber: 3.5 Consensus size: 49
484932 TGAGGTAGCG
* * ** * * *
484942 TGTGTAGTACTAAGTGCAGGCTACTATACGTACCCAAAAACTATGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAA-T-TGGTCACA
* *
484993 TGTGTAGTACTAAGTGCAGGGTACTACATGTACTGGATAATTGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACA
* * *
485042 TGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACA
*
485091 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
485117 TGTGTACCAG
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
49 74 0.69
50 1 0.01
51 33 0.31
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACA
Found at i:492532 original size:16 final size:18
Alignment explanation
Indices: 492501--492533 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
492491 AACTCGTCAC
492501 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
492519 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
492534 AATTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:494636 original size:37 final size:37
Alignment explanation
Indices: 494586--494664 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
494576 TTATTACGAA
* * *
494586 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
494623 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
494660 GTCTT
1 GTCTT
494665 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:494861 original size:47 final size:47
Alignment explanation
Indices: 494783--495652 Score: 1668
Period size: 47 Copynumber: 18.5 Consensus size: 47
494773 CCCTTCGGGA
* * * * * *
494783 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
494830 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
494877 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
494924 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
494971 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495018 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495065 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495112 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495159 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495206 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495253 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495300 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495347 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495394 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495441 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495488 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495535 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495582 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
495629 CTTATCACATATATACACTTTCAC
1 CTTATCACATATATACACTTTCAC
495653 GTATACACAC
Statistics
Matches: 813, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 813 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:500086 original size:69 final size:68
Alignment explanation
Indices: 500002--500141 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 68
499992 AATGCCTTGT
500002 ATCCTATTCCGGCGTCGAATATGGGTAAGGGGTGATACAAGTTTACTAAAGAAGAGCGGGGTGTA
1 ATCCTATTCCGGCGTCGAATATGGGTAAGGGGTGATACAAGTTTACTAAAGAAGAGCGGGGTGTA
500067 TAA
66 TAA
*
500070 ATNCCTATTCCGGCGTCGAATATGGGTAAGGGGTGATACAAGTTTACTAAAGAAGAGCGGTGTGT
1 AT-CCTATTCCGGCGTCGAATATGGGTAAGGGGTGATACAAGTTTACTAAAGAAGAGCGGGGTGT
500135 ATAA
65 ATAA
500139 ATC
1 ATC
500142 TGCCAAATCT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 3 0.04
69 67 0.96
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (68 bp):
ATCCTATTCCGGCGTCGAATATGGGTAAGGGGTGATACAAGTTTACTAAAGAAGAGCGGGGTGTA
TAA
Found at i:502635 original size:46 final size:45
Alignment explanation
Indices: 502568--502742 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 45
502558 TGTAACCCGC
502568 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * * *
502614 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * ***
502660 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* *
502707 CCATAAGTGAACTCGGACTTAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
502743 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 23, Indels: 10
0.75 0.17 0.07
Matches are distributed among these distances:
45 1 0.01
46 67 0.66
47 31 0.31
48 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:502688 original size:93 final size:93
Alignment explanation
Indices: 502576--502746 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
502566 GCCCATAAGT
*** *
502576 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
502641 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
502669 GAACTCGGACTCAACTCAACGAGTTCAAACATTCGCATCCATAAGTGAACTCGGACTTAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
502734 CGAGTTCGGATGC
66 CGAGCTCGGATGC
502747 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:514839 original size:27 final size:27
Alignment explanation
Indices: 514809--514986 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
514799 ATATTGAGTC
* * * *
514809 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
514836 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
514863 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
514891 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
514918 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
514945 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
514972 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
514987 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:514948 original size:82 final size:81
Alignment explanation
Indices: 514830--514985 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
514820 TGCTATATAA
* *
514830 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
514895 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
514912 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
514976 CACTTAGTGC
65 CACTTAGTGC
514986 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:516983 original size:13 final size:13
Alignment explanation
Indices: 516965--516989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
516955 TTTCGGGTAG
516965 AAAATGATTATAT
1 AAAATGATTATAT
516978 AAAATGATTATA
1 AAAATGATTATA
516990 GGAATCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAAATGATTATAT
Found at i:517011 original size:28 final size:28
Alignment explanation
Indices: 516971--517036 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
516961 GTAGAAAATG
*
516971 ATTATAT--AAAATGATTATAGGAATCG
1 ATTATATGGAAAATGATTATAGGAATCA
* *
516997 GTTATATGGAAAATGATTATATGAATCA
1 ATTATATGGAAAATGATTATAGGAATCA
517025 ATTATATGGAAA
1 ATTATATGGAAA
517037 TATTTATGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 6 0.18
28 28 0.82
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (28 bp):
ATTATATGGAAAATGATTATAGGAATCA
Found at i:520057 original size:16 final size:17
Alignment explanation
Indices: 520025--520056 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
520015 AAAGTAGATA
520025 AAAATTTATAATTTTTT
1 AAAATTTATAATTTTTT
520042 AAAA-TTAT-ATTTTTT
1 AAAATTTATAATTTTTT
520057 TTATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAAATTTATAATTTTTT
Found at i:526049 original size:13 final size:13
Alignment explanation
Indices: 526028--526085 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
526018 AAATTTTTCC
526028 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
526041 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* *
526054 CAAGTACTTCTCA
1 AAAGCACTTCTCA
*
526067 AAAGCACTTTTCA
1 AAAGCACTTCTCA
526080 AAAGCA
1 AAAGCA
526086 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:535398 original size:40 final size:40
Alignment explanation
Indices: 535339--535596 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
535329 TGGATGATAA
* * * *
535339 CCGGGCTAAGTCCCAAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
535379 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
535419 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
535459 CCGGGGTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
535499 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
535539 CCGGGCTATGTCTCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
535579 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
535597 TACTTGGCTT
Statistics
Matches: 199, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 15 0.08
40 184 0.92
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:544815 original size:45 final size:44
Alignment explanation
Indices: 544764--544892 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 44
544754 GCTGATGGAT
* * *
544764 AGTAAGCTCTAATGAGCTGAAATGGTAAGCT-TTATCGAGTTGAA
1 AGTAAGCTCTAATGAGCTGAAATAGTAAGCTCATA-CGAGCTGAA
*
544808 CAGTAAGCTCTATTGAGCT-AAATAGTAAGCTCATACGAGCTGAA
1 -AGTAAGCTCTAATGAGCTGAAATAGTAAGCTCATACGAGCTGAA
* * *
544852 ATGGTACGCTCTAATGAGCTGAAAACAGTAAGCTCTTACGA
1 A--GTAAGCTCTAATGAGCTG-AAATAGTAAGCTCATACGA
544893 TCTAGTATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.01
44 19 0.27
45 34 0.48
47 17 0.24
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (44 bp):
AGTAAGCTCTAATGAGCTGAAATAGTAAGCTCATACGAGCTGAA
Found at i:544862 original size:23 final size:23
Alignment explanation
Indices: 544762--544892 Score: 106
Period size: 23 Copynumber: 5.7 Consensus size: 23
544752 AAGCTGATGG
*
544762 ATAGTAAGCTCTAATGAGCTGAA
1 ATAGTAAGCTCTAACGAGCTGAA
* * * *
544785 ATGGTAAGCTTTATCGAGTTG-A
1 ATAGTAAGCTCTAACGAGCTGAA
* **
544807 ACAGTAAGCTCTATTGAGCT-AA
1 ATAGTAAGCTCTAACGAGCTGAA
544829 ATAGTAAGCTC-ATACGAGCTGAA
1 ATAGTAAGCTCTA-ACGAGCTGAA
* * *
544852 ATGGTACGCTCTAATGAGCTGAAA
1 ATAGTAAGCTCTAACGAGCTG-AA
* *
544876 ACAGTAAGCTCTTACGA
1 ATAGTAAGCTCTAACGA
544893 TCTAGTATAT
Statistics
Matches: 82, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
21 1 0.01
22 32 0.39
23 34 0.41
24 15 0.18
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (23 bp):
ATAGTAAGCTCTAACGAGCTGAA
Found at i:549007 original size:56 final size:56
Alignment explanation
Indices: 548883--549040 Score: 199
Period size: 56 Copynumber: 2.8 Consensus size: 56
548873 GAGGGGGTGT
* ** *
548883 TAGGATATTATTATGGGATATTATCTTTTTAGCAATTTAATTCCTAATGGGATGTTA
1 TAGGATATTATTATGGGATATTATC-TTTTAGCAATTTGATTCCTAATGAAATATTA
* * * * *
548940 TAGGATGTTATTACGAGATATTATCTCTTAGTAATTTGATTCCTAATGAAATATTA
1 TAGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGAAATATTA
* * *
548996 TATGATATTATTATGGGGTATTATTTTTTAGCAATTTGATTCCTA
1 TAGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTA
549041 CGTAACTACT
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
56 62 0.74
57 22 0.26
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (56 bp):
TAGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGAAATATTA
Found at i:555377 original size:18 final size:19
Alignment explanation
Indices: 555334--555377 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
555324 ATATGTCAGC
*
555334 TTAATAAATATTTTAAAAAT
1 TTAA-AAATATTTCAAAAAT
555354 TATAAAAATA-TTCAAAAAT
1 T-TAAAAATATTTCAAAAAT
555373 TTAAA
1 TTAAA
555378 GTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 9 0.41
20 6 0.27
21 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATATTTCAAAAAT
Found at i:555383 original size:33 final size:34
Alignment explanation
Indices: 555346--555412 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
555336 AATAAATATT
*
555346 TTAAAAATTATA-AAAATATTC-AAAAATTTAAAG
1 TTAAAAAATATATAAAA-ATTCAAAAAATTTAAAG
555379 TTAAAAAATATATAAAAATTCATAAAAATTTAAA
1 TTAAAAAATATATAAAAATTCA-AAAAATTTAAA
555413 AAGAAAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 15 0.50
34 4 0.13
35 11 0.37
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (34 bp):
TTAAAAAATATATAAAAATTCAAAAAATTTAAAG
Found at i:555397 original size:10 final size:9
Alignment explanation
Indices: 555337--555414 Score: 58
Period size: 10 Copynumber: 8.8 Consensus size: 9
555327 TGTCAGCTTA
*
555337 ATAAATATT
1 ATAAAAATT
*
555346 TTAAAAATT
1 ATAAAAATT
555355 ATAAAAA-T
1 ATAAAAATT
555363 ATTCAAAAATT
1 A-T-AAAAATT
*
555374 -T-AAAGTT
1 ATAAAAATT
555381 A-AAAAATAT
1 ATAAAAAT-T
555390 ATAAAAATT
1 ATAAAAATT
555399 CATAAAAATT
1 -ATAAAAATT
555409 -TAAAAA
1 ATAAAAA
555415 GAAAGCATGA
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
7 5 0.09
8 12 0.21
9 18 0.32
10 20 0.36
11 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:560661 original size:10 final size:9
Alignment explanation
Indices: 560643--560696 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
560633 TTTAAAACCA
560643 TTAAAAATT
1 TTAAAAATT
560652 TTAAATAATT
1 TTAAA-AATT
*
560662 TAAAAAATT
1 TTAAAAATT
* *
560671 AT-AAAATA
1 TTAAAAATT
*
560679 TTAAAAATA
1 TTAAAAATT
560688 TTAAAAATT
1 TTAAAAATT
560697 ATATAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 6 0.16
9 23 0.62
10 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAAAATT
Found at i:560664 original size:18 final size:17
Alignment explanation
Indices: 560643--560696 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
560633 TTTAAAACCA
*
560643 TTAAAAATTTTAAATAAT
1 TTAAAAATATTAAA-AAT
560661 TTAAAAA-ATTATAAAAT
1 TTAAAAATATTA-AAAAT
560678 ATTAAAAATATTAAAAAT
1 -TTAAAAATATTAAAAAT
560696 T
1 T
560697 ATATAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.22
18 21 0.66
19 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTAAAAAT
Found at i:560685 original size:19 final size:20
Alignment explanation
Indices: 560645--560695 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
560635 TAAAACCATT
* *
560645 AAAAATT-TTAAATAATTTA
1 AAAAATTATAAAATAATTAA
560664 AAAAATTATAAAAT-ATTAA
1 AAAAATTATAAAATAATTAA
*
560683 AAATATTA-AAAAT
1 AAAAATTATAAAAT
560696 TATATAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAATAATTAA
Found at i:560693 original size:26 final size:27
Alignment explanation
Indices: 560633--560699 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
560623 GGATGTAGTT
* *
560633 TTTAAAACCATTA-AAAATTTTAAATAA
1 TTTAAAA-AATTATAAAATATTAAATAA
560660 TTTAAAAAATTATAAAATATTAAA-AA
1 TTTAAAAAATTATAAAATATTAAATAA
560686 TATT-AAAAATTATA
1 T-TTAAAAAATTATA
560700 TAAAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (27 bp):
TTTAAAAAATTATAAAATATTAAATAA
Found at i:568113 original size:53 final size:54
Alignment explanation
Indices: 567984--568116 Score: 187
Period size: 56 Copynumber: 2.4 Consensus size: 54
567974 TCCCAGACAG
*
567984 GGTCTTAGTCACACACATATATCGGAGTCACATATCAATGCCAACATATTAAACGT
1 GGTCTTACTCACACACATATATCGGAGTCACATATCAAT--CAACATATTAAACGT
* *
568040 GGTCTTACTCACACACATATATCGGAGTCACATATCGAT-AACGTATTAAACGT
1 GGTCTTACTCACACACATATATCGGAGTCACATATCAATCAACATATTAAACGT
** *
568093 GGTCTTACTCGTACATATATATCG
1 GGTCTTACTCACACACATATATCG
568117 ATGCCATGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
53 34 0.48
56 37 0.52
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (54 bp):
GGTCTTACTCACACACATATATCGGAGTCACATATCAATCAACATATTAAACGT
Found at i:570088 original size:34 final size:33
Alignment explanation
Indices: 570029--570126 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 33
570019 GTGTTTGCAT
*
570029 ACTG-TACTGGAATAGGCTGAA-GCCCAGACTGCC
1 ACTGATACTGTAATAGGC--AAGGCCCAGACTGCC
* *
570062 ACTGATACTGTAATGAGGTAAGGCCCAGACTACC
1 ACTGATACTGTAAT-AGGCAAGGCCCAGACTGCC
* *
570096 ATTGATACTGTAATAGGCCAGGCCCAGACTG
1 ACTGATACTGTAATAGGCAAGGCCCAGACTG
570127 TTACTGCTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
33 20 0.36
34 32 0.58
35 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (33 bp):
ACTGATACTGTAATAGGCAAGGCCCAGACTGCC
Found at i:575323 original size:46 final size:45
Alignment explanation
Indices: 575270--575445 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
575260 TGGTTGAGCA
*
575270 TCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
** *** * *
575316 TTTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
575363 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
575409 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
575446 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.62
47 29 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:575426 original size:93 final size:93
Alignment explanation
Indices: 575267--575437 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
575257 GGATGGTTGA
* ***
575267 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAATGTTTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
575332 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * *
575360 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
575425 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
575438 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:577916 original size:52 final size:51
Alignment explanation
Indices: 577838--577944 Score: 189
Period size: 52 Copynumber: 2.1 Consensus size: 51
577828 CATTATACCA
577838 TCTTCCCTTACAGATTCAAATATGAGATTTGGCAGATTTATACACACCGCT
1 TCTTCCCTTACAGATTCAAATATGAGATTTGGCAGATTTATACACACCGCT
*
577889 NTCTTCCCTTACAGATTCAAATATGAGATTTGGCAGATTTATACACATCGC-
1 -TCTTCCCTTACAGATTCAAATATGAGATTTGGCAGATTTATACACACCGCT
577940 TCTTC
1 TCTTC
577945 TTTAGTAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
50 5 0.09
52 49 0.91
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (51 bp):
TCTTCCCTTACAGATTCAAATATGAGATTTGGCAGATTTATACACACCGCT
Found at i:582425 original size:47 final size:47
Alignment explanation
Indices: 582344--582457 Score: 156
Period size: 47 Copynumber: 2.4 Consensus size: 47
582334 GTGTGTATAC
* * * *
582344 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAAT
* * *
582391 GTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGAT
1 GTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAAT
*
582438 GTGAAAGTGTATAAATGTGA
1 GTGAAAGTGTATATATGTGA
582458 TAAGTCCCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAAT
Found at i:582636 original size:37 final size:37
Alignment explanation
Indices: 582580--582658 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
582570 CCGAGCTCTA
* * *
582580 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
582617 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
582654 AAGAC
1 AAGAC
582659 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:583504 original size:51 final size:51
Alignment explanation
Indices: 583440--583584 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 51
583430 GATACTGGTT
* *
583440 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACAAGTGACCATCACTATCCGATA
* * ** * * *
583491 CACTTAGTAGCCTGCATATAGTACTGTACACGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACAAGTGA-CCATCA-CTATCCGATA
*
583542 CGCATAGTAGCCTGCACATAGTACTACACAAGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACAAGTGACCATCACT
583585 TTCACTTTCA
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
50 3 0.04
51 69 0.92
52 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACAAGTGACCATCACTATCCGATA
Found at i:590402 original size:49 final size:49
Alignment explanation
Indices: 590349--590474 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 49
590339 GCTTGACCAT
* *
590349 TGGTAAGGCATGCTAGTTGCTAACCAGGTGGGAGTATATGATAGGCCAC
1 TGGTAAGGCATGTTAGTTGCTAACCAGGTAGGAGTATATGATAGGCCAC
* * * * * *
590398 TGGTAGGGCATATTAGTTGCTAACCAGATAGGCGTGTATGATGGGCCAC
1 TGGTAAGGCATGTTAGTTGCTAACCAGGTAGGAGTATATGATAGGCCAC
* *
590447 TGGTAAGACATGTTAGTTGTTAACCAGG
1 TGGTAAGGCATGTTAGTTGCTAACCAGG
590475 CTGGTGGGCC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (49 bp):
TGGTAAGGCATGTTAGTTGCTAACCAGGTAGGAGTATATGATAGGCCAC
Found at i:599360 original size:2 final size:2
Alignment explanation
Indices: 599353--599391 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
599343 TTGTACTCAT
* *
599353 TC TC TC TC TC TA TC TC TT TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
599392 TGCTAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:607628 original size:14 final size:14
Alignment explanation
Indices: 607611--607658 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
607601 GAACTAAAAT
607611 AAAAATAAATG-ATA
1 AAAAATAAA-GAATA
*
607625 AAAAATTAAGAATA
1 AAAAATAAAGAATA
*
607639 AAAAACAAAGAAATA
1 AAAAATAAAG-AATA
607654 AAAAA
1 AAAAA
607659 ATAAGGACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAATAAAGAATA
Found at i:607642 original size:15 final size:15
Alignment explanation
Indices: 607622--607663 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
607612 AAAATAAATG
*
607622 ATAAAAAATTAAG-A
1 ATAAAAAAATAAGAA
607636 ATAAAAAACA-AAGAA
1 ATAAAAAA-ATAAGAA
607651 ATAAAAAAATAAG
1 ATAAAAAAATAAG
607664 GACAAAGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (15 bp):
ATAAAAAAATAAGAA
Found at i:608719 original size:273 final size:272
Alignment explanation
Indices: 608216--608737 Score: 769
Period size: 273 Copynumber: 1.9 Consensus size: 272
608206 GTCCAGCCTT
* * * * *
608216 CACACAGCCATGTGCAACCTTCTTCGCTTCTCCCATGCTCGTGTGACAGCCTACACGCTCGTGTG
1 CACACAGCCATGTGCAACCTCCTTCACTTCTCCCACGCTCGTGTGACAGCCTACACGCCCATGTG
* * * *
608281 GCACATCCATGCCTCGCACACGACCGTGTGCCTTGCTCGTGTAACTCTTTGATTTGATTTAAAAA
66 GCACATCCATGCCTCGCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTAACTTGATTTAAAAA
*
608346 TGAAAAAATTAGCTCTAGGTTTCACACGGCCTAGGACATGCCCATGTGTCCAGGACGTGTGGACT
131 TGAAAAAATTAGCTCCAGGTTTCACACGGCCTAGGACATGCCCATGTGTCCAGGACGTGTGGACT
* * *
608411 ATTTTAGGTCGTGTAATAGTCAAATTTTGGAAAAATTAAGTCCTCGTATCCACACGACCTCGGAC
196 ATTTTAGGCCGTGTAATAGTCAAATTTTAGAAAAATTAAGTCCTAGTATCCACACGACCTCGGAC
608476 ATGCCCGTGTGC
261 ATGCCCGTGTGC
* * *
608488 CACACGGCCGTGTGCAACCTCCTTCACTTCTTCCACGCTCGTGTGACAGCCTACACGCCCATGTG
1 CACACAGCCATGTGCAACCTCCTTCACTTCTCCCACGCTCGTGTGACAGCCTACACGCCCATGTG
** * ** * *
608553 GCACAGT-TGTGTCTCGCATGCGGCCGTGTTCCTTTGCCCGTGTAACTCTCTAACTTGATTTAAA
66 GCACA-TCCATGCCTCGCACACGACCGTGTGCC-TTGCCCGTGTAACTCTCTAACTTGATTTAAA
* * *
608617 AATGAAAAAATTAGCTCCAGGTTTCACATGGCCTAGGACATGCCCGTGTTTCCAGG-CTGTGTGG
129 AATGAAAAAATTAGCTCCAGGTTTCACACGGCCTAGGACATGCCCATGTGTCCAGGAC-GTGTGG
608681 ACTATTTTAGGCCGTGTAATAGTCAAATTTTAGAAAAATTAAGTCCTAGTATCCACA
193 ACTATTTTAGGCCGTGTAATAGTCAAATTTTAGAAAAATTAAGTCCTAGTATCCACA
608738 TGGCCAAGGA
Statistics
Matches: 221, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
272 81 0.37
273 140 0.63
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (272 bp):
CACACAGCCATGTGCAACCTCCTTCACTTCTCCCACGCTCGTGTGACAGCCTACACGCCCATGTG
GCACATCCATGCCTCGCACACGACCGTGTGCCTTGCCCGTGTAACTCTCTAACTTGATTTAAAAA
TGAAAAAATTAGCTCCAGGTTTCACACGGCCTAGGACATGCCCATGTGTCCAGGACGTGTGGACT
ATTTTAGGCCGTGTAATAGTCAAATTTTAGAAAAATTAAGTCCTAGTATCCACACGACCTCGGAC
ATGCCCGTGTGC
Found at i:611711 original size:14 final size:16
Alignment explanation
Indices: 611679--611711 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
611669 AACTAAAAAC
611679 AAAAATAAAATGCGAT
1 AAAAATAAAATGCGAT
611695 AAAAAT-AAATG-GAT
1 AAAAATAAAATGCGAT
611709 AAA
1 AAA
611712 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATGCGAT
Done.