Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold305
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: 679795
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 27416 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:599779 original size:9 final size:9
Alignment explanation
Indices: 599765--599801 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
599755 TATAGTTTGA
599765 TATTCGAAT
1 TATTCGAAT
599774 TATTCGAAT
1 TATTCGAAT
*
599783 TATTCGAGT
1 TATTCGAAT
599792 TATTCGAAT
1 TATTCGAAT
599801 T
1 T
599802 TGAAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:599872 original size:9 final size:9
Alignment explanation
Indices: 599855--599885 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
599845 TTAAGTTGAT
599855 TCGAATAAC
1 TCGAATAAC
*
599864 TCGATTAAC
1 TCGAATAAC
599873 TCGAATAAC
1 TCGAATAAC
599882 TCGA
1 TCGA
599886 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:608243 original size:54 final size:54
Alignment explanation
Indices: 608160--608269 Score: 186
Period size: 54 Copynumber: 2.0 Consensus size: 54
608150 CAGTTAAACT
*
608160 AAAGGAGGTTAGTCCATAGAAACCCAGAATCTTTAATTATATAGAAGCTTTGAG
1 AAAGGAGGTTAGTCCATAAAAACCCAGAATCTTTAATTATATAGAAGCTTTGAG
*
608214 AAAGGAGGTTA-TCCCATAAAAACCTAGAATCTTTAATTATATAGAAGCTTTGAG
1 AAAGGAGGTTAGT-CCATAAAAACCCAGAATCTTTAATTATATAGAAGCTTTGAG
608268 AA
1 AA
608270 TCTTTACTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (54 bp):
AAAGGAGGTTAGTCCATAAAAACCCAGAATCTTTAATTATATAGAAGCTTTGAG
Found at i:610505 original size:25 final size:25
Alignment explanation
Indices: 610447--610516 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
610437 ATTGTCTCTC
* *
610447 AAGAGCTTCCCATTATATGGCTCAC
1 AAGAGCTTCCCATTACATGGCTCAA
* * *
610472 ATGACCTTCCTATTACATGGCTCAA
1 AAGAGCTTCCCATTACATGGCTCAA
610497 AAGAGCTTCCCGATTACATG
1 AAGAGCTTCCC-ATTACATG
610517 CTTGTATGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 28 0.78
26 8 0.22
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (25 bp):
AAGAGCTTCCCATTACATGGCTCAA
Found at i:612498 original size:75 final size:76
Alignment explanation
Indices: 612375--612520 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 76
612365 GCTCTAGGTA
* *
612375 GCAATTACCTTTTAGTACCGCATTTCATCCTCAAACTGATGGTCAGTCAGAACGTGTGATTCAAA
1 GCAATTACATTTTAGTACCGCATTTCATCCTCAAACTGATGGTCAGTCAAAACGTGTGATTCAAA
612440 -TCCTTGATAT
66 TTCCTTGATAT
* * * * * *
612450 GCAATTACATTTTAGTACTGCATTTCATTCTTACACTGATGGTTAGTCAAAATGTGTGATTCAAA
1 GCAATTACATTTTAGTACCGCATTTCATCCTCAAACTGATGGTCAGTCAAAACGTGTGATTCAAA
612515 TTCCTT
66 TTCCTT
612521 TATTCTCATC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
75 57 0.92
76 5 0.08
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (76 bp):
GCAATTACATTTTAGTACCGCATTTCATCCTCAAACTGATGGTCAGTCAAAACGTGTGATTCAAA
TTCCTTGATAT
Found at i:612687 original size:54 final size:54
Alignment explanation
Indices: 612605--612710 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
612595 CAGTTAAACT
*
612605 AAAGGAGGTTAGTCCATAGAAACCCAGAATATTTAATTATATAGAAGCTTTGGG
1 AAAGGAGGTTAGTCCATAAAAACCCAGAATATTTAATTATATAGAAGCTTTGGG
* *
612659 AAAGGAGTTTA-TCCCATAAAAACCCAGAATCTTTAATTATATAGAAGCTTTG
1 AAAGGAGGTTAGT-CCATAAAAACCCAGAATATTTAATTATATAGAAGCTTTG
612711 AGAATCTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 1 0.02
54 47 0.98
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (54 bp):
AAAGGAGGTTAGTCCATAAAAACCCAGAATATTTAATTATATAGAAGCTTTGGG
Found at i:614777 original size:24 final size:24
Alignment explanation
Indices: 614745--614936 Score: 101
Period size: 24 Copynumber: 7.9 Consensus size: 24
614735 GCATCTCGCT
614745 ATTTGGCTCTCATGAGCTTCCC-A
1 ATTTGGCTCTCATGAGCTTCCCGA
* * *
614768 ATTACGGCTCTTATGAGCTT-CCTA
1 ATT-TGGCTCTCATGAGCTTCCCGA
614792 ATTAATGGCTCT-ATGGAGCTTCCCG-
1 ATT--TGGCTCTCAT-GAGCTTCCCGA
*
614817 ATATTGGCTCGCATGAGC-TCCCTGA
1 AT-TTGGCTCTCATGAGCTTCCC-GA
* **
614842 ATTTGGCTCTCTTGAGCTTCTAG-
1 ATTTGGCTCTCATGAGCTTCCCGA
* * *
614865 TTTATGGCTCAT-ATGACCTTTCCGA
1 ATT-TGGCTC-TCATGAGCTTCCCGA
* * * *
614890 TAATTGGCTCTCAAGAGCTTCCTGTT
1 -ATTTGGCTCTCATGAGCTTCCCG-A
* *
614916 ATATGGCTCACATGAGCTTCC
1 ATTTGGCTCTCATGAGCTTCC
614937 AGTTACGTGG
Statistics
Matches: 127, Mismatches: 26, Indels: 30
0.69 0.14 0.16
Matches are distributed among these distances:
23 11 0.09
24 59 0.46
25 53 0.42
26 4 0.03
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (24 bp):
ATTTGGCTCTCATGAGCTTCCCGA
Found at i:614826 original size:49 final size:46
Alignment explanation
Indices: 614745--614861 Score: 112
Period size: 49 Copynumber: 2.4 Consensus size: 46
614735 GCATCTCGCT
** *
614745 ATTTGGCTCTCATGAGCTTCCCAATTACGGCTCTTATGAGCTTCCT-A
1 ATTTGGCTCT-ATGAGCTTCCCAATTA-GGCTCGCATGAGCTCCCTGA
614792 ATTAATGGCTCTATGGAGCTTCCCGATATT-GGCTCGCATGAGCTCCCTGA
1 ATT--TGGCTCTAT-GAGCTTCCC-A-ATTAGGCTCGCATGAGCTCCCTGA
*
614842 ATTTGGCTCTCTTGAGCTTC
1 ATTTGGCTCT-ATGAGCTTC
614862 TAGTTTATGG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
47 3 0.05
48 16 0.27
49 32 0.54
50 5 0.08
51 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (46 bp):
ATTTGGCTCTATGAGCTTCCCAATTAGGCTCGCATGAGCTCCCTGA
Found at i:614896 original size:73 final size:72
Alignment explanation
Indices: 614747--614941 Score: 182
Period size: 73 Copynumber: 2.7 Consensus size: 72
614737 ATCTCGCTAT
* *
614747 TTGGCTCTCATGAGCTTCCC--AATTACGGCTCT-TATGAGCTTCCTAATTAATGGCTCTATGGA
1 TTGGCTCTCATGAGC-TCCCTGAATT-TGGCTCTCT-TGAGCTT-CTAGTTAATGGCTCTATGGA
*
614809 GCTTCCCGATA
62 CCTTCCCGATA
* *
614820 TTGGCTCGCATGAGCTCCCTGAATTTGGCTCTCTTGAGCTTCTAGTTTATGGCTCATAT-GACCT
1 TTGGCTCTCATGAGCTCCCTGAATTTGGCTCTCTTGAGCTTCTAGTTAATGGCTC-TATGGACCT
*
614884 TTCCGATAA
65 TCCCGAT-A
* * * * * * *
614893 TTGGCTCTCAAGAGCTTCCTGTTATATGGCTCACATGAGCTTCCAGTTA
1 TTGGCTCTCATGAGCTCCCTG-AATTTGGCTCTCTTGAGCTTCTAGTTA
614942 CGTGGCTCGA
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
72 26 0.26
73 49 0.49
74 26 0.26
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (72 bp):
TTGGCTCTCATGAGCTCCCTGAATTTGGCTCTCTTGAGCTTCTAGTTAATGGCTCTATGGACCTT
CCCGATA
Found at i:614947 original size:25 final size:25
Alignment explanation
Indices: 614894--614975 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
614884 TTCCGATAAT
* * *
614894 TGGCTCTCAAGAGCTTCCTGTTATA
1 TGGCTCACAAGAGCTTCCAGTTACA
* *
614919 TGGCTCACATGAGCTTCCAGTTACG
1 TGGCTCACAAGAGCTTCCAGTTACA
* *
614944 TGGCTCGA-AAGAGTTTCCCGATTACA
1 TGGCTC-ACAAGAGCTTCCAG-TTACA
614970 T-GCTCA
1 TGGCTCA
614976 TATGGGCATA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.85
26 6 0.13
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (25 bp):
TGGCTCACAAGAGCTTCCAGTTACA
Found at i:621163 original size:27 final size:27
Alignment explanation
Indices: 621133--621186 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
621123 AACATAGATG
621133 TACTTGTATATAATCATGTCAACAAGT
1 TACTTGTATATAATCATGTCAACAAGT
*
621160 TACTTGTTTATAATCATGTCAACAAGT
1 TACTTGTATATAATCATGTCAACAAGT
621187 AAATTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (27 bp):
TACTTGTATATAATCATGTCAACAAGT
Found at i:622377 original size:94 final size:94
Alignment explanation
Indices: 622216--622405 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 94
622206 AAGGTGCTTA
622216 TATGCAAGCAATAGAAATGGCCGCACTTAGCTTGAAACAAAATGGTTTCCTATTCTTCTCAATTT
1 TATGCAAGCAATAGAAATGGCCGCACTTAGCTTGAAACAAAATGGTTTCCTATTCTTCTCAATTT
622281 CAACTAAGCATGGTGGAAAATGATGAATC
66 CAACTAAGCATGGTGGAAAATGATGAATC
*
622310 TATGCAAGCAATGGAAATGGCCGCACTTAGCTTGAAACAAAATGGTTTCCTATTCTTCTCAATTT
1 TATGCAAGCAATAGAAATGGCCGCACTTAGCTTGAAACAAAATGGTTTCCTATTCTTCTCAATTT
622375 CAACTAAGCATGGTGGAAAATGATGAATC
66 CAACTAAGCATGGTGGAAAATGATGAATC
622404 TA
1 TA
622406 CTTGTTTTAT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (94 bp):
TATGCAAGCAATAGAAATGGCCGCACTTAGCTTGAAACAAAATGGTTTCCTATTCTTCTCAATTT
CAACTAAGCATGGTGGAAAATGATGAATC
Found at i:625903 original size:20 final size:18
Alignment explanation
Indices: 625799--625904 Score: 60
Period size: 19 Copynumber: 5.7 Consensus size: 18
625789 TCAATATTAG
625799 ATTAAATTTAATATTAAACCTT
1 ATTAAA-TTAATATTAAA---T
625821 ATTAAATTAATA--AAAT
1 ATTAAATTAATATTAAAT
* **
625837 ATTTACCTACA-ATATAAAT
1 ATTAAATTA-ATAT-TAAAT
*
625856 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTAAAT
625873 ATTAAGA-TAATCACTTAAAT
1 ATTAA-ATTAAT-A-TTAAAT
625893 ATTAAATTAATA
1 ATTAAATTAATA
625905 AAATACTATC
Statistics
Matches: 67, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
16 8 0.12
17 13 0.19
18 4 0.06
19 16 0.24
20 14 0.21
21 6 0.09
22 6 0.09
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTAAAT
Found at i:633535 original size:2 final size:2
Alignment explanation
Indices: 633528--633570 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
633518 CATTACTAAA
* *
633528 AC AC AC AC AC AC AC AC AC AG AC AC AC AC AC AC AC AA AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
633570 A
1 A
633571 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.44, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:636857 original size:20 final size:19
Alignment explanation
Indices: 636821--636870 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
636811 CATACTTAGT
636821 TTAA-TAATT-AATAAACC
1 TTAATTAATTAAATAAACC
636838 TTAATTAATTAAACTAAACC
1 TTAATTAATTAAA-TAAACC
636858 TTAATTAACTTAA
1 TTAATTAA-TTAA
636871 CCTTAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.14
18 5 0.17
19 2 0.07
20 14 0.48
21 4 0.14
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATTAATTAAATAAACC
Found at i:636867 original size:15 final size:16
Alignment explanation
Indices: 636842--636876 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
636832 TAAACCTTAA
636842 TTAATTAAACTAAACC
1 TTAATTAAACTAAACC
*
636858 TTAATT-AACTTAACC
1 TTAATTAAACTAAACC
636873 TTAA
1 TTAA
636877 GTATCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAATTAAACTAAACC
Found at i:638471 original size:26 final size:26
Alignment explanation
Indices: 638442--638492 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
638432 ATCATGGCTC
*
638442 GAGACATTGGTAAATGATATCCTTTT
1 GAGACATTGGTAAATGATATACTTTT
638468 GAGACATTGGTAAATGATATACTTT
1 GAGACATTGGTAAATGATATACTTT
638493 CATTGGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (26 bp):
GAGACATTGGTAAATGATATACTTTT
Found at i:639261 original size:26 final size:26
Alignment explanation
Indices: 639205--639263 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
639195 ATTTTACCAA
*
639205 GGGTAAAATCATCAAAATTTTATTAT
1 GGGTAAAATCATCAAAATTTTATTAG
* ** *
639231 AGGTAAAATTGTCAAAATTTTGTTAG
1 GGGTAAAATCATCAAAATTTTATTAG
639257 GGGTAAA
1 GGGTAAA
639264 TTTGAGATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (26 bp):
GGGTAAAATCATCAAAATTTTATTAG
Found at i:640720 original size:42 final size:42
Alignment explanation
Indices: 640673--640757 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
640663 AGAAGATAGA
* *
640673 GACATAGTTGTGATTTACTAGAATGGCAGTACATTAGGCTAT
1 GACATAGCTGTGATTGACTAGAATGGCAGTACATTAGGCTAT
*
640715 GACATAGCTGTGATTGACTAGAATGGTAGTACATTAGGCTAT
1 GACATAGCTGTGATTGACTAGAATGGCAGTACATTAGGCTAT
640757 G
1 G
640758 TATGCGTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (42 bp):
GACATAGCTGTGATTGACTAGAATGGCAGTACATTAGGCTAT
Found at i:650202 original size:4 final size:4
Alignment explanation
Indices: 650193--650227 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
650183 TACAATTCAA
650193 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
650228 TATCACTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:656844 original size:18 final size:18
Alignment explanation
Indices: 656796--656846 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
656786 AAAATCAATT
656796 AAATTATTAAAAAATAGAA
1 AAATTATT-AAAAATAGAA
*
656815 AAA-TATAGAAAAAT-GATA
1 AAATTAT-TAAAAATAGA-A
656833 AAATTATTAAAAAT
1 AAATTATTAAAAAT
656847 TTTAGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.07
18 19 0.70
19 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AAATTATTAAAAATAGAA
Found at i:656856 original size:46 final size:47
Alignment explanation
Indices: 656796--656891 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 47
656786 AAAATCAATT
656796 AAATTATTAAAAAATAGAAAAATAT-A-GAAAAATGATAAAA-TTATTAA
1 AAATTATTAAAAAATAGAAAAATATAAGGAAAAAT--TAAAATTTA-TAA
* * *
656843 AAATT-TTAGAAAATATAAAGATATAAGGAAAAATTAAAATTTATAA
1 AAATTATTAAAAAATAGAAAAATATAAGGAAAAATTAAAATTTATAA
656889 AAA
1 AAA
656892 CAAATAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
46 27 0.63
47 9 0.21
48 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (47 bp):
AAATTATTAAAAAATAGAAAAATATAAGGAAAAATTAAAATTTATAA
Found at i:657075 original size:29 final size:29
Alignment explanation
Indices: 657002--657076 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
656992 TAGATTTCTT
657002 TTAAAAATATAGAAAA-AATTTAAAGTTTA
1 TTAAAAATATA-AAAATAATTTAAAGTTTA
* *
657031 TTAATAATATAAAAATAA-TTAAATTTTA
1 TTAAAAATATAAAAATAATTTAAAGTTTA
657059 TTATAAAATATAAAAATA
1 TTA-AAAATATAAAAATA
657077 CAAAAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 16 0.39
29 25 0.61
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAAAATATAAAAATAATTTAAAGTTTA
Found at i:657519 original size:11 final size:11
Alignment explanation
Indices: 657477--657542 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 11
657467 TTTTCTAAGC
657477 TTTATAA-AAT
1 TTTATAATAAT
657487 TTTAGTAAT--T
1 TTTA-TAATAAT
* *
657497 TTTTTTAT-AT
1 TTTATAATAAT
657507 TTTATAATAAT
1 TTTATAATAAT
*
657518 TTT-TAATACT
1 TTTATAATAAT
657528 TTTATAATAAGT
1 TTTATAATAA-T
657540 TTT
1 TTT
657543 GATTCTGTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.07
10 24 0.55
11 13 0.30
12 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (11 bp):
TTTATAATAAT
Found at i:657519 original size:31 final size:32
Alignment explanation
Indices: 657407--657520 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 32
657397 GTTTTGATTC
*
657407 TTTTTATGATTTTTATAAT-ATTTTAG-AA-TT
1 TTTTTAT-AGTTTTATAATAATTTTAGTAATTT
* *
657437 TTTCTATA-TTTGT-TTATAGATTTT--TAATTT
1 TTTTTATAGTTT-TATAATA-ATTTTAGTAATTT
*
657467 TTTTCTA-AGCTTTATAA-AATTTTAGTAATTT
1 TTTT-TATAGTTTTATAATAATTTTAGTAATTT
657498 TTTTTATA-TTTTATAATAATTTT
1 TTTTTATAGTTTTATAATAATTTT
657521 TAATACTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
28 6 0.09
29 9 0.14
30 28 0.42
31 23 0.35
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTTTATAGTTTTATAATAATTTTAGTAATTT
Found at i:657530 original size:21 final size:20
Alignment explanation
Indices: 657497--657542 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
657487 TTTAGTAATT
*
657497 TTTTTTATATTTTATAATAA
1 TTTTTAATATTTTATAATAA
657517 TTTTTAATACTTTTATAATAA
1 TTTTTAATA-TTTTATAATAA
657538 GTTTT
1 -TTTT
657543 GATTCTGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 11 0.48
22 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTAATATTTTATAATAA
Found at i:658244 original size:19 final size:17
Alignment explanation
Indices: 658222--658284 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
658212 AAATTACAAA
*
658222 AAAATTTAAAATAGTTTT
1 AAAATTCAAAATA-TTTT
658240 CAAAAATTCAAAATAATTTTT
1 --AAAATTCAAAAT-A-TTTT
658261 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTT-T
658279 AAAATT
1 AAAATT
658285 TTCAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 3 0.08
18 8 0.21
19 12 0.31
20 11 0.28
21 5 0.13
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATTCAAAATATTTT
Found at i:658244 original size:20 final size:19
Alignment explanation
Indices: 658221--658282 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
658211 AAAATTACAA
* *
658221 AAAAATTTAAAATAGTTTT
1 AAAAATTCAAAATAATTTT
658240 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
658260 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
658279 AAAA
1 AAAA
658283 TTTTCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 4 0.11
19 16 0.43
20 17 0.46
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:658281 original size:18 final size:19
Alignment explanation
Indices: 658242--658284 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
658232 ATAGTTTTCA
*
658242 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
658261 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
658279 AAAATT
1 AAAATT
658285 TTCAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:658318 original size:10 final size:10
Alignment explanation
Indices: 658303--658337 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
658293 TTATATTTTA
658303 AAAAAATTCT
1 AAAAAATTCT
658313 AAAAAATTCT
1 AAAAAATTCT
*
658323 AAAAACTTCT
1 AAAAAATTCT
658333 AAAAA
1 AAAAA
658338 TATATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:665657 original size:2 final size:2
Alignment explanation
Indices: 665652--665677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
665642 TCCCCCCCTC
665652 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
665678 GATTTATGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:677104 original size:53 final size:54
Alignment explanation
Indices: 677000--677105 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
676990 TTATGCCTTC
* * *
677000 ATCCTGATTTGTTGAAGTTTTTTCTTTATCAGATTGATAACTAGTAACTTTTAT
1 ATCCTGATCTATTGAAGTTTTTTCTTCATCAGATTGATAACTAGTAACTTTTAT
* *
677054 ATCCTGATCTATTGAAGTTTTTTCTTCATCA-ATTTATAACTAGTAGCTTTTA
1 ATCCTGATCTATTGAAGTTTTTTCTTCATCAGATTGATAACTAGTAACTTTTA
677106 AGTTTTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 19 0.40
54 28 0.60
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (54 bp):
ATCCTGATCTATTGAAGTTTTTTCTTCATCAGATTGATAACTAGTAACTTTTAT
Found at i:678365 original size:27 final size:27
Alignment explanation
Indices: 678335--678410 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
678325 TTAATGGCCA
*
678335 CTTCCATCACTGCTTGTGTCATGGTTG
1 CTTCCATAACTGCTTGTGTCATGGTTG
*
678362 CTTCCATAACTGTTTGTGTCATGGTTG
1 CTTCCATAACTGCTTGTGTCATGGTTG
*
678389 CTTCCATAACTGCTTGCGTCAT
1 CTTCCATAACTGCTTGTGTCAT
678411 CAATGTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (27 bp):
CTTCCATAACTGCTTGTGTCATGGTTG
Done.