Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1555
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: 43673
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4935 original size:27 final size:27
Alignment explanation
Indices: 4877--5145 Score: 341
Period size: 27 Copynumber: 10.1 Consensus size: 27
4867 AGGGGTACAA
*
4877 CAGTTATTTTACCCTTCG-GGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
4903 CAGTCATTTTAGCCTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
4930 CGGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * * *
4957 CGGTTATTTTACCATTTTG-GGGTATTT
1 CAGTCATTTTACC-CTTCGAGGGTATTT
4984 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
5011 TAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
5038 TAGTCATTTTACCCTTCGA--GTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
5063 C-GATCATTTTACCCTTCAAGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTT
* *
5090 CAGTCATTTTACCCTTTGGGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * *
5117 TAGTCATTTTAGCCTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
5144 CA
1 CA
5146 CCCTTCGAGA
Statistics
Matches: 213, Mismatches: 23, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
24 1 0.00
25 21 0.10
26 18 0.08
27 169 0.79
28 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:5099 original size:133 final size:133
Alignment explanation
Indices: 4882--5143 Score: 391
Period size: 133 Copynumber: 2.0 Consensus size: 133
4872 TACAACAGTT
* * *
4882 ATTTTACCCTTCGGGGTATTTCAGTCATTTTAGCCTTTGAGGGTATTTCGGTCATTTTACCCTTC
1 ATTTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTCGA-GGTATTTCGATCATTTTACCCTTC
* * * *
4947 GAGGGTATTTCGGTTATTTTACCATTTTGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
65 AAGGGTATTTCAGTCATTTTACCATTTGGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
5012 AGTC
130 AGTC
*
5016 ATTTTACCCTTCGAGGGTATTTTAGTCATTTTACCCTTCGA-GTATTTCGATCATTTTACCCTTC
1 ATTTTACCCTTCG-GGGTATTTCAGTCATTTTACCCTTCGAGGTATTTCGATCATTTTACCCTTC
* * * *
5080 AAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTTAGTCATTTTAGCCTTTGAGGGTATTT
65 AAGGGTATTTCAGTCATTTTACCATTTGGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
5144 CACCCTTCGA
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
133 78 0.68
134 13 0.11
135 24 0.21
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (133 bp):
ATTTTACCCTTCGGGGTATTTCAGTCATTTTACCCTTCGAGGTATTTCGATCATTTTACCCTTCA
AGGGTATTTCAGTCATTTTACCATTTGGGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTA
GTC
Found at i:5197 original size:25 final size:27
Alignment explanation
Indices: 5140--5197 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5130 CTTTGAGGGT
* *
5140 ATTTCACCCTTCGAGAGTATGTTGGTC
1 ATTTTACCCTTCGAGAGTATGTTGATC
*
5167 ATTTTACCCTTCG-GGGTAT-TTGATC
1 ATTTTACCCTTCGAGAGTATGTTGATC
5192 ATTTTA
1 ATTTTA
5198 GGCCCATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.39
26 5 0.18
27 12 0.43
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGAGTATGTTGATC
Found at i:5943 original size:13 final size:13
Alignment explanation
Indices: 5925--5949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5915 GGCTAGCAAA
5925 GAAGAGAAGAGGG
1 GAAGAGAAGAGGG
5938 GAAGAGAAGAGG
1 GAAGAGAAGAGG
5950 AGAATATTTA
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:0.52, T:0.00
Consensus pattern (13 bp):
GAAGAGAAGAGGG
Found at i:6089 original size:12 final size:12
Alignment explanation
Indices: 6072--6096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6062 CGGCAAGCAG
6072 AGAGAAAAGAAA
1 AGAGAAAAGAAA
6084 AGAGAAAAGAAA
1 AGAGAAAAGAAA
6096 A
1 A
6097 TAGCAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAGAAAAGAAA
Found at i:18057 original size:29 final size:29
Alignment explanation
Indices: 18013--18215 Score: 192
Period size: 29 Copynumber: 7.0 Consensus size: 29
18003 GTGCTAAAAA
* * *
18013 ATGGTCGTAACTATCCCTTTTCATACTCG
1 ATGGTCGTCACCATCCCTTTTCATAATCG
***
18042 ATGGTCAAAACCATCCCTTTTCATTAATCG
1 ATGGTCGTCACCATCCCTTTTCA-TAATCG
* * *
18072 ATGGTCGTTACCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAATCG
** *
18101 ATAATCATCACCATCCCTTTTCATAATCG
1 ATGGTCGTCACCATCCCTTTTCATAATCG
* * * * *
18130 ATAGCCG-AAGCTATCCCTTTTCATATTCG
1 ATGGTCGTCA-CCATCCCTTTTCATAATCG
** *
18159 ATGGTCGTCACCATCCCTTTTCATTGTTG
1 ATGGTCGTCACCATCCCTTTTCATAATCG
*
18188 ATGGTCGTCACCATCCCTTTTCAAAATC
1 ATGGTCGTCACCATCCCTTTTCATAATC
18216 AATAGCCGAA
Statistics
Matches: 139, Mismatches: 32, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
28 1 0.01
29 112 0.81
30 26 0.19
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.36
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCATAATCG
Found at i:18188 original size:87 final size:87
Alignment explanation
Indices: 18025--18335 Score: 315
Period size: 87 Copynumber: 3.6 Consensus size: 87
18015 GGTCGTAACT
* * * * * * * *
18025 ATCCCTTTTCATACTCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTTACCATCCCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCA-TATTCGATGGTCGTCACCATCCCT
18090 TTTCATAGTTGATAATCATCACC
65 TTTCATAGTTGATAATCATCACC
18113 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGTCACCATCCCTT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGTCACCATCCCTT
* ** *
18178 TTCATTGTTGATGGTCGTCACC
66 TTCATAGTTGATAATCATCACC
* * * ** **
18200 ATCCCTTTTCAAAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGTC-AAATTTATCCCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGTCA-CCATCCC-
* * **
18264 TTTTTATA-TTCGATAAT--TGAAGTT
64 TTTTCATAGTT-GATAATCAT-CA-CC
* *
18288 ATCCCTTTTCATAATCGATAGCTGAAGCTATCCCTTTTCATGTTCGAT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTCGAT
18336 AATCATCGAT
Statistics
Matches: 188, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
86 2 0.01
87 98 0.52
88 88 0.47
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (87 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGTCACCATCCCTT
TTCATAGTTGATAATCATCACC
Found at i:18204 original size:58 final size:58
Alignment explanation
Indices: 18013--18210 Score: 220
Period size: 58 Copynumber: 3.4 Consensus size: 58
18003 GTGCTAAAAA
* * **
18013 ATGGTCGTAACTATCCCTTTTCATACTCGATGGTCAAAACCATCCCTTTTCATTAATCG
1 ATGGTCGTAACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATT-ATCG
* ** *
18072 ATGGTCGTTACCATCCCTTTTCATAGTT-GATAATCATCACCATCCCTTTTCATAATCG
1 ATGGTCGTAACCATCCCTTTTCATA-TTCGATGGTCATCACCATCCCTTTTCATTATCG
* * * * * *
18130 ATAGCCG-AAGCTATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATTGTTG
1 ATGGTCGTAA-CCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATTATCG
*
18188 ATGGTCGTCACCATCCCTTTTCA
1 ATGGTCGTAACCATCCCTTTTCA
18211 AAATCAATAG
Statistics
Matches: 113, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
57 3 0.03
58 64 0.57
59 45 0.40
60 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (58 bp):
ATGGTCGTAACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATTATCG
Found at i:18334 original size:29 final size:29
Alignment explanation
Indices: 18113--18336 Score: 145
Period size: 29 Copynumber: 7.7 Consensus size: 29
18103 AATCATCACC
* *
18113 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATATTCGATAGCTGAAGCT
* * *
18142 ATCCCTTTTCATATTCGAT-GGTCGTCA-CC
1 ATCCCTTTTCATATTCGATAGCT-G-AAGCT
* * * *
18171 ATCCCTTTTCAT-TGTTGAT-GGTCGTCA-CC
1 ATCCCTTTTCATAT-TCGATAGCT-G-AAGCT
* * * *
18200 ATCCCTTTTCAAAATCAATAGCCGAAGCT
1 ATCCCTTTTCATATTCGATAGCTGAAGCT
* **
18229 ATCCCTTTTCATATTCGATAG-TCAAATTT
1 ATCCCTTTTCATATTCGATAGCT-GAAGCT
* ** *
18258 ATCCCTTTTTTATATTCGATAATTGAAGTT
1 ATCCC-TTTTCATATTCGATAGCTGAAGCT
*
18288 ATCCCTTTTCATAATCGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCTGAAGCT
*
18317 ATCCCTTTTCATGTTCGATA
1 ATCCCTTTTCATATTCGATA
18337 ATCATCGATA
Statistics
Matches: 154, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 3 0.02
29 125 0.81
30 25 0.16
31 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCTGAAGCT
Found at i:18542 original size:38 final size:37
Alignment explanation
Indices: 18499--18573 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 37
18489 AAATTGTAGA
18499 AATGACAAAGTATAGGGGCATTTTAGTAAATTTTCATT
1 AATGACAAAGTATAGGGGCATTTTAGT-AATTTTCATT
* *
18537 AATGACAAAGTATAGGGGCATTTTGGTAGTTTTCATT
1 AATGACAAAGTATAGGGGCATTTTAGTAATTTTCATT
18574 CTCCTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.37
Consensus pattern (37 bp):
AATGACAAAGTATAGGGGCATTTTAGTAATTTTCATT
Found at i:19876 original size:23 final size:23
Alignment explanation
Indices: 19824--19905 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
19814 ATTATGTTGT
* *
19824 ATATTTGG-TGTG-TTGGAGGCT
1 ATATTTGGTTGTGTTTAGAGGCA
*
19845 ATATCTGGTTGTGTTTAGATGG-A
1 ATATTTGGTTGTGTTTAGA-GGCA
* * * *
19868 ATATTTGGTTGTATCTGGAGGCT
1 ATATTTGGTTGTGTTTAGAGGCA
19891 ATATTTGGTTGTGTT
1 ATATTTGGTTGTGTT
19906 GGAGGGTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
21 7 0.15
22 6 0.13
23 32 0.68
24 2 0.04
ACGTcount: A:0.17, C:0.05, G:0.32, T:0.46
Consensus pattern (23 bp):
ATATTTGGTTGTGTTTAGAGGCA
Found at i:25257 original size:20 final size:20
Alignment explanation
Indices: 25229--25267 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25219 CAATTTAAAA
25229 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
25249 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
25268 AGGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:25329 original size:32 final size:32
Alignment explanation
Indices: 25289--25374 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
25279 ACTTTTTCGA
*
25289 AAAATATTTTCAGGAAATC-TGCCAAACAAC-AG
1 AAAATATTTTCAGCAAATCAT-CCAAAC-ACTAG
*
25321 AAAATATTTTACA-CAGATTCATCCAAACACTAG
1 AAAATATTTT-CAGCA-AATCATCCAAACACTAG
*
25354 AAAATATTTTCAGTAAATCAT
1 AAAATATTTTCAGCAAATCAT
25375 TTTCCAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
32 20 0.44
33 24 0.53
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACACTAG
Found at i:25378 original size:14 final size:13
Alignment explanation
Indices: 25355--25397 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
25345 AAACACTAGA
25355 AAAT-ATTTTCAG
1 AAATCATTTTCAG
25367 TAAATCATTTTCCAG
1 -AAATCATTTT-CAG
*
25382 AAATCATTTTCCG
1 AAATCATTTTCAG
25395 AAA
1 AAA
25398 AACATTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 9 0.33
14 15 0.56
15 3 0.11
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATCATTTTCAG
Found at i:30313 original size:186 final size:186
Alignment explanation
Indices: 29997--30371 Score: 669
Period size: 186 Copynumber: 2.0 Consensus size: 186
29987 TGATAACACT
*
29997 GTAGATAGTGTATACTGAAAATAGTAGAGAAACTAAAAACTGTAGTAAGACTGCGATTCGTGATA
1 GTAGATAGTGTATACTAAAAATAGTAGAGAAACTAAAAACTGTAGTAAGACTGCGATTCGTGATA
*
30062 ACAAACTCTAAACATCTGATACTGTTTTGCATAAAATATCTACTAATAGATATCGAAACTGTAAC
66 ACAAACTCTAAACATCTGATACTGTTTTGCATAAAATATCTACTAATAGATATCCAAACTGTAAC
*
30127 TAATTCATAAAACTGATAACACAGATAAGCTACGAATTCTACAATGAGTGCACGAG
131 TAATTCATAAAACTGATAACACAAATAAGCTACGAATTCTACAATGAGTGCACGAG
30183 GTAGATAGTGTATACTAAAAATAGTAGAGAAACTAAAAACTGTAGTAAGACTGCGATTCGTGATA
1 GTAGATAGTGTATACTAAAAATAGTAGAGAAACTAAAAACTGTAGTAAGACTGCGATTCGTGATA
* *
30248 ACAAACTTTAAACATCTGATACTGTTTTGCATAAAATATCTACTAATAGATATCCAAATTGTAAC
66 ACAAACTCTAAACATCTGATACTGTTTTGCATAAAATATCTACTAATAGATATCCAAACTGTAAC
* * * *
30313 TGATTCATAAAATTTATAACACAAATAAGCTACGAATTCTACGATGAGTGCACGAG
131 TAATTCATAAAACTGATAACACAAATAAGCTACGAATTCTACAATGAGTGCACGAG
30369 GTA
1 GTA
30372 TCCGCGGACG
Statistics
Matches: 180, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 180 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (186 bp):
GTAGATAGTGTATACTAAAAATAGTAGAGAAACTAAAAACTGTAGTAAGACTGCGATTCGTGATA
ACAAACTCTAAACATCTGATACTGTTTTGCATAAAATATCTACTAATAGATATCCAAACTGTAAC
TAATTCATAAAACTGATAACACAAATAAGCTACGAATTCTACAATGAGTGCACGAG
Found at i:37682 original size:23 final size:23
Alignment explanation
Indices: 37645--37773 Score: 145
Period size: 23 Copynumber: 5.7 Consensus size: 23
37635 TATTTGGTTG
37645 TATATTT-GTTGTGTTGGGAGGC
1 TATATTTGGTTGTGTTGGGAGGC
* ** *
37667 TATATTTGGTTGTGTTCGGTTGA
1 TATATTTGGTTGTGTTGGGAGGC
* *
37690 TATTTTTGGTTGTGTTGGGAGAC
1 TATATTTGGTTGTGTTGGGAGGC
* * *
37713 TATATTTGGTTGTGTTTGAAGGG
1 TATATTTGGTTGTGTTGGGAGGC
*
37736 TATATTTGGTTGTGTTGGAAGG-
1 TATATTTGGTTGTGTTGGGAGGC
*
37758 TATGTTTGGTTGTGTT
1 TATATTTGGTTGTGTT
37774 TTGAGTGTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
22 22 0.25
23 67 0.75
ACGTcount: A:0.14, C:0.02, G:0.34, T:0.50
Consensus pattern (23 bp):
TATATTTGGTTGTGTTGGGAGGC
Found at i:37703 original size:46 final size:45
Alignment explanation
Indices: 37640--37773 Score: 166
Period size: 46 Copynumber: 3.0 Consensus size: 45
37630 GGATATATTT
37640 GGTTGTATATTT-GTTGTGTTGGGAGGCTATATTTGGTTGTGTTC
1 GGTTGTATATTTGGTTGTGTTGGGAGGCTATATTTGGTTGTGTTC
* * *
37684 GGTTGATATTTTTGGTTGTGTTGGGAGACTATATTTGGTTGTGTTT
1 GGTTG-TATATTTGGTTGTGTTGGGAGGCTATATTTGGTTGTGTTC
* * *
37730 GAAG-GGTATATTTGGTTGTGTTGGAAGG-TATGTTTGGTTGTGTT
1 G--GTTGTATATTTGGTTGTGTTGGGAGGCTATATTTGGTTGTGTT
37774 TTGAGTGTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
44 5 0.06
45 21 0.27
46 50 0.64
47 1 0.01
48 1 0.01
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.49
Consensus pattern (45 bp):
GGTTGTATATTTGGTTGTGTTGGGAGGCTATATTTGGTTGTGTTC
Found at i:37728 original size:69 final size:67
Alignment explanation
Indices: 37645--37773 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 67
37635 TATTTGGTTG
* ** *
37645 TATATTTGTTGTGTTGGGAGGCTATATTTGGTTGTGTTCGGTTGATATTTTTGGTTGTGTTGGGA
1 TATATTTGTTGTGTTGGAAGGCTATATTTGGTTGTGTT-GGAAGATATGTTTGGTTGTGTTGGGA
37710 GAC
65 GAC
* * *
37713 TATATTTGGTTGTGTTTGAAGGGTATATTTGGTTGTGTTGGAAGGTATGTTTGGTTGTGTT
1 TATATTT-GTTGTGTTGGAAGGCTATATTTGGTTGTGTTGGAAGATATGTTTGGTTGTGTT
37774 TTGAGTGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
68 25 0.47
69 28 0.53
ACGTcount: A:0.14, C:0.02, G:0.34, T:0.50
Consensus pattern (67 bp):
TATATTTGTTGTGTTGGAAGGCTATATTTGGTTGTGTTGGAAGATATGTTTGGTTGTGTTGGGAG
AC
Found at i:41332 original size:30 final size:28
Alignment explanation
Indices: 41286--41346 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
41276 AATTTGGTTA
*
41286 AAAAGAATTTTAAAAATGAGATTGTATTTG
1 AAAAGAATTTTAAAAATG-GATT-TAATTG
* *
41316 AAAATAATTTTGAAAATGGATTTAATTG
1 AAAAGAATTTTAAAAATGGATTTAATTG
41344 AAA
1 AAA
41347 TTAAGAACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 4 0.14
30 16 0.57
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (28 bp):
AAAAGAATTTTAAAAATGGATTTAATTG
Found at i:42617 original size:23 final size:23
Alignment explanation
Indices: 42591--42717 Score: 127
Period size: 23 Copynumber: 5.7 Consensus size: 23
42581 TATTTGGTTG
*
42591 TATATTTGGTTATGTTGGGAAGC
1 TATATTTGGTTGTGTTGGGAAGC
* *
42614 TATATTTGGTTGTGTT-TGAAGG
1 TATATTTGGTTGTGTTGGGAAGC
**
42636 TATATTTGGTTGT-AAGGG--GC
1 TATATTTGGTTGTGTTGGGAAGC
* * *
42656 TATATTTGGTTGTGTTTGGAGGG
1 TATATTTGGTTGTGTTGGGAAGC
* *
42679 TATATTTGGTTGTGTTTGGAGGC
1 TATATTTGGTTGTGTTGGGAAGC
*
42702 TATGTTTGGTTGTGTT
1 TATATTTGGTTGTGTT
42718 CAGTGGGTGA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 14 0.16
21 2 0.02
22 18 0.21
23 53 0.61
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (23 bp):
TATATTTGGTTGTGTTGGGAAGC
Found at i:42695 original size:65 final size:66
Alignment explanation
Indices: 42591--42714 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
42581 TATTTGGTTG
42591 TATATTTGGTTATGTTGGGAAGCTATATTTGGTTGTGTTTGAAGG-TATATTTGGTTGTAAGGGG
1 TATATTTGGTTATGTTGGGAAGCTATATTTGGTTGTGTTTGAAGGCTATATTTGGTTGTAAGGGG
42655 C
66 C
* * * * * *
42656 TATATTTGGTTGTGTTTGGAGGGTATATTTGGTTGTGTTTGGAGGCTATGTTTGGTTGT
1 TATATTTGGTTATGTTGGGAAGCTATATTTGGTTGTGTTTGAAGGCTATATTTGGTTGT
42715 GTTCAGTGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
65 40 0.77
66 12 0.23
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (66 bp):
TATATTTGGTTATGTTGGGAAGCTATATTTGGTTGTGTTTGAAGGCTATATTTGGTTGTAAGGGG
C
Done.