Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1378
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: 72211
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2797 original size:378 final size:385
Alignment explanation
Indices: 2046--2797 Score: 977
Period size: 390 Copynumber: 2.0 Consensus size: 385
2036 TAATTAAATT
* * *
2046 TTAATCATTACATAACACTTTAATTAATTTTTCCAACACGGATGCTCGGGGTTACACTTTGCTTT
1 TTAATCATTACAAAACACTTTAATTAATTTTTCCAACACGGATGCTCGAGGTTACACTTTACTTT
* * ** * * * * *
2111 GGTTATTGATGAGATGAGCACTTTGATTTTTCCAAGGCGTGTTTTTGGGTTATACTTTGTTTGTC
66 GCTTATCGATGAGACAAGCACTTTAATTTTTCCAAAGCGTGTCTTTGGGTTATACTTTCTTTGTA
** *
2176 CATGTACTGACTTCTTCGGTAATTGGTTTGGAAAGTCTAGCCCTTCAATGATAAAACTCTTTCCA
131 CATGTACTGACTTCTTCGACAATTGGTTTGGAAAGTCTAACCCTTCAATGATAAAACTCTTTCCA
*
2241 AGAGATGAAGGGAATGCTTAAACAGATTTTCTCCGAACCTTTATTTTTTCATTTATTTATTTTTT
196 AGAGATGAAGGGAATACTT-AACAGATTTTCTCCGAACCTTTA----TT-ATTTATTTATTTTTT
*
2306 CTTTGAACACATTTCATATGTTCCCACTTAAATGAATTTGCAAAAAATTTATTTTTCTTTTTATT
255 CTTTGAACACATTTCATATGTTCCCACTTAAATGAATTTGCAAAAAATTTATTTCTCTTTTTATT
*
2371 ATTTATAATTTCCAAAAGAAAGTAGCATATGCATGAATTGGTTAAAGTTCTTTAGCTAAAGTAGC
320 ATTTATAATTTCCAAAAGAAAGTAGCATAGGCATGAATTGGTTAAAGTTCTTTAGCTAAAGTAGC
2436 C
385 C
* * * * * *
2437 TTAATCATTACAAAACTCTTTAATTAA-TTTTCCAAGACGGGTGTTTGAGGTTATACTTTACTTT
1 TTAATCATTACAAAACACTTTAATTAATTTTTCCAACACGGATGCTCGAGGTTACACTTTACTTT
* *
2501 GCTTATCGATGAGGCAAGCACTTTAATTTTTCCAAAGCGTGTCTTTGGGTTATAGTTTACTTTG-
66 GCTTATCGATGAGACAAGCACTTTAATTTTTCCAAAGCGTGTCTTTGGGTTATACTTT-CTTTGT
* * * * *
2565 ACTTTTATTGACTTTTTCGACAATTGG-TTGG-AAGTGTAACCCTTCAATGATAAAACTCTTTCC
130 ACATGTACTGACTTCTTCGACAATTGGTTTGGAAAGTCTAACCCTTCAATGATAAAACTCTTTCC
* *
2628 AAGGGATGAAGGGAATACTT-A-AGATTTTCTCCTAACCTTTA-T-TTT-TTTATTTTTTCTTTG
195 AAGAGATGAAGGGAATACTTAACAGATTTTCTCCGAACCTTTATTATTTATTTATTTTTTCTTTG
* *
2688 AACACATTTTCATATGTTCCCACTTAAATGAATTTGCAAGAAATTTCTTGTCT-TTTTTATTTAT
260 AACACA-TTTCATATGTTCCCACTTAAATGAATTTGCAAAAAATTTATT-TCTCTTTTTA-TTAT
* * * * *
2752 TTATAATTTCCGAAGGGAAG-AGCATGGGCATGACTTGGTTAAAGTT
322 TTATAATTTCCAAAAGAAAGTAGCATAGGCATGAATTGGTTAAAGTT
2798 GCTAAAGTAG
Statistics
Matches: 317, Mismatches: 40, Indels: 21
0.84 0.11 0.06
Matches are distributed among these distances:
377 21 0.07
378 72 0.23
379 23 0.07
380 1 0.00
385 19 0.06
386 1 0.00
388 48 0.15
389 4 0.01
390 99 0.31
391 29 0.09
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (385 bp):
TTAATCATTACAAAACACTTTAATTAATTTTTCCAACACGGATGCTCGAGGTTACACTTTACTTT
GCTTATCGATGAGACAAGCACTTTAATTTTTCCAAAGCGTGTCTTTGGGTTATACTTTCTTTGTA
CATGTACTGACTTCTTCGACAATTGGTTTGGAAAGTCTAACCCTTCAATGATAAAACTCTTTCCA
AGAGATGAAGGGAATACTTAACAGATTTTCTCCGAACCTTTATTATTTATTTATTTTTTCTTTGA
ACACATTTCATATGTTCCCACTTAAATGAATTTGCAAAAAATTTATTTCTCTTTTTATTATTTAT
AATTTCCAAAAGAAAGTAGCATAGGCATGAATTGGTTAAAGTTCTTTAGCTAAAGTAGCC
Found at i:2952 original size:27 final size:28
Alignment explanation
Indices: 2887--2960 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 28
2877 TACATTGATT
* *
2887 TTTAAGTAA-ATAAAAAATATTTAATTA
1 TTTAAATAATATAAAAAATATTTAATAA
**
2914 TTTATTTAATATAAAAAAT-TTTAA-AA
1 TTTAAATAATATAAAAAATATTTAATAA
*
2940 TTTAAATATATATTAAAAATA
1 TTTAAATA-ATATAAAAAATA
2961 CTAGTATCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 7 0.18
27 22 0.58
28 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTAAATAATATAAAAAATATTTAATAA
Found at i:3464 original size:14 final size:14
Alignment explanation
Indices: 3447--3474 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3437 GGGATTACCA
3447 CCAGTTAATTAAGT
1 CCAGTTAATTAAGT
3461 CCAGTTAATTAAGT
1 CCAGTTAATTAAGT
3475 TTCCATCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
CCAGTTAATTAAGT
Found at i:3656 original size:2 final size:2
Alignment explanation
Indices: 3651--3687 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3641 GCACACACAC
*
3651 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3688 CACGATTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11292 original size:28 final size:28
Alignment explanation
Indices: 11230--11284 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
11220 CAAATGCCAC
11230 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
11258 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
11285 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:12594 original size:22 final size:22
Alignment explanation
Indices: 12552--12596 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12542 TATAAAAATA
**
12552 ATAAAAATATAACGTTATATAT
1 ATAAAAATATAAAATTATATAT
12574 ATAAAAATATCAAAATT-TATAT
1 ATAAAAATAT-AAAATTATATAT
12596 A
1 A
12597 ATAAGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAATATAAAATTATATAT
Found at i:12808 original size:4 final size:4
Alignment explanation
Indices: 12794--12827 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
12784 AAGAAAATCT
12794 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
12828 CCTGCTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:26352 original size:13 final size:14
Alignment explanation
Indices: 26333--26399 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 14
26323 AAAAAAAAAT
26333 TAAAATATAATATA
1 TAAAATATAATATA
26347 -AAAATATACGATATA
1 TAAAATATA--ATATA
*
26362 AAAAATAATAAATATA
1 TAAAAT-AT-AATATA
*
26378 TGAAATAT-ATATA
1 TAAAATATAATATA
26391 TAAAATATA
1 TAAAATATA
26400 TCAAATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 20 0.45
15 7 0.16
16 14 0.32
17 2 0.05
18 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAAATATAATATA
Found at i:26400 original size:15 final size:15
Alignment explanation
Indices: 26333--26400 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
26323 AAAAAAAAAT
26333 TAAAATATA-ATATA
1 TAAAATATATATATA
*
26347 -AAAATATACGATATA
1 TAAAATATA-TATATA
* *
26362 AAAAATA-ATAAATA
1 TAAAATATATATATA
*
26376 TATGAA-ATATATATA
1 TA-AAATATATATATA
26391 TAAAATATAT
1 TAAAATATAT
26401 CAAATTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.19
14 8 0.19
15 20 0.48
16 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (15 bp):
TAAAATATATATATA
Found at i:29690 original size:2 final size:2
Alignment explanation
Indices: 29683--29721 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29673 ATCCTTCCTT
29683 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29722 TTCACATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30187 original size:2 final size:2
Alignment explanation
Indices: 30180--30204 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30170 GGACAAAACA
30180 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
30205 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30209 original size:2 final size:2
Alignment explanation
Indices: 30204--30229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30194 ACACACACAC
30204 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
30230 GATTAAAGTC
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:32136 original size:28 final size:27
Alignment explanation
Indices: 32081--32151 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
32071 GCCACCCATT
32081 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
32108 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
32136 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
32152 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:41883 original size:11 final size:13
Alignment explanation
Indices: 41865--41898 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
41855 TGACACGATA
41865 TAAAAATATAA-T
1 TAAAAATATAATT
41877 T-AAAATATAATT
1 TAAAAATATAATT
41889 TAAAAATATA
1 TAAAAATATA
41899 CGATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 3 0.15
13 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAATATAATT
Found at i:41934 original size:29 final size:29
Alignment explanation
Indices: 41901--41956 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41891 AAAATATACG
41901 ATATAAAAAA-ATAAAAATATGATATGAAT
1 ATATAAAAAATATAAAAAT-TGATATGAAT
* *
41930 ATATAAAAAATATTAAAATTTATATGA
1 ATATAAAAAATATAAAAATTGATATGA
41957 TAAGAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (29 bp):
ATATAAAAAATATAAAAATTGATATGAAT
Found at i:42164 original size:4 final size:4
Alignment explanation
Indices: 42155--42188 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
42145 GAAAATCTTA
*
42155 AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
42189 CCTGCTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:47860 original size:22 final size:22
Alignment explanation
Indices: 47827--47895 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
47817 CAATATAAAA
47827 ATAATAAAAATATAATGTTATAT
1 ATAATAAAAATATAAT-TTATAT
*
47850 ATAA-AAAAATATCAAAATT-TAT
1 ATAATAAAAATAT--AATTTATAT
*
47872 ATAATAAAAAT-T-ATTAATAT
1 ATAATAAAAATATAATTTATAT
47892 ATAA
1 ATAA
47896 AAATCGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
19 2 0.05
20 7 0.18
22 16 0.41
23 12 0.31
24 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (22 bp):
ATAATAAAAATATAATTTATAT
Found at i:49106 original size:34 final size:34
Alignment explanation
Indices: 49068--49252 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
49058 GTAAAAATCA
*
49068 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
49102 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
49136 TCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
49170 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
49204 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
49237 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
49253 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:53712 original size:34 final size:34
Alignment explanation
Indices: 53666--53848 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
53656 GTAAAAACCA
*
53666 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
53700 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
53734 TCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
53768 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
53802 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
53835 CCATTTAATCAACA
1 CCATTTAATCAACA
53849 TATATTAGCT
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:60855 original size:17 final size:17
Alignment explanation
Indices: 60833--60866 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
60823 ATCTTTTGTA
60833 CTAAAAA-ATTGAAAATT
1 CTAAAAATATT-AAAATT
60850 CTAAAAATATTAAAATT
1 CTAAAAATATTAAAATT
60867 AATTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (17 bp):
CTAAAAATATTAAAATT
Found at i:61125 original size:34 final size:34
Alignment explanation
Indices: 61070--61286 Score: 303
Period size: 34 Copynumber: 6.4 Consensus size: 34
61060 CGGTTGGTTC
61070 TGTTGATTAAAT-GGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
* *
61103 TGTTGATTAAATAGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
* * * *
61137 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
* * *
61171 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
61205 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
* * *
61239 TGTTGACTAAATGGGAGATTTGGTAGG-TTGCCAT
1 TGTTGATTAAATGGGTGATTTGGT-GGTTTACCAT
61273 TGTTGATTAAATGG
1 TGTTGATTAAATGG
61287 TGGTTTTTAC
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
33 12 0.07
34 153 0.92
35 2 0.01
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
Found at i:61245 original size:102 final size:102
Alignment explanation
Indices: 61070--61286 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 102
61060 CGGTTGGTTC
* * * *
61070 TGTTGATTAAAT-GGTGATTTGGTGGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTGC
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTAC
61134 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
61171 TGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTAC
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTAC
* *
61236 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
61273 TGTTGATTAAATGG
1 TGTTGATTAAATGG
61287 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 12 0.11
102 96 0.89
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.41
Consensus pattern (102 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:66148 original size:15 final size:13
Alignment explanation
Indices: 66104--66180 Score: 58
Period size: 14 Copynumber: 6.1 Consensus size: 13
66094 TTTCGACATC
66104 ATATAAAAA-AGTA
1 ATATAAAAATA-TA
66117 AT-T-AAAATATA
1 ATATAAAAATATA
66128 ATATAAAAATATA
1 ATATAAAAATATA
66141 CGATATAAAAA-AT-
1 --ATATAAAAATATA
66154 A-ATAAAAATATA
1 ATATAAAAATATA
* *
66166 ACATTAAATATATA
1 ATA-TAAAAATATA
66180 A
1 A
66181 AAATATCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
10 7 0.13
11 11 0.20
12 4 0.07
13 11 0.20
14 12 0.22
15 9 0.17
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:66179 original size:39 final size:39
Alignment explanation
Indices: 66104--66179 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
66094 TTTCGACATC
* *
66104 ATATAAAAAAGTAATTAAAATATAATATAAAAATATACG
1 ATATAAAAAAGTAATAAAAATATAACATAAAAATATACG
*
66143 ATATAAAAAA-TAATAAAAATATAACATTAAATATATA
1 ATATAAAAAAGTAATAAAAATATAACA-TAAAAATATA
66180 AAAATATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 14 0.42
39 19 0.58
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (39 bp):
ATATAAAAAAGTAATAAAAATATAACATAAAAATATACG
Found at i:66180 original size:25 final size:26
Alignment explanation
Indices: 66121--66180 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
66111 AAAGTAATTA
66121 AAATATA-ATATAAAAATATACGATAT
1 AAATATATA-ATAAAAATATACGATAT
*
66147 AAA-AAATAATAAAAATATAAC-AT-T
1 AAATATATAATAAAAATAT-ACGATAT
66171 AAATATATAA
1 AAATATATAA
66181 AAATATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 4 0.14
25 19 0.66
26 6 0.21
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATATATAATAAAAATATACGATAT
Found at i:66199 original size:22 final size:22
Alignment explanation
Indices: 66150--66193 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
66140 ACGATATAAA
*
66150 AAATA-ATAAAAATATAACATT
1 AAATATATAAAAATATAAAATT
66171 AAATATATAAAAATATCAAAATT
1 AAATATATAAAAATAT-AAAATT
66194 TATATAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATATATAAAAATATAAAATT
Found at i:67671 original size:7 final size:8
Alignment explanation
Indices: 67654--67679 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
67644 TTTCCAAACC
67654 TTTATTTT
1 TTTATTTT
67662 TTTATTTT
1 TTTATTTT
67670 TTTATTTT
1 TTTATTTT
67678 TT
1 TT
67680 CTTTGAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:71445 original size:36 final size:37
Alignment explanation
Indices: 71376--71447 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
71366 TTTTCGACAT
* *
71376 GATATAAAAAAGTAATTAAAATAATATAAAAATATAC
1 GATATAAAAAAGTAATAAAAATAATACAAAAATATAC
*
71413 GATATAAAAAA-TAATAAAAAT-ATGACATAAATATA
1 GATATAAAAAAGTAATAAAAATAAT-ACAAAAATATA
71448 AAAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 2 0.06
36 18 0.58
37 11 0.35
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (37 bp):
GATATAAAAAAGTAATAAAAATAATACAAAAATATAC
Done.