Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1837
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: 37503
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:857 original size:26 final size:26
Alignment explanation
Indices: 828--880 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
818 TTTTTGAAAA
828 TAAATTTGTAAAAAGGGGAGAGATAT
1 TAAATTTGTAAAAAGGGGAGAGATAT
* *
854 TAAATTTGTTAAAGGGGGAGAGATAT
1 TAAATTTGTAAAAAGGGGAGAGATAT
880 T
1 T
881 TTGAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (26 bp):
TAAATTTGTAAAAAGGGGAGAGATAT
Found at i:940 original size:14 final size:13
Alignment explanation
Indices: 913--937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
903 AAAAGGGGAG
913 ATTATTTTTGAAC
1 ATTATTTTTGAAC
926 ATTATTTTTGAA
1 ATTATTTTTGAA
938 ACAAAAAGGG
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:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTATTTTTGAAC
Found at i:5848 original size:27 final size:27
Alignment explanation
Indices: 5795--5868 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
5785 CAAAGTTCTA
*
5795 TTTTAATATCTAATTAAAATATAAATT
1 TTTTAATATCTAAATAAAATATAAATT
* *
5822 TTTTAATAT-TAAGATAAAATTTTAATT
1 TTTTAATATCTAA-ATAAAATATAAATT
* *
5849 ATTT-ATAATCTATATAAAAT
1 TTTTAAT-ATCTAAATAAAAT
5869 GTTTAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.13
27 32 0.82
28 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (27 bp):
TTTTAATATCTAAATAAAATATAAATT
Found at i:9023 original size:20 final size:20
Alignment explanation
Indices: 9000--9037 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8990 GAAAACGGTT
*
9000 AATTGTCTTTAAAAATAAAA
1 AATTATCTTTAAAAATAAAA
*
9020 AATTATCTTTAATAATAA
1 AATTATCTTTAAAAATAA
9038 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
AATTATCTTTAAAAATAAAA
Found at i:9139 original size:16 final size:17
Alignment explanation
Indices: 9089--9139 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
9079 TATCTTTTCT
*
9089 AATATTATTAAATTAAA
1 AATATTATTAAATTATA
* * *
9106 AATAATATT-CATTCTA
1 AATATTATTAAATTATA
9122 AATATTATTAAATT-TA
1 AATATTATTAAATTATA
9138 AA
1 AA
9140 ATAAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTATTAAATTATA
Found at i:9749 original size:2 final size:2
Alignment explanation
Indices: 9737--9772 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9727 ATCCAAGACA
*
9737 AT AT AT TT 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 AT AT
9773 GTGCCGACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16659 original size:9 final size:9
Alignment explanation
Indices: 16601--16659 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
16591 TCTCTCTCAT
*
16601 TATCTCTCA
1 TATCTCTCC
16610 TATCTCTCC
1 TATCTCTCC
* *
16619 T-CCTAT-C
1 TATCTCTCC
*
16626 -ATCCCTCC
1 TATCTCTCC
*
16634 TATCTCTAC
1 TATCTCTCC
16643 TATCTCTCC
1 TATCTCTCC
16652 TATCTCTC
1 TATCTCTC
16660 ATCCTATCAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 31 0.82
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:16665 original size:42 final size:42
Alignment explanation
Indices: 16578--16691 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
16568 TCTTTCCTCC
* * * *
16578 TCCTATCATCCCTTCTCTCTC-ATTATCTCTCATATCTCTCC
1 TCCTATCATCCCTCCTATCTCTACTATCTCTCATATCTCTCA
*
16619 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCA
1 TCCTATCATCCCTCCTATCTCTACTATCTCTCATATCTCTCA
* * *
16661 TCCTATCATCCCTCTTATCTCTTCTTTCTCT
1 TCCTATCATCCCTCCTATCTCTACTATCTCT
16692 TTGAGGGCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 19 0.30
42 45 0.70
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (42 bp):
TCCTATCATCCCTCCTATCTCTACTATCTCTCATATCTCTCA
Found at i:19984 original size:18 final size:17
Alignment explanation
Indices: 19961--19994 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19951 AAATGGCATG
*
19961 GAAAAAAGAAAATGAAAT
1 GAAAAAA-AAAAAGAAAT
19979 GAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAGAAA
19995 AATAAAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAAAAGAAAT
Found at i:20007 original size:24 final size:23
Alignment explanation
Indices: 19962--20009 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19952 AATGGCATGG
*
19962 AAAAAAGAAAATGAAATGAAAAA
1 AAAAAAGAAAATGAAAAGAAAAA
*
19985 AAAAAAGAAAAAT-AAAAGCAAAA
1 AAAAAAG-AAAATGAAAAGAAAAA
20008 AA
1 AA
20010 TCAAGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.06
Consensus pattern (23 bp):
AAAAAAGAAAATGAAAAGAAAAA
Found at i:20850 original size:36 final size:36
Alignment explanation
Indices: 20803--20875 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
20793 GTGGGGACTA
20803 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
1 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
20839 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
1 AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
20875 A
1 A
20876 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (36 bp):
AGTTGAAAATATGTAAAAGTTAAAAGGCATAATGGT
Found at i:21371 original size:19 final size:19
Alignment explanation
Indices: 21347--21411 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
21337 TAGCCAAACT
21347 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
21366 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
21379 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
21400 TGTATCGATACA
1 TGTATCGATACA
21412 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:21383 original size:13 final size:13
Alignment explanation
Indices: 21365--21390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21355 TACACAAAAT
21365 ATGTATCGATACA
1 ATGTATCGATACA
21378 ATGTATCGATACA
1 ATGTATCGATACA
21391 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21388 original size:32 final size:33
Alignment explanation
Indices: 21347--21411 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
21337 TAGCCAAACT
21347 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
21379 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
21412 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:23305 original size:22 final size:21
Alignment explanation
Indices: 23269--23330 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
23259 TTTTCTTAGT
23269 TAATTC-TTTATTTTCTTTTGGC
1 TAATTCATTTATTTTCTTTT--C
*
23291 -AATTCATTAATTTTCTTTTC
1 TAATTCATTTATTTTCTTTTC
23311 TAATTCATTTATTTTCTTTT
1 TAATTCATTTATTTTCTTTT
23331 TAAGAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 23 0.64
22 12 0.33
ACGTcount: A:0.19, C:0.13, G:0.03, T:0.65
Consensus pattern (21 bp):
TAATTCATTTATTTTCTTTTC
Found at i:23803 original size:3 final size:3
Alignment explanation
Indices: 23795--23819 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23785 AACCTCTTGC
23795 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
23820 TATTACCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:25908 original size:92 final size:92
Alignment explanation
Indices: 25742--25977 Score: 375
Period size: 92 Copynumber: 2.6 Consensus size: 92
25732 CCACCCATAT
* * * *
25742 ATTCCTAAT-ATATCCCTTTCTTTTAGCCATTACATGGTATTGATGCATCATAAAGCCTGATTTC
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
*
25806 CTTAGGGCAAGGATATCCTGACCACTC
66 CTTAGGGCAAGGATATCCCGACCACTC
*
25833 ATTCCTAATCATATCCCTTTCTTTTGGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
* *
25898 CTTTGGGCAAGGATATCCCGACCACTT
66 CTTAGGGCAAGGATATCCCGACCACTC
* *
25925 ATTCCCAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGTATCACA
1 ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACA
25978 TGACCATAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
91 9 0.07
92 124 0.93
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (92 bp):
ATTCCTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACAAAGCCTAATTTC
CTTAGGGCAAGGATATCCCGACCACTC
Found at i:26453 original size:47 final size:46
Alignment explanation
Indices: 26382--26492 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 46
26372 ATTTTACTTG
* * *
26382 GTCAAAC-CTTTTTCATTATCGTTTGACGTGATGGTTCTTGCCTTA
1 GTCAAACATTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
* * *
26427 TTCAAACATTTTTTTCATTCTTGTTTGACGTTATGGTTCTTGCCCTA
1 GTCAAACA-TTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
26474 GTCAAACATTTTTTCATTC
1 GTCAAACATTTTTTCATTC
26493 CTATTTAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
45 6 0.11
46 11 0.19
47 40 0.70
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.48
Consensus pattern (46 bp):
GTCAAACATTTTTTCATTCTCGTTTGACGTGATGGTTCTTGCCCTA
Found at i:26747 original size:160 final size:162
Alignment explanation
Indices: 26472--26777 Score: 347
Period size: 160 Copynumber: 1.9 Consensus size: 162
26462 GTTCTTGCCC
* * * * * *
26472 TAGTCAAACATTTTTTCATTCCTATTTAACTATACCTAGTCAAACTCTTTTCATTACCATTTGGC
1 TAGTCAAACATCTTTTCATTCCGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACCATTTGAC
** * * * * *
26537 GTGATGGTTCTTATTCTGGTCAAATAACTTTTCATTCTCGTTTGACTATA-CTTGATCAAAC-TC
66 GTGATGGTTCTTACCCTAGTCAAACAACTTTTCATTCTCATTTAACTATACCTAG-TCAAACTTC
26600 TTTCATTACC-GTTTGACGGGATAGTTTTCACCT
130 TTTCATT-CCTGTTTGACGGGATAGTTTTCACCT
*
26633 TAGTCAAACATCTTTTCATTCACGA-TTGACT-GACCAAGTCAAACTCTTTTCAGT-CCTATTTG
1 TAGTCAAACATCTTTTCATTC-CGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACC-ATTTG
* * **
26695 ATGTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTC-CTATTTAACTATACCTAGTCAAACT
64 ACGTGATGGTTCTTACCCTAGTCAAACAACTTTTCATTCTC-ATTTAACTATACCTAGTCAAACT
*
26759 TTTTTCATTCCTGTTTGAC
128 TCTTTCATTCCTGTTTGAC
26778 TGTACCTGGT
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
159 3 0.03
160 72 0.60
161 43 0.36
162 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (162 bp):
TAGTCAAACATCTTTTCATTCCGATTTAACTAGACCAAGTCAAACTCTTTTCAGTACCATTTGAC
GTGATGGTTCTTACCCTAGTCAAACAACTTTTCATTCTCATTTAACTATACCTAGTCAAACTTCT
TTCATTCCTGTTTGACGGGATAGTTTTCACCT
Found at i:26769 original size:35 final size:35
Alignment explanation
Indices: 26711--26802 Score: 123
Period size: 35 Copynumber: 2.6 Consensus size: 35
26701 TGGTTCTTGC
26711 CCTAGTCAAACATTTTTTCATTCCTATTTAACTATA
1 CCTAGTCAAAC-TTTTTTCATTCCTATTTAACTATA
* * *
26747 CCTAGTCAAACTTTTTTCATTCCTGTTTGACTGTA
1 CCTAGTCAAACTTTTTTCATTCCTATTTAACTATA
*
26782 CCTGGTCAAA-TTCTTTTCATT
1 CCTAGTCAAACTT-TTTTCATT
26803 ACCGTTTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.04
35 38 0.75
36 11 0.22
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.46
Consensus pattern (35 bp):
CCTAGTCAAACTTTTTTCATTCCTATTTAACTATA
Found at i:26776 original size:81 final size:81
Alignment explanation
Indices: 26436--26777 Score: 315
Period size: 80 Copynumber: 4.2 Consensus size: 81
26426 ATTCAAACAT
* * *
26436 TTTTTTCATTCTTGTTTGACGTTATGGTTCTTGCCCTAGTCAAACATTTTTTCATTCCTATTTAA
1 TTTTTTCATTCCTGTTTGACGTGATGGTTCTTGCCCTAGTCAAACATCTTTTCATTCCTATTTAA
26501 CTATACCTAGTCAAAC
66 CTATACCTAGTCAAAC
* * * *** * * * *
26517 TCTTTTCATTACC-ATTTGGCGTGATGGTTCTTATTCTGGTCAAATAACTTTTCATT-CTCGTTT
1 TTTTTTCATT-CCTGTTTGACGTGATGGTTCTTGCCCTAGTCAAACATCTTTTCATTCCT-ATTT
* *
26580 GACTATA-CTTGATCAAAC
64 AACTATACCTAG-TCAAAC
* * * *
26598 -TCTTTCATTACC-GTTTGACGGGATAGTT-TT-CACCTTAGTCAAACATCTTTTCATTCACGA-
1 TTTTTTCATT-CCTGTTTGACGTGATGGTTCTTGC-CC-TAGTCAAACATCTTTTCATTC-CTAT
* * *
26658 TTGACT-GACCAAGTCAAAC
62 TTAACTATACCTAGTCAAAC
* * * * *
26677 TCTTTTCAGTCCTATTTGATGTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTCCTATTTAA
1 TTTTTTCATTCCTGTTTGACGTGATGGTTCTTGCCCTAGTCAAACATCTTTTCATTCCTATTTAA
26742 CTATACCTAGTCAAAC
66 CTATACCTAGTCAAAC
26758 TTTTTTCATTCCTGTTTGAC
1 TTTTTTCATTCCTGTTTGAC
26778 TGTACCTGGT
Statistics
Matches: 200, Mismatches: 47, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
79 14 0.07
80 95 0.47
81 88 0.44
82 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (81 bp):
TTTTTTCATTCCTGTTTGACGTGATGGTTCTTGCCCTAGTCAAACATCTTTTCATTCCTATTTAA
CTATACCTAGTCAAAC
Found at i:26797 original size:116 final size:115
Alignment explanation
Indices: 26633--26883 Score: 274
Period size: 116 Copynumber: 2.2 Consensus size: 115
26623 GTTTTCACCT
* * *
26633 TAGTCAAACATCTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGT-CCTATTTGAT
1 TAGTCAAAC-TTTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGTACC-ATTTAAC
* * *
26697 GTGATGGTTCTTGCCCTAGTCAAACATTTTTTCATTC-CTATTTAACTATACC
64 GTGATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTC-ATTTAACTATACC
* ** * * *
26749 TAGTCAAACTTTTTTCATTC-CTGTTTGACTGTACCTGGTCAAATTCTTTTCATTACCGTTTAAC
1 TAGTCAAACTTTTTTCATTCAC-GATTGACTG-ACCAAGTCAAACTCTTTTCAGTACCATTTAAC
* * * *
26813 GTGATGGTTATTGCCTTGGTCAAACATCTGTTCATTCTCGTTTAACTATAGC
64 GTGATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTCATTTAACTATACC
* *
26865 TAATCAAACTTTTGTCATT
1 TAGTCAAACTTTTTTCATT
26884 ACCATTTGAT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
114 1 0.01
115 18 0.16
116 91 0.81
117 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (115 bp):
TAGTCAAACTTTTTTCATTCACGATTGACTGACCAAGTCAAACTCTTTTCAGTACCATTTAACGT
GATGGTTATTGCCCTAGTCAAACATCTGTTCATTCTCATTTAACTATACC
Found at i:29870 original size:16 final size:17
Alignment explanation
Indices: 29849--29881 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29839 GATTTTTGAA
29849 AATTTTATTTA-GTTTT
1 AATTTTATTTATGTTTT
29865 AATTTTATTTATGTTTT
1 AATTTTATTTATGTTTT
29882 TAACTAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
AATTTTATTTATGTTTT
Found at i:30197 original size:10 final size:10
Alignment explanation
Indices: 30182--30228 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
30172 CAGCAAGTGA
30182 AAGAAAAAAG
1 AAGAAAAAAG
30192 AAG-AAAAAG
1 AAGAAAAAAG
30201 AA-AGAAAAAG
1 AAGA-AAAAAG
30211 AGAGAAAAAAG
1 A-AGAAAAAAG
30222 AA-AAAAA
1 AAGAAAAA
30229 CTAAGCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 13 0.39
10 11 0.33
11 8 0.24
12 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:30200 original size:9 final size:9
Alignment explanation
Indices: 30186--30228 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
30176 AAGTGAAAGA
30186 AAAAAGAAG
1 AAAAAGAAG
30195 AAAAAGAAAG
1 AAAAAG-AAG
30205 AAAAAGAGAG
1 AAAAAGA-AG
30215 AAAAAAGAA-
1 -AAAAAGAAG
30224 AAAAA
1 AAAAA
30229 CTAAGCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 7 0.23
10 12 0.39
11 7 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:30205 original size:20 final size:19
Alignment explanation
Indices: 30180--30227 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
30170 TTCAGCAAGT
30180 GAAAGAAAAAAGAAGAAAAA
1 GAAAGAAAAAAG-AGAAAAA
*
30200 GAAAG-AAAAAGAGAGAAA
1 GAAAGAAAAAAGAGAAAAA
30218 -AAAGAAAAAA
1 GAAAGAAAAAA
30228 ACTAAGCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 6 0.23
20 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAGAGAAAAA
Found at i:31760 original size:144 final size:144
Alignment explanation
Indices: 31515--31942 Score: 650
Period size: 144 Copynumber: 3.0 Consensus size: 144
31505 TTTAGCCCTA
* * * * *
31515 TAGGGGTATTGGGTCCTTTT-CTGTCGAAGGTA-CC-TCATAAGGCA-TTTTCGTAATTTTTTAG
1 TAGGGGTACTAGGTACTTTTAC-GTCGAAGGTACCCTTCA-AGGGCATTTTTTGTAA-TTTTTAG
*
31576 GATCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCA
63 AATCGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCA
31641 ACCCTTTTCAAGTCTTT
128 ACCCTTTTCAAGTCTTT
31658 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
1 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
31723 CGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAACC
66 CGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAACC
31788 CTTTTCAAGTCTTT
131 CTTTTCAAGTCTTT
31802 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
1 TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
* * ** ** * * * *
31867 CGAGTCCTAGGTTATGACTCTTACACCAAAGGTGCAGATATAGGATAGATTCACTC-TTTCAACC
66 CGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAACC
31931 CTTTTCAAGTCT
131 CTTTTCAAGTCT
31943 CTTAAGATCA
Statistics
Matches: 265, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
143 47 0.18
144 207 0.78
145 11 0.04
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (144 bp):
TAGGGGTACTAGGTACTTTTACGTCGAAGGTACCCTTCAAGGGCATTTTTTGTAATTTTTAGAAT
CGAGTCCTAGGTTGTCACTCTTATGCCAAAGGTATACACATAGGATAGGTTCAATCTTTTCAACC
CTTTTCAAGTCTTT
Found at i:35375 original size:17 final size:17
Alignment explanation
Indices: 35331--35366 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
35321 ACAATTTTTG
35331 AAAAATAAAATAAAACAT
1 AAAAAT-AAATAAAACAT
35349 AAAAATAAATAAAA-AT
1 AAAAATAAATAAAACAT
35365 AA
1 AA
35367 TAGATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAAACAT
Found at i:35537 original size:13 final size:13
Alignment explanation
Indices: 35518--35551 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35508 GAATTTTTTG
*
35518 AAAAATTAAATTT
1 AAAAATTAAAATT
*
35531 TAAAATTAAAATT
1 AAAAATTAAAATT
35544 AAAAATTA
1 AAAAATTA
35552 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAATTAAAATT
Done.