Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 92 of 310
Found at i:29408027 original size:48 final size:48
Alignment explanation
Indices: 29407950--29408074 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 48
29407940 ACCATATTTA
* * *
29407950 ATGTTTGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCGATGAT
1 ATGTGTGCCAGTGTAAGACCATGTATGGGAAATGGCATCAGCGATGAT
* *
29407998 ATGTGTGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGCGATGAT
1 ATGTGTGCCAGTGTAAGACCATGTATGGGAAATGGCATCAGCGATGAT
* * *
29408046 ATGTGTGCTAGTATAAGACAATGTATGGG
1 ATGTGTGCCAGTGTAAGACCATGTATGGG
29408075 TCCATGTTGC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.28
Consensus pattern (48 bp):
ATGTGTGCCAGTGTAAGACCATGTATGGGAAATGGCATCAGCGATGAT
Found at i:29409953 original size:21 final size:22
Alignment explanation
Indices: 29409915--29409955 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29409905 CAAAAAGGCT
29409915 TCATTCTCTTATACTCATTCTC
1 TCATTCTCTTATACTCATTCTC
* *
29409937 TCATTTTC-TATATTCATTC
1 TCATTCTCTTATACTCATTC
29409956 ATTCTTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (22 bp):
TCATTCTCTTATACTCATTCTC
Found at i:29412284 original size:21 final size:21
Alignment explanation
Indices: 29412241--29412290 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
29412231 GAGCTCACAT
*
29412241 GCCCGTGTGGTCCAAGGGACAC
1 GCCCGTGTGATCCAA-GGACAC
29412263 GCCCGTGTGATCCTAA-GACAC
1 GCCCGTGTGATCC-AAGGACAC
29412284 GCCCGTG
1 GCCCGTG
29412291 CTGCAGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 12 0.46
23 2 0.08
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (21 bp):
GCCCGTGTGATCCAAGGACAC
Found at i:29414056 original size:7 final size:7
Alignment explanation
Indices: 29414044--29414070 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29414034 AAGTAACATT
29414044 TTTATCA
1 TTTATCA
29414051 TTTATCA
1 TTTATCA
29414058 TTTATCA
1 TTTATCA
29414065 TTTATC
1 TTTATC
29414071 GGTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTATCA
Found at i:29414868 original size:18 final size:18
Alignment explanation
Indices: 29414845--29414879 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29414835 TAAAATTATT
29414845 TTTATT-TCTATTTAATTA
1 TTTATTATCT-TTTAATTA
29414863 TTTATTATCTTTTAATT
1 TTTATTATCTTTTAATT
29414880 TTATCACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATCTTTTAATTA
Found at i:29420300 original size:21 final size:21
Alignment explanation
Indices: 29420276--29420345 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
29420266 CACATACATC
29420276 ATGAACTCAGACCACAACTCA
1 ATGAACTCAGACCACAACTCA
* * * *
29420297 ATGAGCTTAGATGTCACATATATC-
1 ATGAACTCAGA--CCACA-A-CTCA
*
29420321 ATGAACTCAGACCATAACTCA
1 ATGAACTCAGACCACAACTCA
29420342 ATGA
1 ATGA
29420346 GTTTAGATCA
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 3 0.09
23 4 0.11
24 10 0.29
25 2 0.06
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (21 bp):
ATGAACTCAGACCACAACTCA
Found at i:29420322 original size:45 final size:45
Alignment explanation
Indices: 29420263--29420353 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
29420253 CAAAAACATG
29420263 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTTAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTTAGA
* * *
29420308 TGTCACATATATCATGAACTCAGACCATAACTCAATGAGTTTAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTTAGA
29420353 T
1 T
29420354 CACATAGTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTTAGA
Found at i:29429313 original size:17 final size:17
Alignment explanation
Indices: 29429293--29429328 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29429283 TGCTAACTTC
29429293 TTCTTCTTTGTTTTGAT
1 TTCTTCTTTGTTTTGAT
29429310 TTCTTCTTTGTTTTGAT
1 TTCTTCTTTGTTTTGAT
29429327 TT
1 TT
29429329 GAATGAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (17 bp):
TTCTTCTTTGTTTTGAT
Found at i:29434436 original size:48 final size:48
Alignment explanation
Indices: 29434367--29434466 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
29434357 CACATAGTCC
*
29434367 TCTTTCCCTTGTGCAATAAAACCCTCTGGCTGCTCCATGTAAAGCTCT
1 TCTTTCCCTTGTGCAACAAAACCCTCTGGCTGCTCCATGTAAAGCTCT
29434415 TCTTTCCCTTGTGCAACAAAACCCTCTGGCTGCTCCATGTAAAGCTCT
1 TCTTTCCCTTGTGCAACAAAACCCTCTGGCTGCTCCATGTAAAGCTCT
29434463 TCTT
1 TCTT
29434467 CCAAGTCACC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (48 bp):
TCTTTCCCTTGTGCAACAAAACCCTCTGGCTGCTCCATGTAAAGCTCT
Found at i:29446751 original size:20 final size:19
Alignment explanation
Indices: 29446726--29446772 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
29446716 AGGCAACCTA
*
29446726 ATTTTATTATTTTTC-CATTT
1 ATTTTATTAGTTTTCTC--TT
*
29446746 ATTTTAGTAGTTTTCTCTT
1 ATTTTATTAGTTTTCTCTT
29446765 ATTTTATT
1 ATTTTATT
29446773 TTTGTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 13 0.57
21 1 0.04
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (19 bp):
ATTTTATTAGTTTTCTCTT
Found at i:29450220 original size:25 final size:26
Alignment explanation
Indices: 29450187--29450246 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
29450177 TGTGCGAGGT
*
29450187 ATGTAAATTTCATAAATGATGA-TAG
1 ATGTAAATTACATAAATGATGATTAG
*
29450212 ATGTTAATTACATAAATGATGATTAG
1 ATGTAAATTACATAAATGATGATTAG
29450238 ATGATAAAT
1 ATG-TAAAT
29450247 ATATGCTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 20 0.67
26 6 0.20
27 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (26 bp):
ATGTAAATTACATAAATGATGATTAG
Found at i:29462514 original size:35 final size:35
Alignment explanation
Indices: 29462468--29462540 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
29462458 ACACATTCTT
29462468 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
29462503 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
29462538 TAT
1 TAT
29462541 ATCACGTACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:29464004 original size:21 final size:21
Alignment explanation
Indices: 29463978--29464019 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29463968 CATCATCAAC
29463978 TCTTT-CCTCGGATTACCCGTT
1 TCTTTCCCT-GGATTACCCGTT
29463999 TCTTTCCCTGGATTACCCGTT
1 TCTTTCCCTGGATTACCCGTT
29464020 GAACACTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.10, C:0.33, G:0.14, T:0.43
Consensus pattern (21 bp):
TCTTTCCCTGGATTACCCGTT
Found at i:29467443 original size:30 final size:30
Alignment explanation
Indices: 29467404--29467464 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
29467394 TACATGAAAT
29467404 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
29467435 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
29467464 A
1 A
29467465 ATTGCTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 5 0.18
30 9 0.32
31 13 0.46
32 1 0.04
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:29471399 original size:41 final size:40
Alignment explanation
Indices: 29471348--29471428 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 40
29471338 AAGAAAGAGT
29471348 GTATATTTCATGACATTCACGAAATATTGACTTTTCAATG
1 GTATATTTCATGACATTCACGAAATATTGACTTTTCAATG
*
29471388 NGTATTTTTCATGACATTCACGAAATATTGACTTTTCAATG
1 -GTATATTTCATGACATTCACGAAATATTGACTTTTCAATG
29471429 ATGCTTTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (40 bp):
GTATATTTCATGACATTCACGAAATATTGACTTTTCAATG
Found at i:29471655 original size:9 final size:9
Alignment explanation
Indices: 29471641--29471678 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
29471631 AACTTAAATT
29471641 AAAATTATA
1 AAAATTATA
29471650 AAAATTATA
1 AAAATTATA
29471659 AAAATTATA
1 AAAATTATA
29471668 AAAATTATA
1 AAAATTATA
29471677 AA
1 AA
29471679 TAAAGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:29478306 original size:30 final size:30
Alignment explanation
Indices: 29478259--29478315 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29478249 AGACCATTTA
*
29478259 CACACAGGCTGAGCACACGCCCGTGTGAGC
1 CACACAGGCTGAGCACACGCCCATGTGAGC
*
29478289 CACACGGGCT-AGCCACACGCCCATGTG
1 CACACAGGCTGAG-CACACGCCCATGTG
29478316 GCAATCCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.23, C:0.39, G:0.28, T:0.11
Consensus pattern (30 bp):
CACACAGGCTGAGCACACGCCCATGTGAGC
Found at i:29483190 original size:13 final size:13
Alignment explanation
Indices: 29483174--29483201 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29483164 ATTTTCATTC
29483174 TTTATTTCTTTAT
1 TTTATTTCTTTAT
29483187 TTTATTTCTTTAT
1 TTTATTTCTTTAT
29483200 TT
1 TT
29483202 CTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:29483220 original size:21 final size:21
Alignment explanation
Indices: 29483175--29483222 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29483165 TTTTCATTCT
*
29483175 TTATTTCTTTATTTTATTTCT
1 TTATTTCTTTATTTTATTTCA
29483196 TTATTTCTTCT-TTCTTATTT-A
1 TTATTTCTT-TATT-TTATTTCA
29483217 TTATTT
1 TTATTT
29483223 TATTTTCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTCTTTATTTTATTTCA
Found at i:29485017 original size:23 final size:23
Alignment explanation
Indices: 29484979--29485046 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
29484969 TTTCTAGAAG
*
29484979 ATTTAGTATTTTTTAGTATAATAT
1 ATTTAG-ATTTATTAGTATAATAT
* *
29485003 ATTTAGATTTATTAGCAAAATAT
1 ATTTAGATTTATTAGTATAATAT
*
29485026 ATTTGAAATTTATTAGTATAA
1 ATTT-AGATTTATTAGTATAA
29485047 AAATCTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (23 bp):
ATTTAGATTTATTAGTATAATAT
Found at i:29500022 original size:31 final size:31
Alignment explanation
Indices: 29499963--29500022 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
29499953 TAATATATAA
29499963 AAAATATATAAATATTATTAAATATTAAATT
1 AAAATATATAAATATTATTAAATATTAAATT
* * *
29499994 AAAATAATATAATTTTTTTTAAAT-TTAAA
1 AAAAT-ATATAAATATTATTAAATATTAAA
29500023 AATAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AAAATATATAAATATTATTAAATATTAAATT
Found at i:29500949 original size:15 final size:16
Alignment explanation
Indices: 29500920--29500953 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29500910 TTTTTATTTT
*
29500920 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
29500936 TATTTTT-ATAAAATA
1 TATTTTTAATAAAATA
29500951 TAT
1 TAT
29500954 ATATTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:29505206 original size:17 final size:17
Alignment explanation
Indices: 29505184--29505243 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
29505174 TTAAGATAAC
29505184 TATATATAAAATTTTAA
1 TATATATAAAATTTTAA
* * *
29505201 TATATAAAAAATATTAT
1 TATATATAAAATTTTAA
* * **
29505218 TAAATATTAAATTAAAA
1 TATATATAAAATTTTAA
29505235 TA-ATATAAA
1 TATATATAAA
29505244 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
16 6 0.19
17 26 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATATAAAATTTTAA
Found at i:29505713 original size:22 final size:22
Alignment explanation
Indices: 29505666--29505713 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
29505656 ATAATATCTA
* * *
29505666 AATAATAAAATGATAGCAATAT
1 AATAATAAAATGACAGCAAAAG
29505688 AATAATAAAAT-AGCAGCAAAAG
1 AATAATAAAATGA-CAGCAAAAG
29505710 AATA
1 AATA
29505714 CCAAAGAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.21
Consensus pattern (22 bp):
AATAATAAAATGACAGCAAAAG
Found at i:29512219 original size:6 final size:6
Alignment explanation
Indices: 29512210--29512248 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
29512200 CTAAATTAAT
*
29512210 AAAATA AAAATA AAAATA AAAATA AATAATA AAACTA AA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AA
29512249 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:29512231 original size:13 final size:13
Alignment explanation
Indices: 29512210--29512258 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
29512200 CTAAATTAAT
29512210 AAAATAAAAAT-A
1 AAAATAAAAATAA
29512222 AAAATAAAAATAA
1 AAAATAAAAATAA
* *
29512235 ATAATAAAACTAAA
1 AAAATAAAAAT-AA
29512249 TAAAATAAAA
1 -AAAATAAAA
29512259 TAATATCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 2 0.06
15 8 0.26
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:29512263 original size:13 final size:13
Alignment explanation
Indices: 29512201--29512263 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
29512191 AGGCTAAAGC
*
29512201 TAAATTAATAAAA
1 TAAAATAATAAAA
29512214 T-AAA-AATAAAAA
1 TAAAATAAT-AAAA
*
29512226 TAAAAATAA-ATAA
1 T-AAAATAATAAAA
29512239 TAAAACTAAATAAAA
1 TAAAA-T-AATAAAA
29512254 TAAAATAATA
1 TAAAATAATA
29512264 TCTTCTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
11 3 0.08
12 11 0.28
13 10 0.25
14 6 0.15
15 10 0.25
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:29513857 original size:13 final size:13
Alignment explanation
Indices: 29513832--29513887 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
29513822 AGGCCAAAGC
29513832 TAAATTAAT-AAAA
1 TAAA-TAATAAAAA
29513845 TAAATAATAAAAA
1 TAAATAATAAAAA
*
29513858 TAAATAATAAAAC
1 TAAATAATAAAAA
*
29513871 TAAATAAAATAAAA
1 TAAATAATA-AAAA
29513885 TAA
1 TAA
29513888 TATCTTCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.11
13 28 0.74
14 6 0.16
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:29513863 original size:22 final size:21
Alignment explanation
Indices: 29513833--29513887 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
29513823 GGCCAAAGCT
*
29513833 AAATTAATAAAATAAATAATAA
1 AAATAAATAAAATAAA-AATAA
*
29513855 AAATAAAT--AATAAAACTAA
1 AAATAAATAAAATAAAAATAA
*
29513874 ATA-AAATAAAATAA
1 AAATAAATAAAATAA
29513888 TATCTTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 11 0.39
22 7 0.25
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATAAATAAAATAAAAATAA
Found at i:29513876 original size:10 final size:9
Alignment explanation
Indices: 29513833--29513883 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
29513823 GGCCAAAGCT
*
29513833 AAATTAATA
1 AAATAAATA
29513842 AAATAAATA
1 AAATAAATA
29513851 ATAA-AAAT-
1 A-AATAAATA
29513859 AAAT-AATA
1 AAATAAATA
29513867 AAACTAAATA
1 AAA-TAAATA
29513877 AAATAAA
1 AAATAAA
29513884 ATAATATCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.14
8 4 0.11
9 18 0.50
10 9 0.25
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:29514713 original size:14 final size:14
Alignment explanation
Indices: 29514684--29514715 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
29514674 TGTAATGATA
29514684 TTATTGTACTATAT
1 TTATTGTACTATAT
*
29514698 TTATTGTATTATAT
1 TTATTGTACTATAT
29514712 TTAT
1 TTAT
29514716 GTGTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
TTATTGTACTATAT
Found at i:29520436 original size:30 final size:31
Alignment explanation
Indices: 29520385--29520444 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
29520375 CACCACCTTG
29520385 CTGTTTTGCATTTTTTGACCTACACCCGTAA
1 CTGTTTTGCATTTTTTGACCTACACCCGTAA
29520416 CTGTTTTGCATTTTTT-ACCTACACCCGTA
1 CTGTTTTGCATTTTTTGACCTACACCCGTA
29520445 TTTTAACCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.43
Consensus pattern (31 bp):
CTGTTTTGCATTTTTTGACCTACACCCGTAA
Found at i:29527524 original size:18 final size:18
Alignment explanation
Indices: 29527501--29527556 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
29527491 CACACGACAT
*
29527501 AGCAGTTCTCATAAAATA
1 AGCAGTTCACATAAAATA
* *
29527519 AGCAGTGCACATATAATA
1 AGCAGTTCACATAAAATA
* * *
29527537 AGTAATTCGCATAAAATA
1 AGCAGTTCACATAAAATA
29527555 AG
1 AG
29527557 TGGATCACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (18 bp):
AGCAGTTCACATAAAATA
Found at i:29528316 original size:18 final size:18
Alignment explanation
Indices: 29528293--29528356 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
29528283 ATCTCACAAT
*
29528293 ATACAGTTTGGCAAATTA
1 ATACAGTTCGGCAAATTA
* *
29528311 ATACAGTTCGCCATATTA
1 ATACAGTTCGGCAAATTA
* *
29528329 ATACAGATCAGCAAATTA
1 ATACAGTTCGGCAAATTA
*
29528347 ACACAGTTCG
1 ATACAGTTCG
29528357 CTATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (18 bp):
ATACAGTTCGGCAAATTA
Found at i:29528384 original size:36 final size:36
Alignment explanation
Indices: 29528304--29528385 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
29528294 TACAGTTTGG
* * *
29528304 CAAATTAATACAGTTCGCCATATTAATACAGATCAG
1 CAAATTAACACAGTTCGCCATAATAATACAGATCAC
* *
29528340 CAAATTAACACAGTTCGCTATAATAATATA-ATTCAC
1 CAAATTAACACAGTTCGCCATAATAATACAGA-TCAC
*
29528376 CAAGTTAACA
1 CAAATTAACA
29528386 TGGTTCACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (36 bp):
CAAATTAACACAGTTCGCCATAATAATACAGATCAC
Found at i:29538534 original size:16 final size:16
Alignment explanation
Indices: 29538484--29538534 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 16
29538474 ATGGAAATAT
*
29538484 AATCTTTAAGCATATGC
1 AATCTTGAAG-ATATGC
29538501 AATCTTAGATATGATATGC
1 AATCTT-GA-A-GATATGC
29538520 AATCTTGAAGATATG
1 AATCTTGAAGATATG
29538535 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 13 0.43
20 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (16 bp):
AATCTTGAAGATATGC
Found at i:29538553 original size:22 final size:21
Alignment explanation
Indices: 29538495--29538536 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
29538485 ATCTTTAAGC
29538495 ATATGCAATCTT--AGATATG
1 ATATGCAATCTTGAAGATATG
29538514 ATATGCAATCTTGAAGATATG
1 ATATGCAATCTTGAAGATATG
29538535 AT
1 AT
29538537 CTTGTAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
ATATGCAATCTTGAAGATATG
Found at i:29542732 original size:45 final size:46
Alignment explanation
Indices: 29542649--29542757 Score: 127
Period size: 45 Copynumber: 2.4 Consensus size: 46
29542639 GAATCATTTT
* *
29542649 TTATTTCCATTTC-C-ATTTTGAGAAAACCACATTTATTTCCAA-A
1 TTATTTCCATTTCTCTATTTTGAGAAAACCACAATGATTTCCAATA
* * *
29542692 TTATTT-CATTTCTCTATTTTGGAGAAAACCATAATGATTTCTAATT
1 TTATTTCCATTTCTCTATTTT-GAGAAAACCACAATGATTTCCAATA
*
29542738 TTTTTTCCATTTCTCTATTT
1 TTATTTCCATTTCTCTATTT
29542758 CTATTCATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 6 0.11
43 7 0.13
44 5 0.09
45 19 0.35
46 5 0.09
47 13 0.24
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (46 bp):
TTATTTCCATTTCTCTATTTTGAGAAAACCACAATGATTTCCAATA
Found at i:29546743 original size:16 final size:16
Alignment explanation
Indices: 29546724--29546757 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29546714 TTTCTTTTTC
29546724 TTTTTAATTTTTATTG
1 TTTTTAATTTTTATTG
29546740 TTTTTAATTTTTATTG
1 TTTTTAATTTTTATTG
29546756 TT
1 TT
29546758 CATCCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTAATTTTTATTG
Found at i:29546750 original size:22 final size:22
Alignment explanation
Indices: 29546705--29546750 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29546695 AATTTGAGAC
* **
29546705 TTAATTTTTTTTCTTTTTCTTT
1 TTAATTTTTATTCTTTTTAATT
*
29546727 TTAATTTTTATTGTTTTTAATT
1 TTAATTTTTATTCTTTTTAATT
29546749 TT
1 TT
29546751 TATTGTTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TTAATTTTTATTCTTTTTAATT
Found at i:29549916 original size:22 final size:21
Alignment explanation
Indices: 29549867--29549921 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
29549857 ATTTTCGCCA
29549867 TTTCATTGTT-GATCTATTGT
1 TTTCATTGTTAGATCTATTGT
29549887 TTCGTCATTGTTAGATC-ATGTGT
1 TT--TCATTGTTAGATCTAT-TGT
29549910 CTTTCATTGTTA
1 -TTTCATTGTTA
29549922 TACCCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.07
22 19 0.63
23 7 0.23
24 2 0.07
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTCATTGTTAGATCTATTGT
Found at i:29551766 original size:46 final size:46
Alignment explanation
Indices: 29551716--29551818 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 46
29551706 ACACTTTCAC
29551716 GCAAAAT-AAGAAAGAAGAATAAATTGATTTTCTAATCAATTGATAG
1 GCAAAATCAAG-AAGAAGAATAAATTGATTTTCTAATCAATTGATAG
* * *
29551762 GCAAATTCAAGTATAAGAATAAATTGATTTTCTAATCAATTGATAG
1 GCAAAATCAAGAAGAAGAATAAATTGATTTTCTAATCAATTGATAG
29551808 G-AAAATTCAAG
1 GCAAAA-TCAAG
29551819 TATATTTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.06
46 45 0.88
47 3 0.06
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (46 bp):
GCAAAATCAAGAAGAAGAATAAATTGATTTTCTAATCAATTGATAG
Found at i:29551819 original size:46 final size:46
Alignment explanation
Indices: 29551730--29551822 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
29551720 AATAAGAAAG
*
29551730 AAGAATAAATTGATTTTCTAATCAATTGATAGGCAAATTCAAGTAT
1 AAGAATAAATTGATTTTCTAATCAATTGATAGGAAAATTCAAGTAT
29551776 AAGAATAAATTGATTTTCTAATCAATTGATAGGAAAATTCAAGTAT
1 AAGAATAAATTGATTTTCTAATCAATTGATAGGAAAATTCAAGTAT
29551822 A
1 A
29551823 TTTTCAAGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (46 bp):
AAGAATAAATTGATTTTCTAATCAATTGATAGGAAAATTCAAGTAT
Found at i:29552420 original size:41 final size:41
Alignment explanation
Indices: 29552375--29552455 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
29552365 TGAGTTTGAA
29552375 CCAAAATTTGTAAGGTATTATTCTCAATTAATCATGCAGTG
1 CCAAAATTTGTAAGGTATTATTCTCAATTAATCATGCAGTG
29552416 CCAAAATTTGTAAGGTATTATTCTCAATTAATCATGCAGT
1 CCAAAATTTGTAAGGTATTATTCTCAATTAATCATGCAGT
29552456 AATATGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (41 bp):
CCAAAATTTGTAAGGTATTATTCTCAATTAATCATGCAGTG
Found at i:29560389 original size:21 final size:21
Alignment explanation
Indices: 29560351--29560390 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29560341 AAAAAGTCAT
* **
29560351 TTTAGGGTTTTAGTTTAGTAG
1 TTTAGGATTTTAACTTAGTAG
29560372 TTTAGGATTTTAACTTAGT
1 TTTAGGATTTTAACTTAGT
29560391 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTAGGATTTTAACTTAGTAG
Found at i:29565821 original size:12 final size:12
Alignment explanation
Indices: 29565801--29565840 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
29565791 AAATAAAAGG
*
29565801 AAATTAAAATTA
1 AAATAAAAATTA
29565813 AAATAAAAATTA
1 AAATAAAAATTA
29565825 ATAATAATAAATTA
1 A-AATAA-AAATTA
29565839 AA
1 AA
29565841 TGGACTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAAAATTA
Found at i:29573832 original size:49 final size:49
Alignment explanation
Indices: 29573779--29573876 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
29573769 ATGTCTTTTT
*
29573779 AATATGAAGTTTTTATGTTGTAATTGGGCCACTACTAAGCTAATGGATG
1 AATATGAAGTTTTTATGCTGTAATTGGGCCACTACTAAGCTAATGGATG
29573828 AATATGAAGTTTTTATGCTGTAATTGGGCCACTACTAAGCTAATGGATG
1 AATATGAAGTTTTTATGCTGTAATTGGGCCACTACTAAGCTAATGGATG
29573877 GCAATGGTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (49 bp):
AATATGAAGTTTTTATGCTGTAATTGGGCCACTACTAAGCTAATGGATG
Found at i:29574709 original size:51 final size:51
Alignment explanation
Indices: 29574647--29574748 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
29574637 AATTAAACAT
29574647 GGTTTATTTTGAATATAAACTGTTTCTATTAAGATGATTTAAATTTTATAA
1 GGTTTATTTTGAATATAAACTGTTTCTATTAAGATGATTTAAATTTTATAA
29574698 GGTTTATTTTGAATATAAACTGTTTCTATTAAGATGATTTAAATTTTATAA
1 GGTTTATTTTGAATATAAACTGTTTCTATTAAGATGATTTAAATTTTATAA
29574749 CTTTTTAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (51 bp):
GGTTTATTTTGAATATAAACTGTTTCTATTAAGATGATTTAAATTTTATAA
Found at i:29575213 original size:35 final size:34
Alignment explanation
Indices: 29575163--29575261 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 34
29575153 CATAGGTAAG
* *
29575163 TACATGTAAGCTTATATTGAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAA-TTGTATATTCGAC
* * * *
29575198 TGCATGTGAGGTTATATTGAATTTTAGTATTCGAT
1 TACATGTGAGCTTATATTGAATTGTA-TATTCGAC
*
29575233 TACATGTGAACTTATATTGAAATTGTATA
1 TACATGTGAGCTTATATTG-AATTGTATA
29575262 CTCAGATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 4 0.08
35 42 0.81
36 6 0.12
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (34 bp):
TACATGTGAGCTTATATTGAATTGTATATTCGAC
Found at i:29577472 original size:5 final size:5
Alignment explanation
Indices: 29577462--29577488 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29577452 TTGGTGTTAT
29577462 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
29577489 TATTCATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:29577488 original size:49 final size:49
Alignment explanation
Indices: 29577430--29577524 Score: 140
Period size: 49 Copynumber: 1.9 Consensus size: 49
29577420 GCTTTATTTT
29577430 ATATAATATATATTAATGGATTTTGGTGT-TATTAATATA-ATATAATATA
1 ATATAATATATATTAATGG-TTTTGGTGTATA-TAATATATATATAATATA
* *
29577479 ATATAATATATATTCATGGTTTTGTTGTATATAATATATATATAAT
1 ATATAATATATATTAATGGTTTTGGTGTATATAATATATATATAAT
29577525 TATGGTTATG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 15 0.36
49 27 0.64
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.48
Consensus pattern (49 bp):
ATATAATATATATTAATGGTTTTGGTGTATATAATATATATATAATATA
Found at i:29577550 original size:33 final size:34
Alignment explanation
Indices: 29577474--29577551 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
29577464 ATATAATATA
*
29577474 ATATAATATA-ATATATATTCATGGTTTTGTTGT
1 ATATAATATATATATATATTCATGGTTTGGTTGT
*
29577507 ATATAATATATATATA-ATT-ATGGTTATGGTTTT
1 ATATAATATATATATATATTCATGGTT-TGGTTGT
29577540 ATATAATATATA
1 ATATAATATATA
29577552 AATTTATGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 6 0.15
33 30 0.73
34 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.50
Consensus pattern (34 bp):
ATATAATATATATATATATTCATGGTTTGGTTGT
Found at i:29581050 original size:16 final size:16
Alignment explanation
Indices: 29581031--29581061 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29581021 CTTCTTCACT
29581031 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
29581047 TACTTACTTACTTAA
1 TACTCACTTACTTAA
29581062 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:29581067 original size:20 final size:20
Alignment explanation
Indices: 29581028--29581067 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29581018 AAACTTCTTC
* *
29581028 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
29581048 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
29581068 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:29581507 original size:55 final size:54
Alignment explanation
Indices: 29581253--29581507 Score: 224
Period size: 55 Copynumber: 4.8 Consensus size: 54
29581243 ACACGGGTAC
* * *
29581253 CTTACC-ATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * * *
29581302 CTTACC-ATTGACGTGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * *
29581355 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCC-T-TAGAAA
* * * * *
29581410 CTTATCAA-TGCCATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * *
29581463 TCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGCATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29581508 AAACCTTAAT
Statistics
Matches: 164, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
49 37 0.23
52 4 0.02
53 42 0.26
54 12 0.07
55 67 0.41
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:29586666 original size:31 final size:31
Alignment explanation
Indices: 29586613--29586671 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
29586603 TATTTTAGTT
* *
29586613 AATTTAGTTTTTCGGATCAACTCGAATAAAA
1 AATTAAGTTTTTCGGATCAACTCAAATAAAA
* *
29586644 AATTAAGTTTTTCGGTTTAACTCAAATA
1 AATTAAGTTTTTCGGATCAACTCAAATA
29586672 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
AATTAAGTTTTTCGGATCAACTCAAATAAAA
Found at i:29587557 original size:27 final size:27
Alignment explanation
Indices: 29587527--29587579 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
29587517 TTTTAATCAT
29587527 ATCTTTAAATAAATTGGAAAAATATTA
1 ATCTTTAAATAAATTGGAAAAATATTA
29587554 ATCTTTAAATAAATTGGAAAAATATT
1 ATCTTTAAATAAATTGGAAAAATATT
29587580 CTTTTGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (27 bp):
ATCTTTAAATAAATTGGAAAAATATTA
Found at i:29588233 original size:28 final size:27
Alignment explanation
Indices: 29588201--29588254 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
29588191 GTTCATGTCT
*
29588201 TCTCCAACAATCAAACAGTGGGAGGCCA
1 TCTCCAACAATCAAACACTGGG-GGCCA
* *
29588229 TCTCCGACAGTCAAACACTGGGGGCC
1 TCTCCAACAATCAAACACTGGGGGCC
29588255 TCGAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.30, C:0.31, G:0.24, T:0.15
Consensus pattern (27 bp):
TCTCCAACAATCAAACACTGGGGGCCA
Found at i:29589415 original size:37 final size:38
Alignment explanation
Indices: 29589340--29589417 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
29589330 AGTACACTTG
*
29589340 AACATATTTAAATATGGGTGTCAAAATATATAACCCTCA
1 AACATATTTAAATATGGATG-CAAAATATATAACCCTCA
* *
29589379 AACATATTTGAATATGGATG-AAAATATATAATCCTCA
1 AACATATTTAAATATGGATGCAAAATATATAACCCTCA
29589416 AA
1 AA
29589418 TGACCCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 18 0.50
39 18 0.50
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (38 bp):
AACATATTTAAATATGGATGCAAAATATATAACCCTCA
Found at i:29598354 original size:38 final size:38
Alignment explanation
Indices: 29598303--29598384 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
29598293 AAGACAAGAT
29598303 TGAAAAGTAAGTTGTTAAAATAACAATACTGAACCATA
1 TGAAAAGTAAGTTGTTAAAATAACAATACTGAACCATA
*
29598341 TGAAAAGTAAGTTGTTAAAATAATAATACTGAACCATA
1 TGAAAAGTAAGTTGTTAAAATAACAATACTGAACCATA
*
29598379 TCAAAA
1 TGAAAA
29598385 ATCTTCTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (38 bp):
TGAAAAGTAAGTTGTTAAAATAACAATACTGAACCATA
Found at i:29600740 original size:38 final size:38
Alignment explanation
Indices: 29600696--29600771 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
29600686 CATTCTTATT
29600696 CAGCAGTAAAAGAGTTATTTTGAAATAATATGTGAAGA
1 CAGCAGTAAAAGAGTTATTTTGAAATAATATGTGAAGA
29600734 CAGCAGTAAAAGAGTTATTTTGAAATAATATGTGAAGA
1 CAGCAGTAAAAGAGTTATTTTGAAATAATATGTGAAGA
29600772 GAGTAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (38 bp):
CAGCAGTAAAAGAGTTATTTTGAAATAATATGTGAAGA
Found at i:29624112 original size:23 final size:22
Alignment explanation
Indices: 29624067--29624110 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
29624057 ATTGGATTGG
*
29624067 TTTTAATATATTTTTTTATTTA
1 TTTTAATATATTTTATTATTTA
29624089 TTTTAAATATATTTATATTATT
1 TTTT-AATATATTT-TATTATT
29624111 ATAAACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTAATATATTTTATTATTTA
Found at i:29626361 original size:15 final size:15
Alignment explanation
Indices: 29626341--29626372 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29626331 AGTCTAGTCC
29626341 GGGGTACCTAAATTA
1 GGGGTACCTAAATTA
29626356 GGGGTACCTAAATTA
1 GGGGTACCTAAATTA
29626371 GG
1 GG
29626373 TCCATCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (15 bp):
GGGGTACCTAAATTA
Found at i:29627384 original size:14 final size:14
Alignment explanation
Indices: 29627365--29627394 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29627355 TTCGAGACCA
29627365 TTGTGCGAGTTTGG
1 TTGTGCGAGTTTGG
29627379 TTGTGCGAGTTTGG
1 TTGTGCGAGTTTGG
29627393 TT
1 TT
29627395 AATTGGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.40, T:0.47
Consensus pattern (14 bp):
TTGTGCGAGTTTGG
Found at i:29630131 original size:10 final size:10
Alignment explanation
Indices: 29630120--29630158 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
29630110 GATATTTCTT
*
29630120 ATAATTTTTT
1 ATAATTTTTA
*
29630130 ATAATTATTA
1 ATAATTTTTA
29630140 ATAATTTTTAA
1 ATAATTTTT-A
29630151 ATAATTTT
1 ATAATTTT
29630159 GTACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:29631427 original size:11 final size:11
Alignment explanation
Indices: 29631411--29631448 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
29631401 TGTGAATCGA
29631411 TTTTTCTTTCT
1 TTTTTCTTTCT
29631422 TTTTTCTTCTCT
1 TTTTTCTT-TCT
*
29631434 TTTTTCTTCCT
1 TTTTTCTTTCT
29631445 TTTT
1 TTTT
29631449 CCTATTCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:29636629 original size:19 final size:19
Alignment explanation
Indices: 29636579--29636635 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
29636569 TTGATGTTGA
* *
29636579 TAATTTTAATTTTCTCTTTT
1 TAATTATAA-TTTCTATTTT
* * *
29636599 TATTTCTTATTTCTATTTT
1 TAATTATAATTTCTATTTT
*
29636618 TAATTATAATTTTTATTT
1 TAATTATAATTTCTATTT
29636636 CTTTTTAGCA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TAATTATAATTTCTATTTT
Found at i:29641517 original size:150 final size:150
Alignment explanation
Indices: 29641295--29641597 Score: 516
Period size: 150 Copynumber: 2.0 Consensus size: 150
29641285 TAGTCGATAG
* * * * * *
29641295 TGTGATTATGGTTCCCGATGATCCTTGATGTTCGAGCTAGCTTCGGTAATCTATAAAACATGGAA
1 TGTGATGATAGTTCCCGATGATCCCTGATGTCCAAGCTAGCTTCGATAATCTATAAAACATGGAA
29641360 AGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAATAAAGTCATCAAATGAACA
66 AGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAATAAAGTCATCAAATGAACA
*
29641425 TTTACATATCAATTCAAGTA
131 TTTACATAACAATTCAAGTA
* *
29641445 TGTGATGATAGTTCCTGATGATCCCTGATGTCCAAGCTAGCTTTGATAATCTATAAAACATGGAA
1 TGTGATGATAGTTCCCGATGATCCCTGATGTCCAAGCTAGCTTCGATAATCTATAAAACATGGAA
*
29641510 AGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAATAAAGTCATCACATGAACA
66 AGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAATAAAGTCATCAAATGAACA
29641575 TTTACATAACAATTCAAGTA
131 TTTACATAACAATTCAAGTA
29641595 TGT
1 TGT
29641598 TTAACATGGT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (150 bp):
TGTGATGATAGTTCCCGATGATCCCTGATGTCCAAGCTAGCTTCGATAATCTATAAAACATGGAA
AGAACACACAAAGTAAGCTTTAAAAGCTTAGTAAGCCATATACAAATAAAGTCATCAAATGAACA
TTTACATAACAATTCAAGTA
Found at i:29651275 original size:48 final size:48
Alignment explanation
Indices: 29651216--29651308 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
29651206 CGCAGATCGA
29651216 AAGATTAAGTAAGTCAGCAACATTTCTTACTGACTTTCATGGGGGCGG
1 AAGATTAAGTAAGTCAGCAACATTTCTTACTGACTTTCATGGGGGCGG
* *
29651264 AAGATTGAGTAAGTCTGCAACATTTCTTACTGACTTTCATGGGGG
1 AAGATTAAGTAAGTCAGCAACATTTCTTACTGACTTTCATGGGGG
29651309 GAAAAGGCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (48 bp):
AAGATTAAGTAAGTCAGCAACATTTCTTACTGACTTTCATGGGGGCGG
Found at i:29652946 original size:55 final size:55
Alignment explanation
Indices: 29652862--29653026 Score: 258
Period size: 55 Copynumber: 3.0 Consensus size: 55
29652852 TTGGCAGCCC
*
29652862 ATTATTAGTAAACCTATCTAAAAGTTGGGCCTTGGACAATATATTTTCATATTAG
1 ATTATTAGTAAACCTATCTAAAAGTTGGGCCTTGGACAAGATATTTTCATATTAG
** * * *
29652917 ATTATTAGTAGGCCTATCTAAAAGTTGGGCTTTGGACAAGGTATTTTCATATTGG
1 ATTATTAGTAAACCTATCTAAAAGTTGGGCCTTGGACAAGATATTTTCATATTAG
* *
29652972 ATTATTAGTAAACTTATCTAAAAGTTGGGCCTTGAACAAGATATTTTCATATTAG
1 ATTATTAGTAAACCTATCTAAAAGTTGGGCCTTGGACAAGATATTTTCATATTAG
29653027 GGTTGGCTGC
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 97 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (55 bp):
ATTATTAGTAAACCTATCTAAAAGTTGGGCCTTGGACAAGATATTTTCATATTAG
Found at i:29655361 original size:3 final size:3
Alignment explanation
Indices: 29655353--29655380 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29655343 AAACCATACT
29655353 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29655381 AACTTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29658229 original size:30 final size:30
Alignment explanation
Indices: 29658193--29658254 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
29658183 ATAGTATTTT
*
29658193 ATATTTTTGTGGT-ACAGATGTTAGATGGAG
1 ATATTTTTGTGATGA-AGATGTTAGATGGAG
* *
29658223 ATATTTTTTTGATGAATATGTTAGATGGAG
1 ATATTTTTGTGATGAAGATGTTAGATGGAG
29658253 AT
1 AT
29658255 TTAATTGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.44
Consensus pattern (30 bp):
ATATTTTTGTGATGAAGATGTTAGATGGAG
Found at i:29673669 original size:24 final size:24
Alignment explanation
Indices: 29673642--29673721 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
29673632 TTACATGTCA
29673642 TTTACACCTCATTTAATTAGATTT
1 TTTACACCTCATTTAATTAGATTT
* * *
29673666 TTTA-ATCATCATTTAATGACATATCT
1 TTTACA-CCTCATTTAATTAGAT-T-T
* *
29673692 CATTTACACCTTATTTAATTAGACTT
1 --TTTACACCTCATTTAATTAGATTT
29673718 TTTA
1 TTTA
29673722 ATCACAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
23 1 0.02
24 21 0.50
25 1 0.02
26 2 0.05
27 1 0.02
28 15 0.36
29 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTACACCTCATTTAATTAGATTT
Found at i:29679149 original size:49 final size:53
Alignment explanation
Indices: 29679076--29679175 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 53
29679066 AAAGCAAATC
*
29679076 AGCAGCAAAGCAGTTACTAGAAAAAAA-T-A-A-CAGCAGGGCAGAGACGTAA
1 AGCAGCAAAGCAGTTACGAGAAAAAAATTAATAGCAGCAGGGCAGAGACGTAA
*
29679125 AGCAGCAAAGCAGTTGCCGA-AAAAAAATTAATAGCAGCAGGGCAGAGACGT
1 AGCAGCAAAGCAGTT-ACGAGAAAAAAATTAATAGCAGCAGGGCAGAGACGT
29679176 GAAGATAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
49 22 0.50
50 3 0.07
51 1 0.02
52 1 0.02
53 17 0.39
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (53 bp):
AGCAGCAAAGCAGTTACGAGAAAAAAATTAATAGCAGCAGGGCAGAGACGTAA
Found at i:29679368 original size:62 final size:62
Alignment explanation
Indices: 29679220--29679356 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 62
29679210 AAAGCAAATC
* *
29679220 AGCAGCAAAGCAGTTGCTGAAAAAAATAACAGCAAGGCAAAGACGTGAAGCAGAGTAATTGA
1 AGCAGCAAAGCAGTTGCTGAAAAAAATAACAGCAAGGCAAAGACATGAAGCAGAGTAAGTGA
* * * *
29679282 AGCAGCAAAGCAGTTGCTGAAAAAAATAACAGTAGGGCAGAGACATGAAGCAGAG-ACGTGA
1 AGCAGCAAAGCAGTTGCTGAAAAAAATAACAGCAAGGCAAAGACATGAAGCAGAGTAAGTGA
*
29679343 AGCAACAAAGCAGT
1 AGCAGCAAAGCAGT
29679357 CGCAGGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
61 17 0.25
62 51 0.75
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (62 bp):
AGCAGCAAAGCAGTTGCTGAAAAAAATAACAGCAAGGCAAAGACATGAAGCAGAGTAAGTGA
Found at i:29680546 original size:44 final size:44
Alignment explanation
Indices: 29680477--29680568 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
29680467 CCGAAATAAC
29680477 AGTAACAGTACGACACACGAGGTGCCTCATCAACTCGAA-GTCGA
1 AGTAACAGTACGACACACGAGGTGCCTCATCAACTC-AAGGTCGA
* *
29680521 AGTAACAGTACGACACTTA-TA-GTGCCTCATCGACTCAAGGTCGA
1 AGTAACAGTACGACAC--ACGAGGTGCCTCATCAACTCAAGGTCGA
29680565 AGTA
1 AGTA
29680569 TCCCTGAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 2 0.05
44 39 0.91
45 1 0.02
46 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (44 bp):
AGTAACAGTACGACACACGAGGTGCCTCATCAACTCAAGGTCGA
Found at i:29681434 original size:9 final size:9
Alignment explanation
Indices: 29681422--29681461 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29681412 CTGCTGTTCT
29681422 TTTTGTTTC
1 TTTTGTTTC
*
29681431 TTTTATTTC
1 TTTTGTTTC
*
29681440 TTTTCTTTC
1 TTTTGTTTC
*
29681449 TTTAGTTTC
1 TTTTGTTTC
29681458 TTTT
1 TTTT
29681462 ATTTACTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (9 bp):
TTTTGTTTC
Found at i:29681446 original size:14 final size:15
Alignment explanation
Indices: 29681427--29681484 Score: 70
Period size: 14 Copynumber: 4.1 Consensus size: 15
29681417 GTTCTTTTTG
29681427 TTTCTTTTATTT-CT
1 TTTCTTTTATTTACT
* *
29681441 TTTC-TTTCTTTA-G
1 TTTCTTTTATTTACT
29681454 TTTCTTTTATTTAC-
1 TTTCTTTTATTTACT
29681468 TTTCTTTTATTTACT
1 TTTCTTTTATTTACT
29681483 TT
1 TT
29681485 ATTGTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.27
14 25 0.68
15 2 0.05
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTTTTATTTACT
Found at i:29684139 original size:56 final size:54
Alignment explanation
Indices: 29684000--29684153 Score: 193
Period size: 55 Copynumber: 2.8 Consensus size: 54
29683990 TGACATGATA
* * *
29684000 CATGCTAGGTCCGGGAGCTTGTGTAGCCCCATTGAGAGGCATGTAATTATGTGTAG
1 CATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAGAGGC--GTGATTATGTGTAG
* * *
29684056 -ACGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAGAGGCGTGGTTATGTGTTG
1 CATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAGAGGCGTGATTATGTGTAG
* *
29684109 CATGCTAGGTCCGGGTGCTCTTATGTAGCCCTGTTGAGAGGCGTG
1 CATGCTAGGTCCGGGAG--CTTATGTAGCCCTATTGAGAGGCGTG
29684154 CTATGTTATG
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
53 11 0.13
54 14 0.16
55 36 0.42
56 25 0.29
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (54 bp):
CATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAGAGGCGTGATTATGTGTAG
Found at i:29686011 original size:33 final size:34
Alignment explanation
Indices: 29685969--29686037 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
29685959 GGAAGAAGAA
* *
29685969 GGCTTGAAAGGAAAA-AAGAAGAAGAAGATCTAG
1 GGCTTGAAAGGAAAAGAAAAAAAAGAAGATCTAG
29686002 GGCTTGAAAGGAAAAGAAAAAAAAGAAGATCTAG
1 GGCTTGAAAGGAAAAGAAAAAAAAGAAGATCTAG
29686036 GG
1 GG
29686038 TTTAGTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 15 0.45
34 18 0.55
ACGTcount: A:0.52, C:0.06, G:0.30, T:0.12
Consensus pattern (34 bp):
GGCTTGAAAGGAAAAGAAAAAAAAGAAGATCTAG
Found at i:29686128 original size:13 final size:13
Alignment explanation
Indices: 29686112--29686147 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
29686102 TTAGTTAGTG
29686112 TTTATTGTTATTT
1 TTTATTGTTATTT
29686125 TTTAATTGTTATTT
1 TTT-ATTGTTATTT
*
29686139 TTTTTTGTT
1 TTTATTGTT
29686148 TAAGGAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (13 bp):
TTTATTGTTATTT
Found at i:29701117 original size:42 final size:40
Alignment explanation
Indices: 29701069--29701180 Score: 98
Period size: 42 Copynumber: 2.7 Consensus size: 40
29701059 TGTTGTCTTA
* * *
29701069 AATCGATTCTTTGCTTTTTTGAATTGATTGTGTTCTTGATTG
1 AATCGATTCTTTG-TTGTTTGAATAGATTGT-TTATTGATTG
* * *
29701111 ACTCGATTATTTTTGTTGTTTGAATAGATTGTTTATTGTTTG
1 AATCGA-T-TCTTTGTTGTTTGAATAGATTGTTTATTGATTG
* * * *
29701153 AATCGATTCATTATTGCTTAAATAGATT
1 AATCGATTCTTTGTTGTTTGAATAGATT
29701181 CTTTGTTGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 16 0.29
41 1 0.02
42 18 0.32
43 16 0.29
44 5 0.09
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (40 bp):
AATCGATTCTTTGTTGTTTGAATAGATTGTTTATTGATTG
Found at i:29701151 original size:20 final size:20
Alignment explanation
Indices: 29701126--29701191 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
29701116 ATTATTTTTG
*
29701126 TTGTTTGAATAGATTGTTTA
1 TTGTTTGAATAGATTCTTTA
* *
29701146 TTGTTTGAATCGATTCATTA
1 TTGTTTGAATAGATTCTTTA
* * *
29701166 TTGCTTAAATAGATTCTTTG
1 TTGTTTGAATAGATTCTTTA
29701186 TTGTTT
1 TTGTTT
29701192 AACTCAATTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.55
Consensus pattern (20 bp):
TTGTTTGAATAGATTCTTTA
Found at i:29701751 original size:21 final size:22
Alignment explanation
Indices: 29701725--29701780 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
29701715 ACAGCGGTGG
*
29701725 CGGTGAGATTAG-TTACTGTAA
1 CGGTGAGATTAGAATACTGTAA
29701746 CGGTGAGATT-GAATACTGTAA
1 CGGTGAGATTAGAATACTGTAA
*
29701767 TGGTGAGATTAGAA
1 CGGTGAGATTAGAA
29701781 ATAATGGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (22 bp):
CGGTGAGATTAGAATACTGTAA
Found at i:29702157 original size:50 final size:50
Alignment explanation
Indices: 29702077--29702176 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
29702067 TCTTTTATAA
29702077 CAATAGTTTCCCTTAACAGCAGGAAGAGCCCATTTTTGCCTAAACATTTT
1 CAATAGTTTCCCTTAACAGCAGGAAGAGCCCATTTTTGCCTAAACATTTT
* *
29702127 CAATAGTTTCCCTTAACAGTAGGAATAGCCCATTTTTGCCTAAACATTTT
1 CAATAGTTTCCCTTAACAGCAGGAAGAGCCCATTTTTGCCTAAACATTTT
29702177 GAATTTTTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (50 bp):
CAATAGTTTCCCTTAACAGCAGGAAGAGCCCATTTTTGCCTAAACATTTT
Found at i:29707000 original size:36 final size:36
Alignment explanation
Indices: 29706935--29707008 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
29706925 ACTGCAAGTG
* ** *
29706935 GATAGACCCATGTGCCCACCCTTTTTTTGATTAAAT
1 GATAGACCCATGTGCCCACCATTGATTTGAATAAAT
* *
29706971 GATAGATCCATGTGCCCACTATTGATTTGAATAAAT
1 GATAGACCCATGTGCCCACCATTGATTTGAATAAAT
29707007 GA
1 GA
29707009 CCTTACTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (36 bp):
GATAGACCCATGTGCCCACCATTGATTTGAATAAAT
Found at i:29712847 original size:18 final size:18
Alignment explanation
Indices: 29712824--29712886 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
29712814 AATATAAAAC
29712824 ACATTCTATACAAACACA
1 ACATTCTATACAAACACA
* *
29712842 ACATTCAATTTAACATAAAAC-
1 ACATTC--TAT-ACA-AACACA
*
29712863 ACATTCCATACAAACACA
1 ACATTCTATACAAACACA
29712881 ACATTC
1 ACATTC
29712887 AATTTAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 4 0.11
18 15 0.43
19 1 0.03
20 2 0.06
21 9 0.26
22 4 0.11
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (18 bp):
ACATTCTATACAAACACA
Found at i:29712860 original size:39 final size:39
Alignment explanation
Indices: 29712817--29712897 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
29712807 TCACATAAAT
*
29712817 ATAAAACACATTCTATACAAACACAACATTCAATTTAAC
1 ATAAAACACATTCCATACAAACACAACATTCAATTTAAC
29712856 ATAAAACACATTCCATACAAACACAACATTCAATTTAAC
1 ATAAAACACATTCCATACAAACACAACATTCAATTTAAC
29712895 ATA
1 ATA
29712898 TTTACAAGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (39 bp):
ATAAAACACATTCCATACAAACACAACATTCAATTTAAC
Found at i:29712868 original size:21 final size:22
Alignment explanation
Indices: 29712839--29712897 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 22
29712829 CTATACAAAC
29712839 ACAACATTCAATTTAACATAAA
1 ACAACATTCAATTTAACATAAA
* *
29712861 AC-ACATTCCA--T-ACA-AAC
1 ACAACATTCAATTTAACATAAA
29712878 ACAACATTCAATTTAACATA
1 ACAACATTCAATTTAACATA
29712898 TTTACAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 1 0.03
20 1 0.03
21 10 0.34
22 3 0.10
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (22 bp):
ACAACATTCAATTTAACATAAA
Found at i:29713152 original size:90 final size:90
Alignment explanation
Indices: 29712994--29713346 Score: 690
Period size: 90 Copynumber: 3.9 Consensus size: 90
29712984 CGATCTAGCC
*
29712994 TCGAATTTGTGTTATCCGGATCTATATAAATGAA-TTAATCATCAATTTATCACATTTCATATTT
1 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
29713058 ATTTGGACTCAATTTACATTCTACT
66 ATTTGGACTCAATTTACATTCTACT
29713083 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
1 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
29713148 ATTTGGACTCAATTTACATTCTACT
66 ATTTGGACTCAATTTACATTCTACT
29713173 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
1 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
29713238 ATTTGGACTCAATTTACATTCTACT
66 ATTTGGACTCAATTTACATTCTACT
29713263 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
1 TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
29713328 ATTTGGACTCAATTTACAT
66 ATTTGGACTCAATTTACAT
29713347 CCTAGGTAAA
Statistics
Matches: 262, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
89 33 0.13
90 229 0.87
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.44
Consensus pattern (90 bp):
TCGAATTTGTGTTATCCAGATCTATATAAATGAATTTAATCATCAATTTATCACATTTCATATTT
ATTTGGACTCAATTTACATTCTACT
Found at i:29716374 original size:26 final size:25
Alignment explanation
Indices: 29716331--29716384 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
29716321 TTTGAAATCT
*
29716331 AAAAAAGTAAATGAACTAAACTTTAA
1 AAAAAAATAAATGAACTAAA-TTTAA
*
29716357 AAAAAAATACAATG-ACTAAATTTCA
1 AAAAAAATA-AATGAACTAAATTTAA
29716382 AAA
1 AAA
29716385 TTGTCGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 14 0.56
27 4 0.16
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAAAAATAAATGAACTAAATTTAA
Found at i:29723337 original size:21 final size:21
Alignment explanation
Indices: 29723313--29723358 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
29723303 TAAATGAATT
*
29723313 TTGAGAGAATTTGAGAGAGAA
1 TTGAGAGAATATGAGAGAGAA
* *
29723334 TT--GATAATATGAGAGAGAG
1 TTGAGAGAATATGAGAGAGAA
29723353 TTGAGA
1 TTGAGA
29723359 TTGAATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
19 16 0.80
21 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (21 bp):
TTGAGAGAATATGAGAGAGAA
Found at i:29732411 original size:28 final size:28
Alignment explanation
Indices: 29732371--29732428 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
29732361 AGTTATATTA
29732371 CAACAACCAAATTTGTGTTGCAAATCTT
1 CAACAACCAAATTTGTGTTGCAAATCTT
29732399 CAACAACCAAATTTGTGTTGCAAATCTT
1 CAACAACCAAATTTGTGTTGCAAATCTT
29732427 CA
1 CA
29732429 TCATTACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (28 bp):
CAACAACCAAATTTGTGTTGCAAATCTT
Found at i:29733546 original size:21 final size:22
Alignment explanation
Indices: 29733517--29733557 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
29733507 ATTAAATTTA
29733517 TTTATATAA-ATTAATAATATAT
1 TTTATATAATA-TAATAATATAT
29733539 TTTA-ATAATATAATAATAT
1 TTTATATAATATAATAATAT
29733558 GAAAAGTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATATAATATAATAATATAT
Found at i:29733863 original size:82 final size:82
Alignment explanation
Indices: 29733728--29733885 Score: 246
Period size: 82 Copynumber: 1.9 Consensus size: 82
29733718 GCCCTCCCAG
* * * *
29733728 AAAATGAAAATTTTCAATTTACTCCTCTTATAAATAAAAAAAATTATAAATTAATATATAGTGAA
1 AAAATGAAAATTTTCAATTCAATCCTCTTATAAATAAAAAAAATTATAAATTAATATATAATAAA
29733793 ATTACACTTTACCCTTC
66 ATTACACTTTACCCTTC
* *
29733810 AAAATGAAAAGTTTTCAATTCAATCCTCTTGTAAAT-AAAGAAATTATAAATTAATATATAATAA
1 AAAATGAAAA-TTTTCAATTCAATCCTCTTATAAATAAAAAAAATTATAAATTAATATATAATAA
29733874 AATTACACTTTA
65 AATTACACTTTA
29733886 GCCCCCCTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 47 0.68
83 22 0.32
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.36
Consensus pattern (82 bp):
AAAATGAAAATTTTCAATTCAATCCTCTTATAAATAAAAAAAATTATAAATTAATATATAATAAA
ATTACACTTTACCCTTC
Found at i:29737045 original size:50 final size:49
Alignment explanation
Indices: 29736985--29737151 Score: 170
Period size: 50 Copynumber: 3.5 Consensus size: 49
29736975 TGTCGATGAA
* *
29736985 ATGTCTCAAACATGGTCTTACACTGACTCTCACATATCTGTGCTGATGCC
1 ATGTCCCAAACATGGTCTTACACTGACTCTCACAT-TCTGTGCCGATGCC
*
29737035 ATGTCCCAAACATGGTCTTACACTGA----CACATTTTGTAGCCGATG-C
1 ATGTCCCAAACATGGTCTTACACTGACTCTCACATTCTGT-GCCGATGCC
* * * **
29737080 ATGTCCCAGACAT-GTCTTACACTAACTCT--CGTCTCAATGCCGATGCC
1 ATGTCCCAAACATGGTCTTACACTGACTCTCACAT-TCTGTGCCGATGCC
*
29737127 ATGTCCCAGACATGGTCTTACACTG
1 ATGTCCCAAACATGGTCTTACACTG
29737152 GTTCCCGTAA
Statistics
Matches: 99, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
44 11 0.11
45 17 0.17
46 20 0.20
47 16 0.16
48 10 0.10
50 25 0.25
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (49 bp):
ATGTCCCAAACATGGTCTTACACTGACTCTCACATTCTGTGCCGATGCC
Found at i:29737108 original size:94 final size:94
Alignment explanation
Indices: 29736985--29737197 Score: 232
Period size: 94 Copynumber: 2.3 Consensus size: 94
29736975 TGTCGATGAA
* * ** *
29736985 ATGTCTCAAACATGGTCTTACACTGACTCTCACATATCTGTGCTGATGCCATGTCCCAAACATGG
1 ATGTCCCAAACAT-GTCTTACACTAACTCT--CATATCAATGCCGATGCCATGTCCCAAACATGG
**
29737050 TCTTACACT-G-ACACATTTTGTAGCCGATGC
63 TCTTACACTGGTACACATAATGTAGCCGATGC
* * * *
29737080 ATGTCCCAGACATGTCTTACACTAACTCTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCT
1 ATGTCCCAAACATGTCTTACACTAACTCTCATATCAATGCCGATGCCATGTCCCAAACATGGTCT
* * * *
29737145 TACACTGGTTCCCGTAATGTGGCCGATGC
66 TACACTGGTACACATAATGTAGCCGATGC
* *
29737174 ATGTCCCATACATGTCTTGCACTA
1 ATGTCCCAAACATGTCTTACACTA
29737198 GTACACAATT
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
92 36 0.36
93 1 0.01
94 51 0.52
95 11 0.11
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (94 bp):
ATGTCCCAAACATGTCTTACACTAACTCTCATATCAATGCCGATGCCATGTCCCAAACATGGTCT
TACACTGGTACACATAATGTAGCCGATGC
Found at i:29742136 original size:18 final size:19
Alignment explanation
Indices: 29742110--29742152 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
29742100 ATAAAATAGT
*
29742110 TCGAGTTATTT-GAGTTAA-
1 TCGAATTATTTGGA-TTAAC
29742128 TCGAATTATTTGGATTAAC
1 TCGAATTATTTGGATTAAC
29742147 TCGAAT
1 TCGAAT
29742153 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGAATTATTTGGATTAAC
Found at i:29745007 original size:18 final size:18
Alignment explanation
Indices: 29744984--29745018 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29744974 GCTAGCTAAT
29744984 AAAAGAATCTAATCCTGC
1 AAAAGAATCTAATCCTGC
29745002 AAAAGAATCTAATCCTG
1 AAAAGAATCTAATCCTG
29745019 GATTTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAGAATCTAATCCTGC
Found at i:29752549 original size:35 final size:35
Alignment explanation
Indices: 29752503--29752572 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
29752493 CATCGTGGTG
*
29752503 GTGGTGAATCGATTTTCAAAGATCGTTGATTTTCT
1 GTGGTGAATCGATTTTCAAAAATCGTTGATTTTCT
29752538 GTGGTGAATCGATTTTCAAAAATCGTTGATTTTCT
1 GTGGTGAATCGATTTTCAAAAATCGTTGATTTTCT
29752573 TTTATGTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.43
Consensus pattern (35 bp):
GTGGTGAATCGATTTTCAAAAATCGTTGATTTTCT
Found at i:29758900 original size:23 final size:22
Alignment explanation
Indices: 29758869--29758914 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
29758859 TTATGAATCA
*
29758869 TATGTTTTGATATGACTTTGGTT
1 TATGATTTGATATG-CTTTGGTT
* *
29758892 TATGATTTGGTATGTTTTGGTT
1 TATGATTTGATATGCTTTGGTT
29758914 T
1 T
29758915 GGATATAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.15, C:0.02, G:0.24, T:0.59
Consensus pattern (22 bp):
TATGATTTGATATGCTTTGGTT
Found at i:29763625 original size:19 final size:21
Alignment explanation
Indices: 29763579--29763626 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
29763569 ATCGAGTGGT
*
29763579 TAATTAGACTTTAATTAAGTG
1 TAATTAGACTTTAATTAAGAG
29763600 -AATTTAG-C-TTAATTAAGAG
1 TAA-TTAGACTTTAATTAAGAG
29763619 TAATTAGA
1 TAATTAGA
29763627 AAAAAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
19 14 0.61
20 5 0.22
21 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (21 bp):
TAATTAGACTTTAATTAAGAG
Found at i:29763982 original size:9 final size:9
Alignment explanation
Indices: 29763968--29763997 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
29763958 AGATTTTTTT
29763968 ATAAAATAA
1 ATAAAATAA
29763977 ATAAAATAA
1 ATAAAATAA
29763986 ATAAAATAA
1 ATAAAATAA
29763995 ATA
1 ATA
29763998 GTTGAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAAATAA
Found at i:29769609 original size:23 final size:22
Alignment explanation
Indices: 29769578--29769623 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
29769568 TTATGAATCA
*
29769578 TATGTTTTGGTATGACTTTGGTT
1 TATGATTTGGTATG-CTTTGGTT
*
29769601 TATGATTTGGTATGTTTTGGTT
1 TATGATTTGGTATGCTTTGGTT
29769623 T
1 T
29769624 GGATATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.13, C:0.02, G:0.26, T:0.59
Consensus pattern (22 bp):
TATGATTTGGTATGCTTTGGTT
Found at i:29771816 original size:18 final size:19
Alignment explanation
Indices: 29771765--29771819 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
29771755 ATTACAAAAT
29771765 AATTCAAAATAATTT-TCAAA
1 AATTCAAAAT-ATTTAT-AAA
29771785 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
29771804 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
29771820 TCTTTAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 7 0.21
19 15 0.45
20 11 0.33
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:29772641 original size:31 final size:29
Alignment explanation
Indices: 29772590--29772647 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
29772580 AAAGATTATA
*
29772590 AAATAAAAATTTTAATAATTTAGTGATTT
1 AAATAAAAATTTTAATAATTTAATGATTT
*
29772619 AAATAAAATTTTTTAAATAATTTAATGAT
1 AAATAAAA-ATTTT-AATAATTTAATGAT
29772648 AGTATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 4 0.16
31 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (29 bp):
AAATAAAAATTTTAATAATTTAATGATTT
Found at i:29778361 original size:18 final size:20
Alignment explanation
Indices: 29778324--29778363 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29778314 ACTACTTCCA
29778324 ATTAATTAGTTCACTCTTCT
1 ATTAATTAGTTCACTCTTCT
*
29778344 ATTAGTTAGTT-A-TCTTCT
1 ATTAATTAGTTCACTCTTCT
29778362 AT
1 AT
29778364 ACTTATTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTAATTAGTTCACTCTTCT
Found at i:29781593 original size:167 final size:165
Alignment explanation
Indices: 29781370--29781845 Score: 657
Period size: 167 Copynumber: 2.8 Consensus size: 165
29781360 TCCCACACAA
* * *
29781370 CTGCAAATTTGCAATAATAAATTTGACTCAAACGGTGTCGTTTCATTACAAAGCATTAAACTTTT
1 CTGCAAATTTGCAAT-ACAAATTTGACTCCAACGGTGTCGTTTCATTACAAAGCATTAAAATTTT
* * *
29781435 AGTGACATTTTTAAAAAACGCCGCAAAATTGCAATAACCATTTGCCTTAAACAAGTCGTTTCACA
65 AGTGGCATTTTTAAAAAACGCCGCAAAGTTGCAAT-ACCATTTGCCTTAAACAAATCGTTTCACA
*
29781500 ACAGGGAACTAAATTTTTAGTTGCATTTTTCACAAAAG
129 ACAGGGAA-TAAATTTTTAGTGGCATTTTTCACAAAAG
* * * * *
29781538 CTGCAAACTTGCAATACCAATTCGACTCCAATGGCGTCGTTTCATTACAAAGCATTAAAATTTTA
1 CTGCAAATTTGCAATACAAATTTGACTCCAACGGTGTCGTTTCATTACAAAGCATTAAAATTTTA
* *
29781603 GTGGCATTTTTAAGAAATGCCGCAAAGTTGCAATACCATTTGCCTTAAACAACATCGTTTCACAA
66 GTGGCATTTTTAAAAAACGCCGCAAAGTTGCAATACCATTTGCCTTAAACAA-ATCGTTTCACAA
*
29781668 CAGGGAATTAAATTTTTAGTGGCATTTTTCACAAACG
130 CAGGGAA-TAAATTTTTAGTGGCATTTTTCACAAAAG
* * * *
29781705 CCGCAAATTTGCAATACTAATTTGTCTCCAACGGTGTTGTTTCATTACAAAGCATTAAAATTTTA
1 CTGCAAATTTGCAATACAAATTTGACTCCAACGGTGTCGTTTCATTACAAAGCATTAAAATTTTA
** * * * *
29781770 GTGGTGTTTTTAAAAAACGCCACAAAGTTGTAATACCATTTGCCTTAAA-AGACTACGTTTCAGA
66 GTGGCATTTTTAAAAAACGCCGCAAAGTTGCAATACCATTTGCCTTAAACA-AAT-CGTTTCACA
29781834 ACAGGGAATAAA
129 ACAGGGAATAAA
29781846 ATTCTTCCCT
Statistics
Matches: 273, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
166 24 0.09
167 235 0.86
168 14 0.05
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (165 bp):
CTGCAAATTTGCAATACAAATTTGACTCCAACGGTGTCGTTTCATTACAAAGCATTAAAATTTTA
GTGGCATTTTTAAAAAACGCCGCAAAGTTGCAATACCATTTGCCTTAAACAAATCGTTTCACAAC
AGGGAATAAATTTTTAGTGGCATTTTTCACAAAAG
Found at i:29781780 original size:84 final size:83
Alignment explanation
Indices: 29781385--29781811 Score: 356
Period size: 83 Copynumber: 5.1 Consensus size: 83
29781375 AATTTGCAAT
* * *
29781385 AATA-AATTTGACTCAAACGGTGTCGTTTCATTACAAAGCATTAAACTTTTAGTGACATTTTTAA
1 AATACAATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTAA
*
29781449 AAAACGCCGCAAAATTGC
66 AAAACGCCGCAAAGTTGC
* * * ** ** ** * * * *
29781467 AATAACCATTTGCCTTAAAC-AAGTCGTTTCACAACAGGGAACTAAATTTTTAGTTGCATTTTTC
1 AAT-ACAATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTT-
* * *
29781531 ACAAAA-GCTGCAAACTTGC
64 AAAAAACGCCGCAAAGTTGC
* * *
29781550 AATACCAATTCGACTCCAATGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTA
1 AATA-CAATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTA
* *
29781615 AGAAATGCCGCAAAGTTGC
65 AAAAACGCCGCAAAGTTGC
* * * ** * ** ** * * *
29781634 AATACCATTTGCCTTAAACAACATCGTTTCACAACAGGGAATTAAATTTTTAGTGGCATTTTTCA
1 AATACAATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTAA
* *
29781699 CAAACGCCGCAAATTTGC
66 AAAACGCCGCAAAGTTGC
* * * * **
29781717 AATACTAATTTGTCTCCAACGGTGTTGTTTCATTACAAAGCATTAAAATTTTAGTGGTGTTTTTA
1 AATAC-AATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTA
* *
29781782 AAAAACGCCACAAAGTTGT
65 AAAAACGCCGCAAAGTTGC
*
29781801 AATACCATTTG
1 AATACAATTTG
29781812 CCTTAAAAGA
Statistics
Matches: 259, Mismatches: 79, Indels: 13
0.74 0.23 0.04
Matches are distributed among these distances:
82 4 0.02
83 130 0.50
84 125 0.48
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (83 bp):
AATACAATTTGACTCAAACGGCGTCGTTTCATTACAAAGCATTAAAATTTTAGTGGCATTTTTAA
AAAACGCCGCAAAGTTGC
Found at i:29782070 original size:23 final size:20
Alignment explanation
Indices: 29782030--29782078 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 20
29782020 AAAATTTAAA
29782030 GTTTAGTGTTTAAGGTTTCGT
1 GTTTAGTGTTTAAGGTTT-GT
29782051 GTTTAGTGATTATAAGGTTTGT
1 GTTTAGTG-TT-TAAGGTTTGT
29782073 GATTTA
1 G-TTTA
29782079 TGGTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 5 0.20
23 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (20 bp):
GTTTAGTGTTTAAGGTTTGT
Found at i:29782310 original size:21 final size:20
Alignment explanation
Indices: 29782285--29782333 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
29782275 GATTTAGGGT
29782285 TTTAGGGCTAGGGTTATATGG
1 TTTAGGGCTAGGGTT-TATGG
* *
29782306 TTTAGGGGTTATGGTTTATGG
1 TTTA-GGGCTAGGGTTTATGG
29782327 TTTAGGG
1 TTTAGGG
29782334 TTTTATGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.16, C:0.02, G:0.39, T:0.43
Consensus pattern (20 bp):
TTTAGGGCTAGGGTTTATGG
Found at i:29782335 original size:14 final size:14
Alignment explanation
Indices: 29782268--29782336 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
29782258 TAAGATTTGC
*
29782268 GGTTTATGATTTAG
1 GGTTTATGGTTTAG
**
29782282 GGTTT-TAGGGCTAG
1 GGTTTAT-GGTTTAG
29782296 GGTTATATGGTTTAG
1 GGTT-TATGGTTTAG
* *
29782311 GGGTTATGGTTTAT
1 GGTTTATGGTTTAG
*
29782325 GGTTTAGGGTTT
1 GGTTTATGGTTT
29782337 TATGGTGTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 1 0.02
14 32 0.74
15 9 0.21
16 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.36, T:0.46
Consensus pattern (14 bp):
GGTTTATGGTTTAG
Found at i:29784637 original size:26 final size:26
Alignment explanation
Indices: 29784601--29784652 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29784591 GATATTAAAG
*
29784601 GTACTAAAGCTATTTGCAATTTTTTT
1 GTACTAAAGCTATCTGCAATTTTTTT
29784627 GTACTAAAGCTATCTGCAATTTTTTT
1 GTACTAAAGCTATCTGCAATTTTTTT
29784653 TCTCTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (26 bp):
GTACTAAAGCTATCTGCAATTTTTTT
Found at i:29785134 original size:9 final size:9
Alignment explanation
Indices: 29785120--29785268 Score: 133
Period size: 9 Copynumber: 16.6 Consensus size: 9
29785110 AGATGCTAAT
29785120 CATAACTTA
1 CATAACTTA
*
29785129 CATAACTCA
1 CATAACTTA
*
29785138 CATAATTTA
1 CATAACTTA
29785147 CATAACTTA
1 CATAACTTA
29785156 CATAACTTA
1 CATAACTTA
*
29785165 CATAATTTA
1 CATAACTTA
29785174 CATAACTTA
1 CATAACTTA
* *
29785183 CATAAATAAA
1 CATAACT-TA
*
29785193 CAT--CATA
1 CATAACTTA
29785200 TCATAACTTA
1 -CATAACTTA
29785210 CATAACTTA
1 CATAACTTA
** *
29785219 CGCAATTTA
1 CATAACTTA
29785228 CATAACTTA
1 CATAACTTA
*
29785237 CATAA-ATA
1 CATAACTTA
* * *
29785245 TATATCATA
1 CATAACTTA
29785254 TCATAACTTA
1 -CATAACTTA
29785264 CATAA
1 CATAA
29785269 TTTATTACCA
Statistics
Matches: 110, Mismatches: 24, Indels: 12
0.75 0.16 0.08
Matches are distributed among these distances:
7 1 0.01
8 8 0.07
9 88 0.80
10 13 0.12
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:29785154 original size:27 final size:27
Alignment explanation
Indices: 29785120--29785268 Score: 167
Period size: 27 Copynumber: 5.5 Consensus size: 27
29785110 AGATGCTAAT
*
29785120 CATAACTTACATAACTCACATAATTTA
1 CATAACTTACATAACTTACATAATTTA
29785147 CATAACTTACATAACTTACATAATTTA
1 CATAACTTACATAACTTACATAATTTA
* * * *
29785174 CATAACTTACATAAATAAACATCATAT-
1 CATAACTTACATAACT-TACATAATTTA
**
29785201 CATAACTTACATAACTTACGCAATTTA
1 CATAACTTACATAACTTACATAATTTA
* * * *
29785228 CATAACTTACATAAATATATATCATAT-
1 CATAACTTACATAACT-TACATAATTTA
29785255 CATAACTTACATAA
1 CATAACTTACATAA
29785269 TTTATTACCA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
26 5 0.05
27 85 0.83
28 12 0.12
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (27 bp):
CATAACTTACATAACTTACATAATTTA
Found at i:29785205 original size:54 final size:54
Alignment explanation
Indices: 29785120--29785268 Score: 210
Period size: 54 Copynumber: 2.8 Consensus size: 54
29785110 AGATGCTAAT
* * * * *
29785120 CATAACTTACATAACT-CACATAATTTACATAACTTACATAACTTACATAATTTA
1 CATAACTTACATAAATAAACATCATAT-CATAACTTACATAACTTACACAATTTA
*
29785174 CATAACTTACATAAATAAACATCATATCATAACTTACATAACTTACGCAATTTA
1 CATAACTTACATAAATAAACATCATATCATAACTTACATAACTTACACAATTTA
* *
29785228 CATAACTTACATAAATATATATCATATCATAACTTACATAA
1 CATAACTTACATAAATAAACATCATATCATAACTTACATAA
29785269 TTTATTACCA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 79 0.92
55 7 0.08
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (54 bp):
CATAACTTACATAAATAAACATCATATCATAACTTACATAACTTACACAATTTA
Found at i:29789657 original size:28 final size:27
Alignment explanation
Indices: 29789607--29789720 Score: 97
Period size: 28 Copynumber: 3.9 Consensus size: 27
29789597 CTATTCAGAA
*
29789607 ATCAGTGTTAA-CTGGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
29789634 ATCAGTATTAATCTGGGCCATAGCCC-T
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
* *
29789661 ATTACAATATCAGAGTATACTGGGCCTAGCCCAT
1 A-T-CAGTAT--TA--AT-CTGGGCCTAGCCCAT
29789695 ATCAGTATTAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCC-TAGCCC
29789721 TATTACAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
27 19 0.27
28 22 0.31
29 5 0.07
30 1 0.01
31 1 0.01
32 5 0.07
33 9 0.13
34 9 0.13
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAATCTGGGCCTAGCCCAT
Found at i:29789719 original size:61 final size:59
Alignment explanation
Indices: 29789584--29789758 Score: 219
Period size: 61 Copynumber: 2.9 Consensus size: 59
29789574 TCAAGCTTTA
* *
29789584 CTGGGCCTAAGCCCTATTCAGAAATCAGTGT-TAACTGGGCCTTAGCCCATATCAGTATTAAT
1 CTGGGCCT-AGCCCTATT-ACAAATCAGAGTAT-ACTGGGCC-TAGCCCATATCAGTATTAAT
29789646 CTGGGCCATAGCCCTATTACAATATCAGAGTATACTGGGCCTAGCCCATATCAGTATTAAT
1 CTGGGCC-TAGCCCTATTACAA-ATCAGAGTATACTGGGCCTAGCCCATATCAGTATTAAT
* * *
29789707 CTGGGCCGTAGCCCTATTACAAGTC-GAGATATATTGGGCCTTGCCCATATCA
1 CTGGGCC-TAGCCCTATTACAAATCAGAG-TATACTGGGCCTAGCCCATATCA
29789759 ACACAGTTGG
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
59 3 0.03
60 23 0.22
61 44 0.43
62 31 0.30
63 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (59 bp):
CTGGGCCTAGCCCTATTACAAATCAGAGTATACTGGGCCTAGCCCATATCAGTATTAAT
Found at i:29797653 original size:19 final size:19
Alignment explanation
Indices: 29797621--29797671 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29797611 ATCATTTATA
* *
29797621 TTTGCTATTT-CTGGTTGGC
1 TTTG-TATTTGCTGGATGAC
29797640 TTTGTATTTGCTGGATGAC
1 TTTGTATTTGCTGGATGAC
29797659 TTTGTATTTGCTG
1 TTTGTATTTGCTG
29797672 TTTTTGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.53
Consensus pattern (19 bp):
TTTGTATTTGCTGGATGAC
Found at i:29797890 original size:42 final size:42
Alignment explanation
Indices: 29797814--29797931 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
29797804 AAAATGTGAC
* *
29797814 CTTTAGCGGCGTTTTTCACTAAAGCGTCGCTAAAAGTCTTATT
1 CTTTAGCGGCGTTTTTC-TTAAAGCGCCGCTAAAAGTCTTATT
* * * *
29797857 CTTTAGCAGCATTTTTCTTAAAGTGCCGCTAAAAGTCTTGTT
1 CTTTAGCGGCGTTTTTCTTAAAGCGCCGCTAAAAGTCTTATT
29797899 CTTTAGCGGCGTTTTTCTTAAAGCGCCGCTAAA
1 CTTTAGCGGCGTTTTTCTTAAAGCGCCGCTAAA
29797932 GTTCATGTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 51 0.77
43 15 0.23
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTCTTAAAGCGCCGCTAAAAGTCTTATT
Done.