Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold475
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: 1773841
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 12 of 12
Found at i:1743328 original size:115 final size:111
Alignment explanation
Indices: 1743129--1744179 Score: 1168
Period size: 115 Copynumber: 9.2 Consensus size: 111
1743119 TTAGCCCTTC
*
1743129 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCGC-TTCCTA
1 CCAGTCCTCAAAGAGCAGGACGCC---TC--TTTAAAGCCCACACAAGTTGGTGGCACTTTCC-A
* *
1743193 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACAAAAGTTGGTGGCACTTC
60 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
* *
1743245 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
1 CCAGTCCTCAAAGAGCAGGACGCC---TCTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* *
1743310 CCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
62 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
* * * * *
1743360 CCAATCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTC
1 CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
*
1743424 AAAGAGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTC
66 AAAGAGCAGGATGC-----C-TTTTAAAGCCCACACAAGTTGGTGGCACTTT
* * *
1743476 CCAGTCCTCAAAGAGCAGAACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
1 CCAGTCCTCAAAGAGCAGGACGCC---TCTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* * *
1743541 CCTCAAAGAGTAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTT
62 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
* * * *
1743591 -CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAG
1 CCAGTCCTCAAAGAGCAGGACGC---CTC-TTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * *
1743655 TCCCCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
61 TCCTCAAAGAGCAGGATGCC---T-TTT-AAAGCCCACACAAGTTGGTGGCACTTT
* * * *
1743711 CCAATCCTCAAAGAGCAGGATGCCT-TTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTC
1 CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
*
1743774 AAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTT
66 AAAGAGCAGGATGC-----CTTTT-AAAGCCCACACAAGTTGGTGGCACTTT
* *
1743826 CCAGTCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCC
1 CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCT
* ** * *
1743889 CAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
65 CAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
* * *
1743936 CCAGTCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACATAAGTTGGTGGCACCTTT-CAGTCCC
1 CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCT
** * *
1743999 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
65 CAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
* *
1744046 CCAGTCCTCAAAGAGCAGGACACCTC-TTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTC
1 CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
* * *
1744110 AGAGAGCAGGACGCCTTCACCTCTTAAAGCCCACACAAGTAGGTGGCACTTT
66 AAAGAGCAGGATGCC-T----T-TTAAAGCCCACACAAGTTGGTGGCACTTT
**
1744162 TTAGTCCTCAAAGAGCAG
1 CCAGTCCTCAAAGAGCAG
1744180 AATACACTTT
Statistics
Matches: 832, Mismatches: 66, Indels: 74
0.86 0.07 0.08
Matches are distributed among these distances:
109 3 0.00
110 253 0.30
111 7 0.01
112 1 0.00
114 44 0.05
115 273 0.33
116 150 0.18
118 2 0.00
119 5 0.01
120 26 0.03
121 68 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (111 bp):
CCAGTCCTCAAAGAGCAGGACGCCTCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
AAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
Found at i:1743332 original size:27 final size:27
Alignment explanation
Indices: 1743302--1743387 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
1743292 TTGGTGGCAT
1743302 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
* * ** *
1743329 TTTCAAAGCC-CACACA-AGTTGG-TGGCAT
1 TTTCCAATCCTCA-A-AGAGCAGGAT-GC-C
1743357 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
1743384 TTTC
1 TTTC
1743388 AAAGCCCACA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 3 0.07
27 20 0.48
28 16 0.38
29 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (27 bp):
TTTCCAATCCTCAAAGAGCAGGATGCC
Found at i:1744969 original size:21 final size:21
Alignment explanation
Indices: 1744941--1744998 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1744931 AAATTTTATC
*
1744941 CAAATGTATCGATACATATGTA
1 CAAATGTATCGATACAT-TCTA
*
1744963 -GAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
1744983 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1744999 GGGTCCCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:1746275 original size:76 final size:78
Alignment explanation
Indices: 1746181--1746330 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
1746171 TGATTATGAG
* * * * *
1746181 AATAACGGGGTTGGAGTATCCCCGATGA-AG-AATTGATGTTTTGGAAATAAAACCGGGGTTGGA
1 AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
1746244 GTATCCCCTCGAA
66 GTATCCCCTCGAA
*
1746257 AATAACGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1 AATAACGGGGATGGAGTATCCCCGATGA-GAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1746322 AGTATCCCC
65 AGTATCCCC
1746331 GATGATGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 26 0.40
78 2 0.03
79 37 0.57
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (78 bp):
AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
GTATCCCCTCGAA
Found at i:1746540 original size:153 final size:153
Alignment explanation
Indices: 1746262--1746549 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
1746252 TCGAAAATAA
* *
1746262 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTAT
1 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
* * * *
1746327 CCCCGATGATGAAAAATTAGTATTTTGGAAATACAATCGGAGTTGGAGTATCCCCGATTATAG-A
66 CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAT-GCA
1746391 AAATTGGTGTTTTGAAAATAAAAC
130 AAATTGGTGTTTTGAAAATAAAAC
* * ** * *
1746415 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTCTGAG-AATAAAATCGGAGTTGGAGT
1 CGGGGATGGAGTATCCCCGATTATGAG-AAATTAATATT-TGAGAAATAAAAACGGAGTTGGAGT
* * * * *
1746478 GTCCCCGATTG-TGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGATTATG
64 ATCCCCGA-TGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATG
1746542 CAAAATTG
128 CAAAATTG
1746550 AGAAAACTTG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 2 0.02
153 107 0.94
154 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (153 bp):
CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATGCAA
AATTGGTGTTTTGAAAATAAAAC
Found at i:1746547 original size:51 final size:50
Alignment explanation
Indices: 1746262--1746548 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
1746252 TCGAAAATAA
* * * *
1746262 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAA
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTAGAAATAAAAC
* * * * *
1746313 CGGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTGGAAATACAAT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATTAGTGTTTTAGAAATAAAAC
* *
1746364 CGGAGTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAG-AAATAAAAC
* * * *
1746415 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTCT-GAGAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGA-AATAAAAC
* * * * *
1746466 CGGAGTTGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGAAATAAAAC
1746517 CGGGGTTGGAGTATCCCCGATTATGCAAAATT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATT
1746549 GAGAAAACTT
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 3 0.01
51 196 0.97
52 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:1746549 original size:102 final size:101
Alignment explanation
Indices: 1746268--1746549 Score: 370
Period size: 102 Copynumber: 2.8 Consensus size: 101
1746258 ATAACGGGGA
* *
1746268 TGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
* * * *
1746333 TGATGAAAAATTAGTATTTTGGAAATACAATCGGAGT
65 TTATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
**
1746370 TGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCG
* * *
1746434 ATTGTGGAAAATTGGTGTTCT-GAGAATAAAATCGGAGT
64 ATTATGAAAAATTGGTATTCTGGA-AATAAAATCGGAGT
* * *
1746472 TGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
*
1746537 TTATGCAAAATTG
65 TTATGAAAAATTG
1746550 AGAAAACTTG
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
101 3 0.02
102 151 0.96
103 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (101 bp):
TGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGAT
TATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
Found at i:1748928 original size:13 final size:13
Alignment explanation
Indices: 1748910--1748935 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1748900 ACAAAGATCC
1748910 ATGTATCGATACA
1 ATGTATCGATACA
1748923 ATGTATCGATACA
1 ATGTATCGATACA
1748936 CAGAAAAATG
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:1748931 original size:33 final size:33
Alignment explanation
Indices: 1748889--1748955 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1748879 AAAATTTCCA
***
1748889 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1748922 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1748955 A
1 A
1748956 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1748999 original size:19 final size:18
Alignment explanation
Indices: 1748975--1749042 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1748965 CAGTAGCTAA
1748975 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1748994 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1749009 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1749026 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1749043 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1749015 original size:13 final size:13
Alignment explanation
Indices: 1748997--1749021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1748987 ACAATACTTA
1748997 TGTATCGATACAT
1 TGTATCGATACAT
1749010 TGTATCGATACA
1 TGTATCGATACA
1749022 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1749019 original size:32 final size:32
Alignment explanation
Indices: 1748978--1749040 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1748968 TAGCTAATTA
*
1748978 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1749010 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1749041 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1749122 original size:21 final size:21
Alignment explanation
Indices: 1749098--1749154 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1749088 CATTTGTAGG
1749098 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1749119 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1749140 ATGTATCGATACATT
1 ATGTATCGATACATT
1749155 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1749182 original size:20 final size:20
Alignment explanation
Indices: 1749157--1749194 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1749147 GATACATTTA
1749157 AATTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTC
1749177 AATTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTT
1749195 CAAACACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (20 bp):
AATTTTTTTTTTTTTTTTTC
Found at i:1749184 original size:19 final size:19
Alignment explanation
Indices: 1749160--1749197 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1749150 ACATTTAAAT
1749160 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
1749179 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
1749198 ACACTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTCAA
Found at i:1749814 original size:55 final size:55
Alignment explanation
Indices: 1749730--1750462 Score: 1090
Period size: 55 Copynumber: 13.3 Consensus size: 55
1749720 ATAAGTTGTA
* * * * * *
1749730 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1749785 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1749840 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1749895 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1749950 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1750005 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1750060 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1750115 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGATG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1750170 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
1750225 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1750280 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1750335 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1750390 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1750445 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
1750463 AAAAAGCGGA
Statistics
Matches: 634, Mismatches: 33, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
54 16 0.03
55 604 0.95
56 14 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:1750025 original size:26 final size:26
Alignment explanation
Indices: 1749996--1750085 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
1749986 GTGTGGGCTT
1749996 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1750022 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
1750049 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1750077 TGAAAGGTG
1 TGAAAGGTG
1750086 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 8 0.17
28 9 0.19
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1751467 original size:8 final size:8
Alignment explanation
Indices: 1751444--1751487 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
1751434 CTTTTCTCTC
*
1751444 TTTTTCTT
1 TTTTTGTT
1751452 TGTTTTGTT
1 T-TTTTGTT
1751461 TTTTTG-T
1 TTTTTGTT
1751468 TTTTT-TT
1 TTTTTGTT
1751475 TTTTTGTT
1 TTTTTGTT
1751483 TTTTT
1 TTTTT
1751488 TTTGAAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 12 0.38
8 13 0.41
9 7 0.22
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1751468 original size:13 final size:12
Alignment explanation
Indices: 1751444--1751491 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
1751434 CTTTTCTCTC
*
1751444 TTTTTCTTTGTT
1 TTTTTTTTTGTT
1751456 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
*
1751469 TTTTTTTTTTTGT
1 TTTTTTTTTGT-T
1751482 TTTTTTTTTG
1 TTTTTTTTTG
1751492 AAGAGAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:1751479 original size:22 final size:23
Alignment explanation
Indices: 1751444--1751487 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1751434 CTTTTCTCTC
1751444 TTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTCTTTGTTTTGTTTTTTTG
*
1751467 TTTTT-TTTTTTTTGTTTTTTT
1 TTTTTCTTTGTTTTGTTTTTTT
1751488 TTTGAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (23 bp):
TTTTTCTTTGTTTTGTTTTTTTG
Found at i:1764079 original size:76 final size:78
Alignment explanation
Indices: 1763985--1764134 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
1763975 TGATTATGAG
* * * * *
1763985 AATAACGGGGTTGGAGTATCCCCGATGA-AG-AATTGATGTTTTGGAAATAAAACCGGGGTTGGA
1 AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
1764048 GTATCCCCTCGAA
66 GTATCCCCTCGAA
*
1764061 AATAACGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1 AATAACGGGGATGGAGTATCCCCGATGA-GAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1764126 AGTATCCCC
65 AGTATCCCC
1764135 GATGATGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 26 0.40
78 2 0.03
79 37 0.57
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (78 bp):
AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
GTATCCCCTCGAA
Found at i:1764344 original size:153 final size:153
Alignment explanation
Indices: 1764066--1764353 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
1764056 TCGAAAATAA
* *
1764066 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTAT
1 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
* * * *
1764131 CCCCGATGATGAAAAATTAGTATTTTGGAAATACAATCGGAGTTGGAGTATCCCCGATTATAG-A
66 CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAT-GCA
1764195 AAATTGGTGTTTTGAAAATAAAAC
130 AAATTGGTGTTTTGAAAATAAAAC
* * ** * *
1764219 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTCTGAG-AATAAAATCGGAGTTGGAGT
1 CGGGGATGGAGTATCCCCGATTATGAG-AAATTAATATT-TGAGAAATAAAAACGGAGTTGGAGT
* * * * *
1764282 GTCCCCGATTG-TGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGATTATG
64 ATCCCCGA-TGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATG
1764346 CAAAATTG
128 CAAAATTG
1764354 AGAAAACTTG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 2 0.02
153 107 0.94
154 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (153 bp):
CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATGCAA
AATTGGTGTTTTGAAAATAAAAC
Found at i:1764351 original size:51 final size:50
Alignment explanation
Indices: 1764066--1764352 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
1764056 TCGAAAATAA
* * * *
1764066 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAA
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTAGAAATAAAAC
* * * * *
1764117 CGGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTGGAAATACAAT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATTAGTGTTTTAGAAATAAAAC
* *
1764168 CGGAGTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAG-AAATAAAAC
* * * *
1764219 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTCT-GAGAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGA-AATAAAAC
* * * * *
1764270 CGGAGTTGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGAAATAAAAC
1764321 CGGGGTTGGAGTATCCCCGATTATGCAAAATT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATT
1764353 GAGAAAACTT
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 3 0.01
51 196 0.97
52 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:1764353 original size:102 final size:101
Alignment explanation
Indices: 1764072--1764353 Score: 370
Period size: 102 Copynumber: 2.8 Consensus size: 101
1764062 ATAACGGGGA
* *
1764072 TGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
* * * *
1764137 TGATGAAAAATTAGTATTTTGGAAATACAATCGGAGT
65 TTATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
**
1764174 TGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCG
* * *
1764238 ATTGTGGAAAATTGGTGTTCT-GAGAATAAAATCGGAGT
64 ATTATGAAAAATTGGTATTCTGGA-AATAAAATCGGAGT
* * *
1764276 TGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
*
1764341 TTATGCAAAATTG
65 TTATGAAAAATTG
1764354 AGAAAACTTG
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
101 3 0.02
102 151 0.96
103 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (101 bp):
TGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGAT
TATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
Found at i:1766728 original size:13 final size:13
Alignment explanation
Indices: 1766710--1766735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1766700 ACAAAGATCC
1766710 ATGTATCGATACA
1 ATGTATCGATACA
1766723 ATGTATCGATACA
1 ATGTATCGATACA
1766736 CAGAAAAAGT
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:1766819 original size:13 final size:14
Alignment explanation
Indices: 1766794--1766824 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1766784 TATCGATACA
1766794 ATACTTATGTATCG
1 ATACTTATGTATCG
1766808 ATACTT-TGTATCG
1 ATACTTATGTATCG
1766821 ATAC
1 ATAC
1766825 AAAACTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (14 bp):
ATACTTATGTATCG
Found at i:1766823 original size:32 final size:32
Alignment explanation
Indices: 1766782--1766843 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1766772 TAGCTAATTA
*
1766782 TGTATCGATACAATACTTATGTATCGATACTT
1 TGTATCGATACAAAACTTATGTATCGATACTT
1766814 TGTATCGATACAAAACTTATGTATCGATAC
1 TGTATCGATACAAAACTTATGTATCGATAC
1766844 AAATTGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACTT
Found at i:1766846 original size:19 final size:19
Alignment explanation
Indices: 1766779--1766846 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1766769 GTGTAGCTAA
*
1766779 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
1766798 TTATGTATCGAT-----AC
1 TTATGTATCGATACAAAAC
1766812 TT-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1766830 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1766847 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
14 4 0.09
18 4 0.09
19 26 0.60
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1766927 original size:21 final size:21
Alignment explanation
Indices: 1766901--1766957 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1766891 ACATTGTAGG
1766901 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1766922 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1766943 ATGTATCGATACATT
1 ATGTATCGATACATT
1766958 TAAAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1766969 original size:1 final size:1
Alignment explanation
Indices: 1766963--1766996 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
1766953 ACATTTAAAA
**
1766963 TTTTTTTTTTTTTTTTTCATTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1766997 CAAACACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:1766987 original size:17 final size:17
Alignment explanation
Indices: 1766965--1766998 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1766955 ATTTAAAATT
1766965 TTTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTTCA
1766982 TTTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTTCA
1766999 AACACTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTCA
Found at i:1772080 original size:13 final size:13
Alignment explanation
Indices: 1772062--1772086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1772052 CATAAAGTGT
1772062 TGTATCGATACAA
1 TGTATCGATACAA
1772075 TGTATCGATACA
1 TGTATCGATACA
1772087 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1772084 original size:33 final size:33
Alignment explanation
Indices: 1772042--1772108 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1772032 TTCAACGATT
1772042 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1772075 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1772108 T
1 T
1772109 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Done.