Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 7 of 325
Found at i:2234848 original size:21 final size:21
Alignment explanation
Indices: 2234813--2234951 Score: 118
Period size: 21 Copynumber: 6.5 Consensus size: 21
2234803 AGGCACTTTA
2234813 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
2234836 TGTGTCGTATCAGGCACTTCG
1 TGTGTCGTATCAGGCACCTCG
* * ** **
2234857 TGTGTCGTTTTAGGCATTTTA
1 TGTGTCGTATCAGGCACCTCG
*
2234878 TGTGTCGTATTTCAGGCACCTTG
1 TGTGTCGTA--TCAGGCACCTCG
*
2234901 TGTGTTGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * **
2234922 TGTGTCGTTTCAAGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
2234942 TGTGTCGTAT
1 TGTGTCGTAT
2234952 ACTGATCAGG
Statistics
Matches: 95, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
20 11 0.12
21 59 0.62
23 25 0.26
ACGTcount: A:0.14, C:0.20, G:0.26, T:0.40
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:2234863 original size:44 final size:43
Alignment explanation
Indices: 2234800--2234951 Score: 150
Period size: 44 Copynumber: 3.5 Consensus size: 43
2234790 GACTTTACTG
2234800 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCAC-TTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
* ** **
2234844 ATCAGGCACTTCGTGTGTCGT-TTT-AGGCATTTTATGTGTCGT
1 ATCAGGCACTT-ATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
* *
2234886 ATTTCAGGCACCTTGTGTGTTGTA--TCAGGCACCTCGTGTGTCGT
1 A--TCAGGCA-CTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
* *
2234930 TTCAAGCACTTATGTGTCGTAT
1 ATCAGGCACTTATGTGTCGTAT
2234952 ACTGATCAGG
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
41 11 0.13
42 21 0.24
43 6 0.07
44 46 0.53
45 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (43 bp):
ATCAGGCACTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
Found at i:2234911 original size:65 final size:64
Alignment explanation
Indices: 2234801--2234951 Score: 230
Period size: 65 Copynumber: 2.3 Consensus size: 64
2234791 ACTTTACTGA
*
2234801 TCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTT
1 TCAGGCA-TTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTT
* * *
2234866 TTAGGCATTTTATGTGTCGTATTTCAGGCACCTTGTGTGTTGTATCAGGCACCTCGTGTGTCGTT
1 TCAGGCA-TTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTT
* *
2234931 TCAAGCACTTATGTGTCGTAT
1 TCAGGCATTTATGTGTCGTAT
2234952 ACTGATCAGG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 13 0.17
65 65 0.83
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (64 bp):
TCAGGCATTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTT
Found at i:2237558 original size:7 final size:7
Alignment explanation
Indices: 2237546--2237624 Score: 54
Period size: 7 Copynumber: 10.6 Consensus size: 7
2237536 TATATAAAAA
2237546 TATATAT
1 TATATAT
2237553 TATATAT
1 TATATAT
2237560 TATATTAACT
1 TATA-T-A-T
2237570 TA-ATAT
1 TATATAT
2237576 T-TAAGTAT
1 TAT-A-TAT
2237584 TAATATAT
1 T-ATATAT
*
2237592 AATATAT
1 TATATAT
2237599 TATATTAT
1 TATA-TAT
2237607 TATATAT
1 TATATAT
* *
2237614 AATATAA
1 TATATAT
2237621 TATA
1 TATA
2237625 ATATATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.03
7 33 0.57
8 16 0.28
9 3 0.05
10 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:2237618 original size:20 final size:20
Alignment explanation
Indices: 2237547--2237632 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
2237537 ATATAAAAAT
* *
2237547 ATATATTATATATTATATTA
1 ATATATAATATATAATATTA
* *
2237567 A-CT-TAATATTTAAGTATTA
1 ATATATAATATATAA-TATTA
*
2237586 ATATATAATATATTATATTA
1 ATATATAATATATAATATTA
*
2237606 TTATAT-ATAATATAATA-TA
1 ATATATAAT-ATATAATATTA
2237625 ATATATAA
1 ATATATAA
2237633 AACATAAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
18 7 0.14
19 16 0.31
20 20 0.39
21 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
ATATATAATATATAATATTA
Found at i:2237619 original size:17 final size:17
Alignment explanation
Indices: 2237588--2237632 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2237578 AAGTATTAAT
2237588 ATATAATATAT--TATA
1 ATATAATATATAATATA
* *
2237603 TTATTATATATAATATA
1 ATATAATATATAATATA
2237620 ATATAATATATAA
1 ATATAATATATAA
2237633 AACATAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:2238786 original size:29 final size:31
Alignment explanation
Indices: 2238749--2238806 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
2238739 CTAGCGCGCT
2238749 TTCTGATTATTAGCACATT-AGTGCTCTCCG
1 TTCTGATTATTAGCACATTAAGTGCTCTCCG
*
2238779 TTCT-ATTATTAGCACGTTAAGTGCTCTC
1 TTCTGATTATTAGCACATTAAGTGCTCTC
2238807 TGTTTAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (31 bp):
TTCTGATTATTAGCACATTAAGTGCTCTCCG
Found at i:2238827 original size:22 final size:22
Alignment explanation
Indices: 2238798--2238854 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
2238788 TAGCACGTTA
2238798 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
2238821 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
2238842 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
2238855 CGTTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:2241325 original size:47 final size:47
Alignment explanation
Indices: 2241215--2241347 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 47
2241205 ATAATCTCAC
* * *
2241215 CCATAATGAACTCGGAACGCAACTCAATGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* * *
2241261 TCATAATGAACTTGGAACACAACTCAACGAGTTCGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
*
2241307 CCATAGGTGAACTCGGAACGCAACTCAAC-ATGTTCGGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGA-GTTCGGATGC
2241348 CTCATAATTC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 42 0.57
47 32 0.43
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (47 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
Found at i:2256113 original size:16 final size:14
Alignment explanation
Indices: 2256076--2256122 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2256066 AACTCTTGCG
2256076 TAAAA-TAAATAAA
1 TAAAATTAAATAAA
*
2256089 -AAGATTAAAGTAATA
1 TAAAATTAAA-TAA-A
2256104 TAAAATTAAATAAA
1 TAAAATTAAATAAA
2256118 TAAAA
1 TAAAA
2256123 ATCGAACGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 3 0.11
13 4 0.14
14 9 0.32
15 4 0.14
16 8 0.29
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
TAAAATTAAATAAA
Found at i:2256379 original size:13 final size:13
Alignment explanation
Indices: 2256361--2256386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2256351 TGCTGATAGT
2256361 AAAAAACAAAAAA
1 AAAAAACAAAAAA
2256374 AAAAAACAAAAAA
1 AAAAAACAAAAAA
2256387 TTAAGACGAA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:2257235 original size:18 final size:18
Alignment explanation
Indices: 2257214--2257255 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2257204 CATACATGAC
2257214 ATGCAAAACATAATAAAA
1 ATGCAAAACATAATAAAA
* *
2257232 ATGCAGAACATAATAGAA
1 ATGCAAAACATAATAAAA
2257250 ATGCAA
1 ATGCAA
2257256 CAATTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
ATGCAAAACATAATAAAA
Found at i:2271223 original size:12 final size:11
Alignment explanation
Indices: 2271201--2271233 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
2271191 TCCCCCACAC
2271201 TTTTT-CTTTT
1 TTTTTCCTTTT
2271211 TTTTTCCCTTTT
1 TTTTT-CCTTTT
2271223 TTTTTCCTTTT
1 TTTTTCCTTTT
2271234 CTCTCTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 6 0.29
12 10 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:2271472 original size:29 final size:29
Alignment explanation
Indices: 2271407--2271480 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
2271397 AAAGTATTTG
2271407 AAATTTTTTATTTAAATAATTGAACTATT
1 AAATTTTTTATTTAAATAATTGAACTATT
* * *
2271436 AAAGTTTTTATTTAAGTCATT-AAGCTATT
1 AAATTTTTTATTTAAATAATTGAA-CTATT
* *
2271465 AATTTTTTTTTTTAAA
1 AAATTTTTTATTTAAA
2271481 ATCTAGCTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (29 bp):
AAATTTTTTATTTAAATAATTGAACTATT
Found at i:2271796 original size:29 final size:29
Alignment explanation
Indices: 2271725--2271789 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2271715 ACAAATAGAG
*
2271725 AATGTCATAAAATATCGATTTTTACAATT
1 AATGACATAAAATATCGATTTTTACAATT
* *
2271754 AATGTCATAAAATATCGATTTTTACAGTT
1 AATGACATAAAATATCGATTTTTACAATT
2271783 CAATGAC
1 -AATGAC
2271790 TTGAATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
AATGACATAAAATATCGATTTTTACAATT
Found at i:2272199 original size:3 final size:3
Alignment explanation
Indices: 2272191--2272224 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2272181 TATTTGTATA
2272191 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2272225 CGATATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2303888 original size:59 final size:59
Alignment explanation
Indices: 2303819--2303937 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
2303809 AAACGCAACA
*
2303819 TATACTTATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTAAAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTAAAGT
* *
2303878 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTGCCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTAAAGT
2303937 T
1 T
2303938 TTACTCTCAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.53
Consensus pattern (59 bp):
TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTAAAGT
Found at i:2310111 original size:50 final size:50
Alignment explanation
Indices: 2310036--2310135 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2310026 CTTTGAAATG
2310036 TTGATATCAATGTGCTATATCAACTTACCTTGTTTATTAAATCTCCTCAA
1 TTGATATCAATGTGCTATATCAACTTACCTTGTTTATTAAATCTCCTCAA
2310086 TTGATATCAATGTGCTATATCAACTTACCTTGTTTATTAAATCTCCTCAA
1 TTGATATCAATGTGCTATATCAACTTACCTTGTTTATTAAATCTCCTCAA
2310136 AATAGATGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (50 bp):
TTGATATCAATGTGCTATATCAACTTACCTTGTTTATTAAATCTCCTCAA
Found at i:2311756 original size:31 final size:32
Alignment explanation
Indices: 2311711--2311776 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
2311701 TTTAATCACC
* *
2311711 TAATGATTTCAAT-AAAAA-TTATTAAATAATT
1 TAATGAGTTAAATAAAAAATTTATT-AATAATT
2311742 TAATGAGTTAAATAAAAAAATTTATTAATAATT
1 TAATGAGTTAAAT-AAAAAATTTATTAATAATT
2311775 TA
1 TA
2311777 TTATTTCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 11 0.37
33 14 0.47
34 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (32 bp):
TAATGAGTTAAATAAAAAATTTATTAATAATT
Found at i:2320406 original size:39 final size:39
Alignment explanation
Indices: 2320352--2320426 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
2320342 GGCATGTTCA
2320352 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
*
2320391 TTCAAGGTCAACATTTTTACTCTCTTCTCAATTTAA
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAA
2320427 CATTCTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
Found at i:2337122 original size:68 final size:68
Alignment explanation
Indices: 2337013--2337148 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
2337003 CCTTAAAGTT
2337013 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
1 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
2337078 TGC
66 TGC
2337081 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
1 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
2337146 TGC
66 TGC
2337149 TCCTGAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (68 bp):
GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
TGC
Found at i:2348081 original size:86 final size:86
Alignment explanation
Indices: 2347936--2348094 Score: 300
Period size: 86 Copynumber: 1.8 Consensus size: 86
2347926 CGGTTCACAT
2347936 ATTGTAACACCCCTTACCCGAGACCGTTGCCGGAATCGAGTACGAGGCATTACTTAGCTTATCTT
1 ATTGTAACACCCCTTACCCGAGACCGTTGCCGGAATCGAGTACGAGGCATTACTTAGCTTATCTT
*
2348001 CCTAATTCAATGACCACCAAA
66 ACTAATTCAATGACCACCAAA
*
2348022 ATTGTAACACCCCTTACCCGAGACCGTTGCCGGAATCGAGTACGAGGCATTATTTAGCTTATCTT
1 ATTGTAACACCCCTTACCCGAGACCGTTGCCGGAATCGAGTACGAGGCATTACTTAGCTTATCTT
2348087 ACTAATTC
66 ACTAATTC
2348095 GGGGCATAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (86 bp):
ATTGTAACACCCCTTACCCGAGACCGTTGCCGGAATCGAGTACGAGGCATTACTTAGCTTATCTT
ACTAATTCAATGACCACCAAA
Found at i:2351056 original size:45 final size:44
Alignment explanation
Indices: 2350981--2351084 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 44
2350971 TTTTCTTTTC
*
2350981 TTTCTTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTTCTTT-CTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
* *
2351026 TTTCTTTCTTTCTCCCTTCTCTGT-TTTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTC-CT-TCTCTGTTTCGTTTTGCTCTCTG
2351071 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
2351085 TTCTTTGTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
44 7 0.13
45 36 0.68
46 10 0.19
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (44 bp):
TTTCTTTCTTTCTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:2351132 original size:16 final size:18
Alignment explanation
Indices: 2351094--2351134 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2351084 TTTCTTTGTC
*
2351094 ATAT-ATATATAATATAT
1 ATATAATATAAAATATAT
2351111 ATATAATATAAAATAT-T
1 ATATAATATAAAATATAT
2351128 A-ATAATA
1 ATATAATA
2351135 ATCATTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 6 0.27
18 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATATAAAATATAT
Found at i:2351163 original size:11 final size:11
Alignment explanation
Indices: 2351094--2351120 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2351084 TTTCTTTGTC
2351094 ATATATATATA
1 ATATATATATA
2351105 ATATATATATA
1 ATATATATATA
2351116 ATATA
1 ATATA
2351121 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATATATATA
Found at i:2356471 original size:53 final size:53
Alignment explanation
Indices: 2356359--2356523 Score: 194
Period size: 53 Copynumber: 3.1 Consensus size: 53
2356349 CTTACACGGT
* * *
2356359 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGT-TTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAACCCAG-CTATGGTCTTATACGGAGTCACATTA
*
2356413 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAGTCACATTA
** * *
2356466 TCACATTGCACTGATGCCATAACCCAGCTATGGTCTTAAACGG-G-CACACTTA
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAGTCACA-TTA
2356518 TCACAT
1 TCACAT
2356524 ATTTTTCGTC
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
51 5 0.05
52 33 0.33
53 56 0.56
54 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAGTCACATTA
Found at i:2362329 original size:56 final size:56
Alignment explanation
Indices: 2362252--2362427 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
2362242 ATAAGGGATG
*
2362252 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2362308 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2362364 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2362420 ATGGGCAA
1 ATGGGCAA
2362428 CAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:2363787 original size:40 final size:40
Alignment explanation
Indices: 2363556--2363780 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
2363546 TCGAATGATG
* * * *
2363556 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
2363596 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2363636 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2363675 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2363715 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
2363756 -CCGGGCTATGTCCCGAATGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2363781 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2363802 original size:119 final size:119
Alignment explanation
Indices: 2363556--2363813 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
2363546 TCGAATGATG
* *
2363556 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
2363621 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
2363675 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
2363738 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAATGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
2363795 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
2363814 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.72
120 30 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:2365967 original size:17 final size:17
Alignment explanation
Indices: 2365927--2365970 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2365917 ATTATGAGCC
*
2365927 TAAAAAAAACTAAATAG
1 TAAAAAATACTAAATAG
* *
2365944 TATAAAAATACTTATTAG
1 TA-AAAAATACTAAATAG
2365962 TAAAAAATA
1 TAAAAAATA
2365971 ATAATATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
TAAAAAATACTAAATAG
Found at i:2371217 original size:46 final size:46
Alignment explanation
Indices: 2371167--2371342 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
2371157 TGGTTGAGCA
*
2371167 TCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2371213 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
2371258 CATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2371306 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2371343 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2371323 original size:93 final size:93
Alignment explanation
Indices: 2371164--2371335 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
2371154 GGATGGTTGA
* * *
2371164 GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2371229 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
2371257 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2371322 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2371336 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2374110 original size:135 final size:135
Alignment explanation
Indices: 2373931--2374580 Score: 1030
Period size: 135 Copynumber: 4.8 Consensus size: 135
2373921 TTTCGATCCA
* * * * * ** *
2373931 TGGAGATAAGATTCACCGAAATTTGGTCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * * *
2373996 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGTTTAATCGCCG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCCG
2374061 GTACG
131 GTACG
*
2374066 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * *
2374131 ATTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCTG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCCG
2374196 GTACG
131 GTACG
* *
2374201 TGGAGATAAGATTCTCCAAAATTCGATCTACTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * *
2374266 ATTTAGCCTGCTCCACTCCTGCTTAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGTCG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCCG
2374331 GTACG
131 GTACG
* * *
2374336 TGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
*
2374401 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCTG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCCG
2374466 GTACG
131 GTACG
* *
2374471 TGGAGATAAGATTCTCCAAAACTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCGGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * *
2374536 GTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGAT
2374581 ATCTGTCTTT
Statistics
Matches: 477, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 477 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (135 bp):
TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCAATCGCCG
GTACG
Found at i:2374154 original size:45 final size:44
Alignment explanation
Indices: 2374099--2374301 Score: 135
Period size: 45 Copynumber: 4.5 Consensus size: 44
2374089 TGATCTGCTT
* *
2374099 CACTCTTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTACTC
1 CACTCCTGCTCAGTGAAGATAAGATCT-GTATATTTAGCCTACTC
* * ** *
2374144 CACTCCTGCTCAGTGAAGATAAGGT-TG-ATGATTGGAATCTGCTC
1 CACTCCTGCTCAGTGAAGATAAGATCTGTAT-ATT-TAGCCTACTC
* * ** * * * * *
2374188 CA-TCGCTGGT-ACGTGGAGATAAGATTCTCCAAAATTCGATCTACTT
1 CACTC-CTGCTCA-GTGAAGATAAGA-TCTGTATATTTAG-CCTACTC
* *
2374234 CACTCCTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTGCTC
1 CACTCCTGCTCAGTGAAGATAAGATCT-GTATATTTAGCCTACTC
*
2374279 CACTCCTGCTTAGTGAAGATAAG
1 CACTCCTGCTCAGTGAAGATAAG
2374302 GTTGATGATT
Statistics
Matches: 116, Mismatches: 31, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.06
44 23 0.20
45 51 0.44
46 29 0.25
47 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CACTCCTGCTCAGTGAAGATAAGATCTGTATATTTAGCCTACTC
Found at i:2382353 original size:21 final size:21
Alignment explanation
Indices: 2382329--2382373 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2382319 GCTGGCTCAT
*
2382329 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
* *
2382350 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
2382371 CAT
1 CAT
2382374 TTGATCATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:2385886 original size:9 final size:9
Alignment explanation
Indices: 2385872--2385897 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2385862 TAAAAAATGT
2385872 ATTTATTTA
1 ATTTATTTA
2385881 ATTTATTTA
1 ATTTATTTA
2385890 ATTTATTT
1 ATTTATTT
2385898 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTATTTA
Found at i:2398156 original size:2 final size:2
Alignment explanation
Indices: 2398149--2398230 Score: 58
Period size: 2 Copynumber: 45.0 Consensus size: 2
2398139 ATTCTAGTTA
*
2398149 AT AT AT AT AT AT AT AT AT AT AT AT AT GT A- AGT A- AT GAT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT
*
2398190 -T AT -T A- AT AT -T TT AT AT -T AT AT -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2398225 AT AT AT
1 AT AT AT
2398231 GACAAAGAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 24
0.71 0.03 0.26
Matches are distributed among these distances:
1 10 0.15
2 52 0.80
3 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2398296 original size:40 final size:40
Alignment explanation
Indices: 2398239--2398334 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
2398229 ATGACAAAGA
2398239 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
2398280 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
2398320 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
2398335 GAAATAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:2401694 original size:47 final size:46
Alignment explanation
Indices: 2401620--2401768 Score: 141
Period size: 47 Copynumber: 3.2 Consensus size: 46
2401610 GGGAGTTTAG
*
2401620 CGTGCTCTCTGAT-TATTAGCACATCAGTGCTCTCTGTTTAGCACAT
1 CGTGCTCTCTGATAT-TTAGCACGTCAGTGCTCTCTGTTTAGCACAT
2401666 CGGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGAATATTAG--CA-
1 C-GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG--T-TTAGCACAT
* * *
2401713 C--GCTCTCTGATCA-CTAGCACGTTAGTGCTCTCCGTTTAGCACATT
1 CGTGCTCTCTGAT-ATTTAGCACGTCAGTGCTCTCTGTTTAGCACA-T
*
2401758 TGTGCTCTCTG
1 CGTGCTCTCTG
2401769 TACAGTCCCG
Statistics
Matches: 86, Mismatches: 5, Indels: 23
0.75 0.04 0.20
Matches are distributed among these distances:
41 4 0.05
42 1 0.01
43 2 0.02
44 28 0.33
45 1 0.01
46 1 0.01
47 41 0.48
48 3 0.03
49 1 0.01
50 4 0.05
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (46 bp):
CGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACAT
Found at i:2401714 original size:25 final size:24
Alignment explanation
Indices: 2401621--2401713 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 24
2401611 GGAGTTTAGC
2401621 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGA-TATTAGCACATCA
*
2401646 GTGCTCTCTG-T-TTAGCACATCG
1 GTGCTCTCTGATATTAGCACATCA
*
2401668 GTGCTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGATA-TTAGCACATCA
2401693 GTGCTCTCTGAATATTAGCAC
1 GTGCTCTCTG-ATATTAGCAC
2401714 GCTCTCTGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
22 20 0.33
23 2 0.03
25 36 0.59
26 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (24 bp):
GTGCTCTCTGATATTAGCACATCA
Found at i:2401730 original size:19 final size:19
Alignment explanation
Indices: 2401695--2401733 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2401685 GCACGTCAGT
*
2401695 GCTCTCTGAATATTAGCAC
1 GCTCTCTGAATACTAGCAC
2401714 GCTCTCTG-ATCACTAGCAC
1 GCTCTCTGAAT-ACTAGCAC
2401733 G
1 G
2401734 TTAGTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (19 bp):
GCTCTCTGAATACTAGCAC
Found at i:2402681 original size:13 final size:13
Alignment explanation
Indices: 2402665--2402692 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2402655 CGATTTCTTC
2402665 TGGGTATTCTATA
1 TGGGTATTCTATA
2402678 TGGGTATTCTATA
1 TGGGTATTCTATA
2402691 TG
1 TG
2402693 CTCTTTTATC
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:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:2403007 original size:12 final size:12
Alignment explanation
Indices: 2402992--2403031 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2402982 TTCTTCTTTT
2402992 GGATTTTCTCTG
1 GGATTTTCTCTG
* * *
2403004 GGATATTCTTTT
1 GGATTTTCTCTG
2403016 GGATTTTCTCTG
1 GGATTTTCTCTG
2403028 GGAT
1 GGAT
2403032 ATCATCGATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (12 bp):
GGATTTTCTCTG
Found at i:2403017 original size:24 final size:24
Alignment explanation
Indices: 2402985--2403033 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2402975 AGTGATATTC
2402985 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
2403009 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
2403033 T
1 T
2403034 CATCGATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
TTCTTTTGGATTTTCTCTGGGATA
Found at i:2404766 original size:40 final size:40
Alignment explanation
Indices: 2404709--2404804 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
2404699 ATGACAAAGA
2404709 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
2404750 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
2404790 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
2404805 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:2408847 original size:48 final size:52
Alignment explanation
Indices: 2408777--2408875 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
2408767 AATAATTATT
2408777 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
2408825 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
2408876 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:2408857 original size:17 final size:17
Alignment explanation
Indices: 2408832--2408865 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2408822 ATAATTTTAA
*
2408832 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
2408849 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
2408866 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:2408882 original size:17 final size:16
Alignment explanation
Indices: 2408837--2408884 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2408827 TTTAAATTTT
2408837 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
2408854 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
2408868 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
2408885 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:2408939 original size:54 final size:54
Alignment explanation
Indices: 2408881--2409059 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
2408871 ATAATCATAT
2408881 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
2408935 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
2408998 TA
54 -A
*
2409000 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
2409055 ATTAT
1 ATTAT
2409060 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:2408942 original size:61 final size:61
Alignment explanation
Indices: 2408877--2409064 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
2408867 AGTTATAATC
2408877 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
2408938 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
2408997 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
2409058 ATATATT
1 ATATATT
2409065 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:2408956 original size:18 final size:17
Alignment explanation
Indices: 2408925--2408959 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2408915 ATTATTAAGA
2408925 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
2408942 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
2408960 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:2408998 original size:120 final size:120
Alignment explanation
Indices: 2408874--2409096 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
2408864 ATTAGTTATA
2408874 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
2408939 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
2408994 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
2409059 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
2409097 TAAATATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:2409073 original size:18 final size:17
Alignment explanation
Indices: 2409045--2409079 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2409035 ATTATTAAGA
*
2409045 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2409062 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2409080 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2409091 original size:54 final size:54
Alignment explanation
Indices: 2408908--2409093 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
2408898 TTCATATAAG
* *
2408908 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
2408962 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
2409025 AAG
53 -TT
* *
2409028 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
2409082 AATAATAATTAT
1 AATAATAATTAT
2409094 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:2409200 original size:144 final size:147
Alignment explanation
Indices: 2409033--2409304 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
2409023 ATAAGAATAT
*
2409033 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
2409098 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
2409160 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
2409177 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
2409242 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
2409305 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:2409217 original size:18 final size:17
Alignment explanation
Indices: 2409189--2409223 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2409179 ATTATTAAGA
*
2409189 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2409206 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2409224 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2409434 original size:44 final size:45
Alignment explanation
Indices: 2409385--2409479 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
2409375 TTATACCTCT
* *
2409385 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
2409429 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
2409474 ATTACA
1 ATTACA
2409480 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:2409479 original size:16 final size:16
Alignment explanation
Indices: 2409458--2409490 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2409448 TTGATTTGCT
*
2409458 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
2409474 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
2409490 A
1 A
2409491 ATCCAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:2417878 original size:3 final size:3
Alignment explanation
Indices: 2417870--2417896 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2417860 TACTTTATAT
2417870 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2417897 TTTAATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2417952 original size:5 final size:5
Alignment explanation
Indices: 2417942--2417967 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2417932 TATAAGAAAA
2417942 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
2417968 TTACAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:2418056 original size:12 final size:13
Alignment explanation
Indices: 2418039--2418110 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 13
2418029 TTAATTTATT
2418039 TTAATAATAA-TA
1 TTAATAATAATTA
2418051 TTAATAATAATTA
1 TTAATAATAATTA
*
2418064 TT-ATAATTTAATAA
1 TTAATAA--TAATTA
* *
2418078 TTTAATATAAAACTA
1 -TTAATA-ATAATTA
2418093 -TAATAATAATTA
1 TTAATAATAATTA
2418105 -TAATAA
1 TTAATAA
2418111 ATATCTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 25 0.52
13 9 0.19
14 5 0.10
15 5 0.10
16 3 0.06
17 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAATAATAATTA
Found at i:2418098 original size:29 final size:29
Alignment explanation
Indices: 2418043--2418099 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2418033 TTTATTTTAA
* * *
2418043 TAATAATATTAATAATAATTATTATAATT
1 TAATAATATTAATAAAAACTATAATAATT
2418072 TAATAAT-TTAATATAAAACTATAATAAT
1 TAATAATATTAATA-AAAACTATAATAAT
2418100 AATTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATAATATTAATAAAAACTATAATAATT
Found at i:2418123 original size:24 final size:23
Alignment explanation
Indices: 2418069--2418125 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2418059 AATTATTATA
2418069 ATTTAATAATTTAATATAAAACT
1 ATTTAATAATTTAATATAAAACT
* *
2418092 ATAATAATAATTATAATA-AATATCT
1 AT-TTAATAATT-TAATATAA-AACT
2418117 ATTTAATAA
1 ATTTAATAA
2418126 CAAATACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 16 0.57
25 10 0.36
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAATAATTTAATATAAAACT
Found at i:2425399 original size:19 final size:20
Alignment explanation
Indices: 2425359--2425408 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2425349 CTTTATGTAA
2425359 TTAAAATAAATTATATTATT
1 TTAAAATAAATTATATTATT
*
2425379 TTAAAATAATTTAATATT-TT
1 TTAAAATAAATT-ATATTATT
*
2425399 TAAAAATAAA
1 TTAAAATAAA
2425409 ATTTGAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATAAATTATATTATT
Found at i:2425546 original size:17 final size:17
Alignment explanation
Indices: 2425508--2425546 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2425498 GTAATATATA
*
2425508 CAATTTATTATCTTTAT
1 CAATTTATTATCTTCAT
*
2425525 CAATTTATTGTCTTCAT
1 CAATTTATTATCTTCAT
*
2425542 TAATT
1 CAATT
2425547 GCAGATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (17 bp):
CAATTTATTATCTTCAT
Found at i:2426317 original size:29 final size:28
Alignment explanation
Indices: 2426252--2426319 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2426242 CTTTTCACAA
2426252 ATTTAAAATTTAATATTTGTACTTTTAT
1 ATTTAAAATTTAATATTTGTACTTTTAT
* *
2426280 -TTATAAAAATTTAATATTTTTATTTTTAT
1 ATT-T-AAAATTTAATATTTGTACTTTTAT
2426309 ATTTCAAAATT
1 ATTT-AAAATT
2426320 CATATTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 29 0.85
30 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTAAAATTTAATATTTGTACTTTTAT
Found at i:2427984 original size:193 final size:193
Alignment explanation
Indices: 2427761--2428113 Score: 600
Period size: 193 Copynumber: 1.8 Consensus size: 193
2427751 AATTTTTGCT
* * * * *
2427761 TTTTCTAAAGTTAAAAGTCAAAATCATTAAGTTAAAAGATAAAATTATATTGTTTTGATAAATAT
1 TTTTCTAAAGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAATTACATCGTTTTAATAAATAT
*
2427826 TTACTCATTAAATTAAAAAATAAAATAATTATATTATTTATATAGTTAAATAATCTTATACTTTG
66 TTACTCATTAAATTAAAAAATAAAATAATTATATTATTTATATAGTTAAATAATCTTATACTTCG
2427891 TTTACTAATTAAATAATC-GATCCATGTAAAGACAAAAGTACGTCATTTTGATAAATATTTAAC
131 TTTACTAATTAAATAATCAG-TCCATGTAAAGACAAAAGTACGTCATTTTGATAAATATTTAAC
*
2427954 TTTTCTAATGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAATTACATCGTTTTAATAAATAT
1 TTTTCTAAAGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAATTACATCGTTTTAATAAATAT
* * *
2428019 TTACTCATTAAATTAAAAGATAAAATAATTATATTATTTATGTAGTTAAATAATCTTGTACTTCG
66 TTACTCATTAAATTAAAAAATAAAATAATTATATTATTTATATAGTTAAATAATCTTATACTTCG
2428084 TTTACTAATTAAATAATCAGTCCATGTAAA
131 TTTACTAATTAAATAATCAGTCCATGTAAA
2428114 CTCAATATTG
Statistics
Matches: 149, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
193 148 0.99
194 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (193 bp):
TTTTCTAAAGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAATTACATCGTTTTAATAAATAT
TTACTCATTAAATTAAAAAATAAAATAATTATATTATTTATATAGTTAAATAATCTTATACTTCG
TTTACTAATTAAATAATCAGTCCATGTAAAGACAAAAGTACGTCATTTTGATAAATATTTAAC
Found at i:2428255 original size:34 final size:34
Alignment explanation
Indices: 2428212--2428281 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2428202 TTAAGTTCGG
2428212 TTGTCGTCAACTCGTCTAACTCGAATTTTTTTGA
1 TTGTCGTCAACTCGTCTAACTCGAATTTTTTTGA
2428246 TTGTCGTCAACTCGTCTAACTCGAATTTTTTTGA
1 TTGTCGTCAACTCGTCTAACTCGAATTTTTTTGA
2428280 TT
1 TT
2428282 CGACTCGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (34 bp):
TTGTCGTCAACTCGTCTAACTCGAATTTTTTTGA
Found at i:2432905 original size:21 final size:19
Alignment explanation
Indices: 2432864--2432901 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2432854 TTTTGATAAA
*
2432864 TTTTTTATGTGATAGTTAT
1 TTTTTTAAGTGATAGTTAT
*
2432883 TTTTTTAAGTGATATTTAT
1 TTTTTTAAGTGATAGTTAT
2432902 ATTTAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
TTTTTTAAGTGATAGTTAT
Found at i:2433088 original size:21 final size:22
Alignment explanation
Indices: 2433045--2433090 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2433035 AATAAAATAC
2433045 ATTTAATGTTGGTTATGAATTT
1 ATTTAATGTTGGTTATGAATTT
*
2433067 ATTTAATTTTGTGTT-T-AATTT
1 ATTTAATGTTG-GTTATGAATTT
2433088 ATT
1 ATT
2433091 AAATATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (22 bp):
ATTTAATGTTGGTTATGAATTT
Found at i:2435019 original size:17 final size:18
Alignment explanation
Indices: 2434997--2435034 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2434987 TTTTTATACC
2434997 AAATTTAAAT-TAT-AAAT
1 AAATTT-AATCTATAAAAT
2435014 AAATTTAATCTATAAAAT
1 AAATTTAATCTATAAAAT
2435032 AAA
1 AAA
2435035 AGATATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAATCTATAAAAT
Found at i:2441561 original size:29 final size:30
Alignment explanation
Indices: 2441490--2441571 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 30
2441480 TAAATCTTAA
* *
2441490 AATTATAC-ATGAATTTTGATTTAATATGC
1 AATTATACAATGAACTTTAATTTAATATGC
* *
2441519 AATTGTATATATGAACTTTAATTT-A-ATGC
1 AATTATACA-ATGAACTTTAATTTAATATGC
*
2441548 AATTATACAGATGAAACTCTAATT
1 AATTATACA-ATG-AACTTTAATT
2441572 GCGGTTCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 20 0.48
30 10 0.24
31 12 0.29
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (30 bp):
AATTATACAATGAACTTTAATTTAATATGC
Found at i:2444423 original size:39 final size:37
Alignment explanation
Indices: 2444356--2444448 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
2444346 ACCAGAATGG
* *
2444356 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
2444395 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
2444432 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
2444449 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:2444811 original size:3 final size:3
Alignment explanation
Indices: 2444803--2444839 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2444793 ATTCCCACTC
2444803 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2444840 AAAATTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2445584 original size:17 final size:16
Alignment explanation
Indices: 2445552--2445585 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2445542 TTGGCTATTC
*
2445552 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
2445568 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
2445585 T
1 T
2445586 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:2445633 original size:14 final size:14
Alignment explanation
Indices: 2445574--2445624 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2445564 CTTTTGTTTC
*
2445574 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
2445587 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
2445602 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
2445616 TTTTATTTC
1 TTTTATTTC
2445625 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:2445792 original size:14 final size:17
Alignment explanation
Indices: 2445773--2445809 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
2445763 ATTTATTTCT
2445773 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
2445787 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
2445804 TAATAT
1 TAATAT
2445810 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:2447252 original size:23 final size:23
Alignment explanation
Indices: 2447220--2447263 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2447210 AATACTATTT
2447220 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2447243 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2447264 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2447256 original size:13 final size:11
Alignment explanation
Indices: 2447224--2447266 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2447214 CTATTTTCTA
*
2447224 AATAAAATAAT
1 AATAAAATATT
2447235 AAT-AAATATCT
1 AATAAAATAT-T
2447246 AAGTAAAATATT
1 AA-TAAAATATT
2447258 AATAAAATA
1 AATAAAATA
2447267 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2454813 original size:26 final size:26
Alignment explanation
Indices: 2454776--2454835 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 26
2454766 TTTTGTAGTG
2454776 TAATAAATAATTTTTCTAT-TTAA-ATT
1 TAAT-AATAATTTTT-TATATTAATATT
2454802 TAATAATGAATTTTTTATATTAATATT
1 TAATAAT-AATTTTTTATATTAATATT
2454829 TATATAA
1 TA-ATAA
2454836 CTTTTGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.20
26 15 0.50
27 5 0.17
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TAATAATAATTTTTTATATTAATATT
Found at i:2462626 original size:17 final size:18
Alignment explanation
Indices: 2462606--2462640 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2462596 ATCATAAATC
2462606 AATCATAATTA-TCTTTT
1 AATCATAATTACTCTTTT
2462623 AATCATAATTACTCTTTT
1 AATCATAATTACTCTTTT
2462641 GTAACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AATCATAATTACTCTTTT
Found at i:2466267 original size:5 final size:5
Alignment explanation
Indices: 2466257--2466281 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2466247 TAGTAAATTA
2466257 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
2466282 GCACAACTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:2466319 original size:5 final size:5
Alignment explanation
Indices: 2466309--2466336 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2466299 TTTATACTGT
2466309 ACCAA ACCAA ACCAA ACCAA ACCAA ACC
1 ACCAA ACCAA ACCAA ACCAA ACCAA ACC
2466337 GAAGGGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAA
Found at i:2471721 original size:15 final size:16
Alignment explanation
Indices: 2471701--2471741 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2471691 CGTGACATAA
2471701 TTTAAAAATGAAA-AT
1 TTTAAAAATGAAATAT
*
2471716 TTTAAAAATTAAATAT
1 TTTAAAAATGAAATAT
*
2471732 TGTAAAAATG
1 TTTAAAAATG
2471742 GATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (16 bp):
TTTAAAAATGAAATAT
Found at i:2476229 original size:17 final size:18
Alignment explanation
Indices: 2476186--2476233 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
2476176 AATGAATGAC
*
2476186 TGTTACTGAATAACTTAAT
1 TGTTACTGAAT-ACCTAAT
*
2476205 TGTTACTGAATACCTGAT
1 TGTTACTGAATACCTAAT
2476223 T-TTACTGAATA
1 TGTTACTGAATA
2476234 ATTGACTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 10 0.37
18 6 0.22
19 11 0.41
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
TGTTACTGAATACCTAAT
Found at i:2476341 original size:18 final size:18
Alignment explanation
Indices: 2476050--2476345 Score: 186
Period size: 18 Copynumber: 16.1 Consensus size: 18
2476040 AAAGGTATAA
* *
2476050 AATAACTGATTATTACTG
1 AATAATTGATTGTTACTG
* * *
2476068 AATAATTAACTGTTACCG
1 AATAATTGATTGTTACTG
2476086 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* * *
2476104 GAT-ATTAGACTGTTATTG
1 AATAATT-GATTGTTACTG
* *
2476122 AATAATTGAATATTACTG
1 AATAATTGATTGTTACTG
**
2476140 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* * *
2476158 AATAACTGATTGTCACTA
1 AATAATTGATTGTTACTG
*
2476176 AATGAA-TGACTGTTACTG
1 AAT-AATTGATTGTTACTG
*
2476194 AATAACTTAATTGTTACTG
1 AATAA-TTGATTGTTACTG
**
2476213 AATACCTGATT-TTACTG
1 AATAATTGATTGTTACTG
*
2476230 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
2476249 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
* * * *
2476274 AATAACTGGTTATTATTG
1 AATAATTGATTGTTACTG
*
2476292 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
2476310 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
2476328 AATAAATAATTGTT-CTG
1 AATAATTGATTGTTACTG
2476345 A
1 A
2476346 TTGTTAATGA
Statistics
Matches: 211, Mismatches: 53, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
17 23 0.11
18 150 0.71
19 22 0.10
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:2477591 original size:13 final size:14
Alignment explanation
Indices: 2477573--2477603 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2477563 CTTTCTCATG
2477573 TTTTC-TCATTTTC
1 TTTTCTTCATTTTC
2477586 TTTTCTTCATTTTC
1 TTTTCTTCATTTTC
2477600 TTTT
1 TTTT
2477604 TTTCCTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTCATTTTC
Found at i:2478181 original size:18 final size:17
Alignment explanation
Indices: 2478154--2478196 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2478144 ATATTTTAAG
*
2478154 TATAAGATATTTAATATA
1 TATAATATA-TTAATATA
*
2478172 TATAATATATTATTATA
1 TATAATATATTAATATA
2478189 -ATAATATA
1 TATAATATA
2478197 ATATAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATAATATATTAATATA
Found at i:2478195 original size:21 final size:20
Alignment explanation
Indices: 2478160--2478217 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
2478150 TAAGTATAAG
2478160 ATATTTAATATATATAATATA
1 ATATTTAATA-ATATAATATA
*
2478181 TTATTATAATAATATAATATA
1 ATATT-TAATAATATAATATA
2478202 ATATTTAA-AATA-AATA
1 ATATTTAATAATATAATA
2478218 AAAGAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 3 0.09
21 18 0.53
22 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTAATAATATAATATA
Found at i:2478229 original size:18 final size:17
Alignment explanation
Indices: 2478208--2478241 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2478198 TATAATATTT
2478208 AAAATAAATAAAAGAAAC
1 AAAATAAA-AAAAGAAAC
*
2478226 AAAATAGAAAAAGAAA
1 AAAATAAAAAAAGAAA
2478242 GAACAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAAAGAAAC
Found at i:2478290 original size:33 final size:33
Alignment explanation
Indices: 2478218--2478290 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
2478208 AAAATAAATA
*
2478218 AAAG-AAACAAAATAGAAAAAGAAAGAACAGAG
1 AAAGAAAACAAAATAGAAAAAGAAAGAAAAGAG
* * * *
2478250 AATGAAAACGAAATAG-AAAGGAAAGAAAAAGGG
1 AAAGAAAACAAAATAGAAAAAGAAAG-AAAAGAG
2478283 AAAGAAAA
1 AAAGAAAA
2478291 AGAATGGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (33 bp):
AAAGAAAACAAAATAGAAAAAGAAAGAAAAGAG
Found at i:2479467 original size:61 final size:61
Alignment explanation
Indices: 2479393--2479507 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
2479383 TTTTTATCAT
2479393 CCCAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAATAAT-TTTTATCATCTATTAA
1 CCCAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAATAATATTTT-TCATCTATTAA
* *
2479454 CCCAATTAGCTTTTCAAATAAATTTACAATCATTTAAATAATAATATTTTTCAT
1 CCCAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAATAATATTTTTCAT
2479508 TCATATGTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
61 47 0.92
62 4 0.08
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.41
Consensus pattern (61 bp):
CCCAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAATAATATTTTTCATCTATTAA
Found at i:2479667 original size:18 final size:18
Alignment explanation
Indices: 2479646--2479773 Score: 98
Period size: 18 Copynumber: 7.1 Consensus size: 18
2479636 AGTCACTCTT
*
2479646 TAACAGTCAGTTATTCAG
1 TAACAGTCAATTATTCAG
*
2479664 TAAC-GATAAATTATTCAG
1 TAACAG-TCAATTATTCAG
*
2479682 TAACAATCAATTATTCAG
1 TAACAGTCAATTATTCAG
* ** **
2479700 TAACAATCTTTTACACAG
1 TAACAGTCAATTATTCAG
* *
2479718 TAGCAGTCAGTTA-TCTAG
1 TAACAGTCAATTATTC-AG
* *
2479736 TTACAGTCAGTTATTCAG
1 TAACAGTCAATTATTCAG
**
2479754 TAGTAGTCAATTATTCAG
1 TAACAGTCAATTATTCAG
2479772 TA
1 TA
2479774 CATTTATTTA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
17 2 0.02
18 83 0.95
19 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TAACAGTCAATTATTCAG
Found at i:2479978 original size:45 final size:47
Alignment explanation
Indices: 2479888--2479993 Score: 144
Period size: 45 Copynumber: 2.3 Consensus size: 47
2479878 CCGTAATGGT
*
2479888 AACAGTAACAGTAGCGGTACACAGAGTACCTCATCAGAACAAATCCGG
1 AACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCAGAACAAATCCGG
* * *
2479936 AACAGTAACAGTA-AGGT-ACAGAGTACCTCTTCGGAACGAATCCGG
1 AACAGTAACAGTAGAGGTAACAGAGTACCTCATCAGAACAAATCCGG
*
2479981 AATAGTAACAGTA
1 AACAGTAACAGTA
2479994 CGGCGACACT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 37 0.70
47 3 0.06
48 13 0.25
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTAGAGGTAACAGAGTACCTCATCAGAACAAATCCGG
Found at i:2480764 original size:20 final size:20
Alignment explanation
Indices: 2480739--2480778 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2480729 ATTTAAGTAT
2480739 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
2480759 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
2480779 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:2481018 original size:20 final size:18
Alignment explanation
Indices: 2480989--2481033 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
2480979 AACGAAAAGC
2480989 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
2481007 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
2481026 AGGGAAAA
1 AGGGAAAA
2481034 ATTGAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:2483502 original size:19 final size:19
Alignment explanation
Indices: 2483470--2483508 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2483460 AATACTTATT
* * *
2483470 TATTATTTATACATGTGTA
1 TATTATTAACACATATGTA
2483489 TATTATTAACACATATGTA
1 TATTATTAACACATATGTA
2483508 T
1 T
2483509 CCATTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATTATTAACACATATGTA
Found at i:2484535 original size:29 final size:30
Alignment explanation
Indices: 2484476--2484533 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2484466 TCCGAGCCTT
*
2484476 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2484506 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2484534 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2484763 original size:13 final size:13
Alignment explanation
Indices: 2484745--2484776 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2484735 TTTCCAGCAA
2484745 TTATGAATTTATT
1 TTATGAATTTATT
2484758 TTATGAATTTATT
1 TTATGAATTTATT
*
2484771 TGATGA
1 TTATGA
2484777 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2484984 original size:50 final size:50
Alignment explanation
Indices: 2484871--2485112 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
2484861 ATTTGGGTAA
* * *
2484871 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
2484927 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2484977 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2485027 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
2485077 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
2485113 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2485060 original size:100 final size:103
Alignment explanation
Indices: 2484871--2485120 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
2484861 ATTTGGGTAA
2484871 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
2484936 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
2484977 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
2485039 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
2485077 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
2485121 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:2490294 original size:19 final size:19
Alignment explanation
Indices: 2490262--2490300 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2490252 ATACTTATTT
* * *
2490262 TATTATTTATACATGTGTA
1 TATTATTAACACATATGTA
2490281 TATTATTAACACATATGTA
1 TATTATTAACACATATGTA
2490300 T
1 T
2490301 CCATTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATTATTAACACATATGTA
Found at i:2491550 original size:13 final size:13
Alignment explanation
Indices: 2491532--2491563 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2491522 TTTCCAGAAA
2491532 TTATGAATTTATT
1 TTATGAATTTATT
2491545 TTATGAATTTATT
1 TTATGAATTTATT
*
2491558 TGATGA
1 TTATGA
2491564 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2491769 original size:49 final size:49
Alignment explanation
Indices: 2491658--2491896 Score: 223
Period size: 49 Copynumber: 4.7 Consensus size: 49
2491648 ATTTGGGTAA
* * * *
2491658 AGAGATCCATGTAAGACACATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCTGTAAGAC-CATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
2491714 AGAGGTCCCTGTAAAACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2491763 AGAGGTCCCATGTAAGACCATGTC-GGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2491812 AGAGGTCCCTATAAGACCATGT-TCGGGACATGGCATGCGCACC-ATCACG
1 AGAGGTCCCTGTAAGACCATGTCT-GGGACATGGCATGGGCACCGA-GACG
** *
2491861 AGAACATCTCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTC-CCTGTAAGACCATGTCTGGGACATGGC
2491897 TTTGGCATGT
Statistics
Matches: 157, Mismatches: 19, Indels: 19
0.81 0.10 0.10
Matches are distributed among these distances:
48 13 0.08
49 61 0.39
50 16 0.10
51 24 0.15
52 4 0.03
54 2 0.01
55 23 0.15
56 14 0.09
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (49 bp):
AGAGGTCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2491862 original size:98 final size:103
Alignment explanation
Indices: 2491664--2491904 Score: 289
Period size: 98 Copynumber: 2.3 Consensus size: 103
2491654 GTAAAGAGAT
*
2491664 CCATGTAAGACACATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCTGTAAA
1 CCATGTAAGAC-CATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCCTATAAA
* * **
2491729 ACCATGTCTGGGACATGGCATGGGCACCGAGACGAG-AGGTC
62 ACCATGTCTGGGACATGGCATGCGCACCGACACGAGAACATC
* * *
2491770 CCATGTAAGACCATGTC-GGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCTATAAGACCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCTATAAAACCA
2491831 TGT-TCGGGACATGGCATGCGCACC-ATCACGAGAACATC
66 TGTCT-GGGACATGGCATGCGCACCGA-CACGAGAACATC
* *
2491869 TCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
2491905 GTTATTATCA
Statistics
Matches: 120, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
97 2 0.02
98 46 0.38
99 21 0.17
100 16 0.13
103 2 0.02
104 16 0.13
105 6 0.05
106 11 0.09
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCTATAAAACCA
TGTCTGGGACATGGCATGCGCACCGACACGAGAACATC
Found at i:2664198 original size:22 final size:22
Alignment explanation
Indices: 2664173--2664215 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664163 TATCTAAACA
2664173 ATAACAACAAAATAGTAACAAT
1 ATAACAACAAAATAGTAACAAT
* * *
2664195 ATAATAGCAAAATGGTAACAA
1 ATAACAACAAAATAGTAACAA
2664216 AACAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAT
Found at i:2665463 original size:37 final size:37
Alignment explanation
Indices: 2665406--2665557 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
2665396 TATGATCACT
*
2665406 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
2665441 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
2665478 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
2665523 ATATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
2665558 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:2665545 original size:46 final size:46
Alignment explanation
Indices: 2665474--2666064 Score: 668
Period size: 46 Copynumber: 12.6 Consensus size: 46
2665464 TAAGTGTAGC
* * **
2665474 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665520 CACATATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665566 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTA-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665611 CTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCTGAAGCTAT
1 C-ACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665664 CACTTATCACTTTGTCACTTGATCAGATAAG--T----GTAGC---
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665701 CACTTATCACTTTGTCTCTTGATCAGATAAG--TAG-CTAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665744 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665790 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665842 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
2665894 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2665940 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
2665986 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
2666038 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2666065 AGTACTCAAA
Statistics
Matches: 487, Mismatches: 28, Indels: 60
0.85 0.05 0.10
Matches are distributed among these distances:
37 31 0.06
40 7 0.01
43 31 0.06
44 1 0.00
45 4 0.01
46 233 0.48
48 2 0.00
49 1 0.00
50 3 0.01
51 3 0.01
52 170 0.35
53 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:2665644 original size:52 final size:52
Alignment explanation
Indices: 2665563--2665676 Score: 169
Period size: 52 Copynumber: 2.2 Consensus size: 52
2665553 TAGCCGAAGC
2665563 TATCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTA-CTACT
1 TATCACTT-TCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATC-ACT
* *
2665616 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTATAGCTGAAGCTATCACT
1 TATCACTTT-CACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2665668 TATCACTTT
1 TATCACTTT
2665677 GTCACTTGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
52 45 0.79
53 12 0.21
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:2665668 original size:98 final size:96
Alignment explanation
Indices: 2665474--2666064 Score: 685
Period size: 98 Copynumber: 6.3 Consensus size: 96
2665464 TAAGTGTAGC
* * * ** *
2665474 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT-C--A-CA-TATCACTTTG
1 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATACTTATCACTTTCAC-TTG
*
2665534 TCTCTTGATCAGATAAGTATAGCCGAAGCTAT
65 TCACTTGATCAGATAAGTATAGCCGAAGCTAT
2665566 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTACTACTTATCACTTTCCACTT
1 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTA-TACTTATCACTTT-CACTT
*
2665631 GTCACTTGATCAGATAAGTATAGCTGAAGCTAT
64 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665664 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-C----C---ACTTATCAC--T---TTGT
1 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATACTTATCACTTTCACTTGT
* *
2665716 CTCTTGATCAGATAAG--TAG-CTAAGCTAT
66 CACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665744 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT-ACTTATCAC-TTTCACTT
*
2665809 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
64 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
2665842 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC--T
1 CACTTATCACTTT--A----TCACTTGATCAGATAAGTATAGCCGAAGCTAT-ACTTATCACTTT
2665905 ---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
59 CACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
2665940 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTA-TACTTATCACTTT-CACTT
* ** *
2666005 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
64 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
2666038 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTATCACTTGATCAGA
2666065 AGTACTCAAA
Statistics
Matches: 433, Mismatches: 28, Indels: 70
0.82 0.05 0.13
Matches are distributed among these distances:
80 41 0.09
81 4 0.01
83 19 0.04
85 1 0.00
87 1 0.00
89 18 0.04
92 79 0.18
93 3 0.01
94 2 0.00
95 19 0.04
96 2 0.00
97 6 0.01
98 195 0.45
99 3 0.01
101 1 0.00
104 39 0.09
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (96 bp):
CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATACTTATCACTTTCACTTGT
CACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:2665706 original size:37 final size:37
Alignment explanation
Indices: 2665664--2665781 Score: 164
Period size: 37 Copynumber: 3.0 Consensus size: 37
2665654 CTGAAGCTAT
*
2665664 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2665701 CACTTATCACTTTGTCTCTTGATCAGATAAGTAGCTAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGT-G-T-AGC
*
2665741 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2665781 C
1 C
2665782 GAAGCTATCA
Statistics
Matches: 73, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
37 32 0.44
38 1 0.01
39 1 0.01
40 6 0.08
41 1 0.01
43 32 0.44
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:2665821 original size:52 final size:52
Alignment explanation
Indices: 2665741--2666058 Score: 426
Period size: 52 Copynumber: 6.3 Consensus size: 52
2665731 GTAGCTAAGC
* *
2665741 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2665794 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
2665846 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2665898 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2665944 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
2665990 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2666042 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
2666059 ATCAGAAGTA
Statistics
Matches: 239, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 84 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:2669176 original size:49 final size:49
Alignment explanation
Indices: 2669121--2669266 Score: 238
Period size: 49 Copynumber: 3.0 Consensus size: 49
2669111 TTCGTTTTCT
* * *
2669121 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* *
2669170 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
2669219 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT
2669267 GTTGCCATGG
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 83 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:2670572 original size:37 final size:37
Alignment explanation
Indices: 2670511--2670656 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
2670501 TACGTATGAT
* *
2670511 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
2670546 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2670583 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
2670620 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2670657 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:2670673 original size:46 final size:45
Alignment explanation
Indices: 2670620--2670885 Score: 343
Period size: 45 Copynumber: 5.6 Consensus size: 45
2670610 TAAGTGTAGC
* *
2670620 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC-GAAGCTAT
* *
2670666 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CGAAGCTAT
2670712 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAG-CGAAGCTAT
2670764 CACTTATCACTTTCACTTGTCACTTGATCAGATAAGTGTAGCGAAGCTAT
1 CACTTATCAC--T---TTGTCACTTGATCAGATAAGTGTAGCGAAGCTAT
* *
2670814 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCGAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCGAAGCTAT
*
2670859 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2670886 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 7, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
45 58 0.28
46 52 0.25
47 1 0.00
48 1 0.00
49 1 0.00
50 19 0.09
51 31 0.15
52 43 0.21
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCGAAGCTAT
Found at i:2670739 original size:52 final size:51
Alignment explanation
Indices: 2670663--2670879 Score: 304
Period size: 52 Copynumber: 4.3 Consensus size: 51
2670653 TAGCTAAAGC
* *
2670663 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAG-CGAAGCTATCACT
*
2670716 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAG-CGAAGCTATCACT
*
2670768 TATCAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCGAAGCTATCACT
*
2670818 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCGAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCGAAGCTATCACT
2670863 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
2670880 ATCAGAAGTA
Statistics
Matches: 152, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
45 42 0.28
48 1 0.01
49 1 0.01
50 19 0.12
51 31 0.20
52 46 0.30
53 12 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCGAAGCTATCACT
Found at i:2679455 original size:13 final size:13
Alignment explanation
Indices: 2679437--2679474 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2679427 CAGTAATTCT
2679437 ATATTTTTTAAAA
1 ATATTTTTTAAAA
*
2679450 ATATTTTGTTCAAA
1 ATATTTT-TTAAAA
2679464 AT-TTTTTTAAA
1 ATATTTTTTAAA
2679475 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 11 0.50
14 7 0.32
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (13 bp):
ATATTTTTTAAAA
Found at i:2679502 original size:20 final size:22
Alignment explanation
Indices: 2679477--2679529 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2679467 TTTTTAAATA
*
2679477 TTAAAAATAAAT-ATAA-ATTG
1 TTAAAAATAAATGAAAATATTG
* *
2679497 TTAAAAATATATGAAAATATTT
1 TTAAAAATAAATGAAAATATTG
2679519 TTAAAAATAAA
1 TTAAAAATAAA
2679530 AAAATCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 3 0.11
22 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
TTAAAAATAAATGAAAATATTG
Found at i:2679533 original size:20 final size:20
Alignment explanation
Indices: 2679477--2679534 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
2679467 TTTTTAAATA
*
2679477 TTAAAAATAAATATAA-ATTG
1 TTAAAAATAAA-AAAATATTG
* *
2679497 TTAAAAATATATGAAAATATTT
1 TTAAAAATA-A-AAAAATATTG
2679519 TTAAAAATAAAAAAAT
1 TTAAAAATAAAAAAAT
2679535 CTAAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 14 0.45
21 5 0.16
22 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAAAATAAAAAAATATTG
Found at i:2681148 original size:27 final size:28
Alignment explanation
Indices: 2681100--2681164 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
2681090 ACACATTTAA
* *
2681100 AAATATATATCATTTTTTTATAT-TATAT
1 AAATATA-ATCATTTATGTATATATATAT
*
2681128 AAATATAATTATTTATGTATATAATATAT
1 AAATATAATCATTTATGTATAT-ATATAT
2681157 AAATATAA
1 AAATATAA
2681165 AATACTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.38
28 7 0.22
29 13 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATATAATCATTTATGTATATATATAT
Done.