Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 120 of 172
Found at i:39870122 original size:8 final size:8
Alignment explanation
Indices: 39870098--39870134 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
39870088 TCAAAGTACA
39870098 ATTTTATT
1 ATTTTATT
*
39870106 A-TATATT
1 ATTTTATT
39870113 ATTTTATT
1 ATTTTATT
39870121 ATTTTATT
1 ATTTTATT
39870129 ATTTTA
1 ATTTTA
39870135 GAGAGAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTTATT
Found at i:39871840 original size:18 final size:19
Alignment explanation
Indices: 39871817--39871859 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
39871807 ATTTAATTTT
* *
39871817 TATATAAAAATTACAT-AA
1 TATATAAAAATAAAATAAA
39871835 TATATAAAAATAAAATAAA
1 TATATAAAAATAAAATAAA
39871854 TATATA
1 TATATA
39871860 TATCATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TATATAAAAATAAAATAAA
Found at i:39876116 original size:2 final size:2
Alignment explanation
Indices: 39876109--39876240 Score: 264
Period size: 2 Copynumber: 66.0 Consensus size: 2
39876099 GTTTATAAAG
39876109 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39876151 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39876193 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39876235 CT CT CT
1 CT CT CT
39876241 TGGCTTATGC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 130 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:39883096 original size:13 final size:13
Alignment explanation
Indices: 39883078--39883102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39883068 TTTTTTATAG
39883078 AAATATAATAATA
1 AAATATAATAATA
39883091 AAATATAATAAT
1 AAATATAATAAT
39883103 TATTTATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:39883573 original size:12 final size:12
Alignment explanation
Indices: 39883556--39883580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39883546 TTGGTGGCAC
39883556 AAAAAAATAAAA
1 AAAAAAATAAAA
39883568 AAAAAAATAAAA
1 AAAAAAATAAAA
39883580 A
1 A
39883581 TCACTTGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:39884018 original size:23 final size:23
Alignment explanation
Indices: 39883957--39884011 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
39883947 AAATCCGCTC
**
39883957 ATATTATTTTTAA-AAAATATTT
1 ATATTATTTTTAATTTAATATTT
39883979 ATATTATTTTTAATTTAATATTT
1 ATATTATTTTTAATTTAATATTT
*
39884002 -TATTTTTTTT
1 ATATTATTTTT
39884012 CTATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATATTATTTTTAATTTAATATTT
Found at i:39884658 original size:15 final size:14
Alignment explanation
Indices: 39884631--39884680 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
39884621 CAAAATTCAA
39884631 AAAATATAAAAATT
1 AAAATATAAAAATT
39884645 AAAAT-TAATCAAATT
1 AAAATATAA--AAATT
39884660 AAAATATAAAAATT
1 AAAATATAAAAATT
39884674 -AAATATA
1 AAAATATA
39884681 CACCTTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 10 0.30
16 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:39884658 original size:23 final size:23
Alignment explanation
Indices: 39884632--39884675 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39884622 AAAATTCAAA
*
39884632 AAATATAAAA-ATTAAAATTAATC
1 AAAT-TAAAATATAAAAATTAATC
39884655 AAATTAAAATATAAAAATTAA
1 AAATTAAAATATAAAAATTAA
39884676 ATATACACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATTAAAATATAAAAATTAATC
Found at i:39890706 original size:13 final size:11
Alignment explanation
Indices: 39890678--39890720 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
39890668 AGTTAAATAT
39890678 TATTTTATTAA
1 TATTTTATTAA
39890689 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
39890702 TA-TTTATTAT
1 TATTTTATTAA
39890712 TATTTTATT
1 TATTTTATT
39890721 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:39890707 original size:23 final size:23
Alignment explanation
Indices: 39890681--39890724 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39890671 TAAATATTAT
39890681 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
39890704 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
39890725 AAATGGTAGT
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:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:39899646 original size:30 final size:30
Alignment explanation
Indices: 39899611--39899667 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
39899601 TAGGCATTTC
*
39899611 CACACGAGTAAACCACACGCCCGTGTGAGG
1 CACACGAGCAAACCACACGCCCGTGTGAGG
* **
39899641 CACACGGGCAGTCCACACGCCCGTGTG
1 CACACGAGCAAACCACACGCCCGTGTG
39899668 TCATGGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.11
Consensus pattern (30 bp):
CACACGAGCAAACCACACGCCCGTGTGAGG
Found at i:39903735 original size:23 final size:23
Alignment explanation
Indices: 39903690--39903732 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39903680 CTATCATTTT
39903690 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
39903713 TCTAAGTAAAA-ATTAATAAA
1 TCTAAATAAAATAATAATAAA
39903733 ATAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:39905860 original size:44 final size:44
Alignment explanation
Indices: 39905812--39905902 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
39905802 TTTGAAATAA
* *
39905812 AATAGAAATTGTGATAATTTCACATTTTAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
* **
39905856 AATAGAAGTTGTGATAATTACTTATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
39905900 AAT
1 AAT
39905903 TTAAAATTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (44 bp):
AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
Found at i:39906376 original size:32 final size:31
Alignment explanation
Indices: 39906339--39906420 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
39906329 TATTTTATGT
* * *
39906339 TAATTACTACAATTAAAAATATAATATTTAAAA
1 TAATTA-TA-AATTAAAAACATAAAAATTAAAA
39906372 -AATTATTAAATATTAAAAACATAAAAATTAAAA
1 TAATTA-T-AA-ATTAAAAACATAAAAATTAAAA
39906405 TTAATTATAAATTAAA
1 -TAATTATAAATTAAA
39906421 TAAAAATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
32 13 0.32
33 22 0.54
34 1 0.02
35 5 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
TAATTATAAATTAAAAACATAAAAATTAAAA
Found at i:39906528 original size:4 final size:4
Alignment explanation
Indices: 39906519--39906545 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39906509 TTTATTTTTC
39906519 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
39906546 TTGCTTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:39908414 original size:30 final size:31
Alignment explanation
Indices: 39908366--39908430 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
39908356 TATTTACTTC
* *
39908366 TAAATTTATTTGTACACAT-GTATATGTTTTT
1 TAAATCTATTTGTACACATAAT-TATGTTTTT
*
39908397 TAAATCTA-TTGTGCACATAATTATGTTTTT
1 TAAATCTATTTGTACACATAATTATGTTTTT
39908427 TAAA
1 TAAA
39908431 AATCTGTCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (31 bp):
TAAATCTATTTGTACACATAATTATGTTTTT
Found at i:39908442 original size:28 final size:29
Alignment explanation
Indices: 39908388--39908443 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
39908378 TACACATGTA
*
39908388 TATGTTTTTTAAATCTATTGTGCACATAAT
1 TATGTTTTTTAAA-CAATTGTGCACATAAT
39908418 TATGTTTTTTAAA-AATCTGT-CACATA
1 TATGTTTTTTAAACAAT-TGTGCACATA
39908444 TGGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 3 0.12
30 13 0.54
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (29 bp):
TATGTTTTTTAAACAATTGTGCACATAAT
Found at i:39913513 original size:6 final size:6
Alignment explanation
Indices: 39913502--39913533 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39913492 ATTATGCAAT
39913502 CCATCA CCATCA CCATCA CCATCA CCATCA CC
1 CCATCA CCATCA CCATCA CCATCA CCATCA CC
39913534 TACCCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATCA
Found at i:39919053 original size:20 final size:20
Alignment explanation
Indices: 39919028--39919069 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39919018 ATGACTCACC
39919028 ATTGTTAATTTAGTCGAAAA
1 ATTGTTAATTTAGTCGAAAA
39919048 ATTGTTAATTTAGTCGAAAA
1 ATTGTTAATTTAGTCGAAAA
39919068 AT
1 AT
39919070 AATTTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
ATTGTTAATTTAGTCGAAAA
Found at i:39919074 original size:16 final size:17
Alignment explanation
Indices: 39919032--39919077 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
39919022 CTCACCATTG
39919032 TTAATTTAGTCGAAAAA
1 TTAATTTAGTCGAAAAA
39919049 TTGTTAATTTAGTCGAAAAA
1 ---TTAATTTAGTCGAAAAA
39919069 -TAATTTAGT
1 TTAATTTAGT
39919078 AACCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
20 17 0.65
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (17 bp):
TTAATTTAGTCGAAAAA
Found at i:39922436 original size:3 final size:3
Alignment explanation
Indices: 39922428--39922453 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39922418 ATATGTTCAA
39922428 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39922454 AACGCGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39926015 original size:21 final size:21
Alignment explanation
Indices: 39925978--39926028 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
39925968 AAGGTTAAAA
*
39925978 TAAATATATGATGAATATATT
1 TAAATATATGATAAATATATT
*
39925999 TAAA-ATATGCATAAATATATA
1 TAAATATATG-ATAAATATATT
*
39926020 TATATATAT
1 TAAATATAT
39926029 ATATAAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
TAAATATATGATAAATATATT
Found at i:39932805 original size:17 final size:18
Alignment explanation
Indices: 39932785--39932824 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39932775 AAAATATTTG
*
39932785 TTTTTCATA-AATTTTTA
1 TTTTTCAAACAATTTTTA
*
39932802 TTTTTTAAACAATTTTTA
1 TTTTTCAAACAATTTTTA
39932820 TTTTT
1 TTTTT
39932825 TAAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCAAACAATTTTTA
Found at i:39932837 original size:19 final size:18
Alignment explanation
Indices: 39932794--39932828 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39932784 GTTTTTCATA
39932794 AATTTTTATTTTTTAAAC
1 AATTTTTATTTTTTAAAC
39932812 AATTTTTATTTTTTAAA
1 AATTTTTATTTTTTAAA
39932829 ATATATTTTT
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTTATTTTTTAAAC
Found at i:39933719 original size:5 final size:5
Alignment explanation
Indices: 39933711--39933736 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39933701 CAATTTTCTT
39933711 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
39933737 CATATTTAAA
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):
TTTTA
Found at i:39933967 original size:5 final size:5
Alignment explanation
Indices: 39933959--39933984 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39933949 CAATTTTCTT
39933959 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
39933985 CATATTTAAA
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):
TTTTA
Found at i:39934117 original size:248 final size:248
Alignment explanation
Indices: 39933679--39934174 Score: 992
Period size: 248 Copynumber: 2.0 Consensus size: 248
39933669 AATTAGAAGT
39933679 CACCTTTAGACTGTACTATAGTCAATTTTCTTTTTTATTTTATTTTATTTTATTTTATCATATTT
1 CACCTTTAGACTGTACTATAGTCAATTTTCTTTTTTATTTTATTTTATTTTATTTTATCATATTT
39933744 AAAATTCTCCTACTTAAAATATATTTATATATTCAAAATTATATTAAACCCATTTATGACATGTT
66 AAAATTCTCCTACTTAAAATATATTTATATATTCAAAATTATATTAAACCCATTTATGACATGTT
39933809 TTTAGTTAATTGTTTATAAAATCCTTAAACCTTTATCTTTATCTATATATTATATAAAATAAGGA
131 TTTAGTTAATTGTTTATAAAATCCTTAAACCTTTATCTTTATCTATATATTATATAAAATAAGGA
39933874 AGCTTTAGGAAATAAATAGATTAAAGGATAAAATAGGAATAGTGGTATTTTGG
196 AGCTTTAGGAAATAAATAGATTAAAGGATAAAATAGGAATAGTGGTATTTTGG
39933927 CACCTTTAGACTGTACTATAGTCAATTTTCTTTTTTATTTTATTTTATTTTATTTTATCATATTT
1 CACCTTTAGACTGTACTATAGTCAATTTTCTTTTTTATTTTATTTTATTTTATTTTATCATATTT
39933992 AAAATTCTCCTACTTAAAATATATTTATATATTCAAAATTATATTAAACCCATTTATGACATGTT
66 AAAATTCTCCTACTTAAAATATATTTATATATTCAAAATTATATTAAACCCATTTATGACATGTT
39934057 TTTAGTTAATTGTTTATAAAATCCTTAAACCTTTATCTTTATCTATATATTATATAAAATAAGGA
131 TTTAGTTAATTGTTTATAAAATCCTTAAACCTTTATCTTTATCTATATATTATATAAAATAAGGA
39934122 AGCTTTAGGAAATAAATAGATTAAAGGATAAAATAGGAATAGTGGTATTTTGG
196 AGCTTTAGGAAATAAATAGATTAAAGGATAAAATAGGAATAGTGGTATTTTGG
39934175 TTTTTTACTT
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 248 1.00
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (248 bp):
CACCTTTAGACTGTACTATAGTCAATTTTCTTTTTTATTTTATTTTATTTTATTTTATCATATTT
AAAATTCTCCTACTTAAAATATATTTATATATTCAAAATTATATTAAACCCATTTATGACATGTT
TTTAGTTAATTGTTTATAAAATCCTTAAACCTTTATCTTTATCTATATATTATATAAAATAAGGA
AGCTTTAGGAAATAAATAGATTAAAGGATAAAATAGGAATAGTGGTATTTTGG
Found at i:39934529 original size:20 final size:20
Alignment explanation
Indices: 39934504--39934552 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
39934494 TATGTTGGAT
39934504 TTTTTATATAATTATTCCTA
1 TTTTTATATAATTATTCCTA
* * *
39934524 TTTTTATGTATTTATTTCTA
1 TTTTTATATAATTATTCCTA
39934544 TTTATTATA
1 TTT-TTATA
39934553 CATTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATATAATTATTCCTA
Found at i:39942406 original size:72 final size:72
Alignment explanation
Indices: 39942257--39943683 Score: 1023
Period size: 72 Copynumber: 18.7 Consensus size: 72
39942247 AACATGTGAA
* *
39942257 CTGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA-ATTTTT-AAAACAGAAATTGAAATTACC
39942321 TCAGCGTGTC
63 TCAGCGTGTC
*
39942331 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATTACCTCA
39942396 GCGTGTC
66 GCGTGTC
* * *
39942403 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAA-CAGAAATTGAAATTACCTC
*
39942468 AACGTGTC
65 AGCGTGTC
* *
39942476 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATTACCTCA
**
39942541 ATGTGTC
66 GCGTGTC
* * * *
39942548 TTGGGGCTCAACTTATTTCTCGCAATATGAGTTG-ATTCTTTCAAAAACATAATAACGAAAATAG
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT-TTT--AAAAC------A-G-AAATTG
* ** **
39942612 AAATGGAAAATACCTCG-GT-
55 AAAT--TACCT-CAGCGTGTC
* * * ** *
39942631 GTGACCTGAG-GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATT
1 CTGA---G-GCTC-AA-CTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATT
39942694 ACCTCAGCGTGTC
60 ACCTCAGCGTGTC
* *
39942707 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATTACCTCA
39942771 GCGTGTC
66 GCGTGTC
* *
39942778 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAACAACAGAAATTGAAATTA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----ATTTTTAA-AACAGAAATTGAAATTA
39942843 CCTCAGCGTGTC
61 CCTCAGCGTGTC
*
39942855 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTTAA-AACAGAAATTGAAATTACC
*
39942920 TCAGCGTGTT
63 TCAGCGTGTC
** * * *
39942930 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATTGAAAAACAGAA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT-TAAAACAGAAATT--------GAA
* ** **
39942994 ATGGAAAATACCTCAGCATGTC
57 AT--TACCT-CAGC-G--TGTC
** * ** * ** ** **
39943016 CTGAGGCTCAACTCACCTCTTGCAATATGAGTTG-ATTTAGAAAACAGACATAAAAACAGAAATT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAAT-TGAA-ATTACCT
* **
39943080 GAAAGTGACTCAAC
64 CAGCGTG--T---C
* ** *
39943094 ACGTGA-GC-CAAGGCTCAACTCACCTT-TCGCAATATGAGTTGATTTTTTTGAAAGTAGAATTT
1 -C-TGAGGCTCAA--CTC-A-T----TTCTCGCAATATGAGTTGA-ATTTTT-AAAACAGAAATT
* * *
39943156 GAAAATACCTCGGCGTGCC
54 GAAATTACCTCAGCGTGTC
* **
39943175 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGAAAAAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTT---AAAACAGAAATTGAAATTACC
39943239 TCAGCGTGTC
63 TCAGCGTGTC
** *
39943249 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGAAAAACATAAATTGAACAAGAAT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTT--AAAACAGAAATTG----A-AA-
*
39943313 TGGAAATACCTCAACGTGTC
58 T-----TACCTCAGCGTGTC
* ** * *
39943333 TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTT-TT-AAAA-CAGAAATTGAAATTACC
**
39943398 TCAATGTGTC
63 TCAGCGTGTC
* ** * *
39943408 TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTT-AAAACAGAAATTGAAATTACCT
39943473 CAGCGTGTC
64 CAGCGTGTC
*** * * *
39943482 CTGAGGCTCAACTCGCCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATTGAAATTACCTC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT-TAAAACAGAAATTGAAATTACCTC
39943546 AGCGTGTC
65 AGCGTGTC
* * *
39943554 CTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTTGACAACAGAAATTGAAATTA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----ATTTTT-AAAACAGAAATTGAAATTA
39943619 CCTCAGCGTGTC
61 CCTCAGCGTGTC
** * * *
39943631 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT-TAAAACAGAAATT
39943684 AAAAGTCTTA
Statistics
Matches: 1120, Mismatches: 139, Indels: 190
0.77 0.10 0.13
Matches are distributed among these distances:
71 95 0.08
72 229 0.20
73 96 0.09
74 172 0.15
75 130 0.12
76 12 0.01
77 140 0.12
78 10 0.01
79 11 0.01
80 15 0.01
81 8 0.01
82 12 0.01
83 4 0.00
84 51 0.05
85 37 0.03
86 59 0.05
87 9 0.01
88 30 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (72 bp):
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTAAAACAGAAATTGAAATTACCTCA
GCGTGTC
Found at i:39942720 original size:71 final size:71
Alignment explanation
Indices: 39942604--39942986 Score: 514
Period size: 71 Copynumber: 5.2 Consensus size: 71
39942594 ACATAATAAC
* * * * * * **
39942604 GAAAATAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
39942669 GATTTT
66 GATTTT
*
39942675 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTT
1 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
39942740 GATTTT
66 GATTTT
*
39942746 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTT
1 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
39942811 GATTTTTTTTT
66 GA-----TTTT
*
39942822 TAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 GAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
39942887 TGATTTTTTT
65 TGA---TTTT
* * ** *
39942897 TAACAACAGAAATTGAAATTACCTCAGCGTGTTCTGAGGCTCAACTCACCTCTAGCAATATGAGT
1 GAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
39942962 TGATTTT
65 TGATTTT
*
39942969 GAAAAACAAAAATTGAAA
1 G-AAAACAGAAATTGAAA
39942987 AACAGAAATG
Statistics
Matches: 288, Mismatches: 17, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
71 129 0.45
72 17 0.06
73 2 0.01
75 71 0.25
76 6 0.02
77 63 0.22
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (71 bp):
GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
GATTTT
Found at i:39942934 original size:75 final size:75
Alignment explanation
Indices: 39942610--39943669 Score: 837
Period size: 74 Copynumber: 13.9 Consensus size: 75
39942600 TAACGAAAAT
* * * * *
39942610 AGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---T
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39942672 TTTGAA-AAC
66 TTTGAACAAC
* **
39942681 AGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA---T
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39942743 TTTGAA-AAC
66 TTTGAACAAC
* **
39942752 AGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
*
39942817 TTTTTTAACAAC
64 TTTTTGAACAAC
**
39942829 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
39942894 TTTTAACAAC
66 TTTGAACAAC
* *
39942904 AGAAATTGAAATTACCTCAGCGTGTTCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA---T
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
39942966 TTTGAAAAAC
66 TTTGAACAAC
* * *** ** * * * * * **
39942976 AAAAATTGAAA-AACAGAAATG-GAAAATACCTCAGCATGTCCTGAGGCTCAACTCAC-CTCT-T
1 AGAAATTGAAATTAC-CTCA-GCG--TGT-CCT--G-A-G-GCTCA-ACTCACCTCTCGCAATAT
* * *
39943037 GCAATATGAGTTGATTTAGAA-AAC
55 G-AGT-TGA-TT-TTTTTGAACAAC
* ** ** ** * ** *
39943061 AGACATAAAAACAGAAATTGAAAGTGACTCAACACGTGA-GC-CAAGGCTCAACTCACCTTTCGC
1 AGAAAT-TGAA-ATTACCTCAGCGTG--T---C-C-TGAGGCTCAA----C---TCACCTCTCGC
**
39943124 AATATGAGTTGATTTTTTTGAA-AGT
50 AATATGAGTTGATTTTTTTGAACAAC
* * * * *
39943149 AGAATTTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
39943212 TTTGAAAAAAC
66 TTTG-AACAAC
39943223 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
39943286 TTTGAAAAAC
66 TTTGAACAAC
* * *
39943296 ATAAATTGAACAAGAATTGGAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
1 AGAAATTG----A-AA-T-----TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
*
39943361 GAGTTGATTTTCTTGAA-AAGC
55 GAGTTGATTTTTTTGAACAA-C
* ** *
39943382 AGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39943447 TTTG-ACAAC
66 TTTGAACAAC
* *
39943456 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCGCCTCTAGCAATATGAGTTGA---T
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
39943518 TTTGAAAAAC
66 TTTGAACAAC
* ** *
39943528 AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---T
39943593 TTTTTTG-ACAAC
63 TTTTTTGAACAAC
*
39943605 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39943670 GAAAAACAAA
Statistics
Matches: 813, Mismatches: 107, Indels: 135
0.77 0.10 0.13
Matches are distributed among these distances:
71 131 0.16
72 86 0.11
73 16 0.02
74 147 0.18
75 130 0.16
76 6 0.01
77 126 0.15
78 8 0.01
79 6 0.01
80 10 0.01
81 16 0.02
82 1 0.00
84 48 0.06
85 10 0.01
86 29 0.04
87 7 0.01
88 14 0.02
89 5 0.01
90 10 0.01
91 5 0.01
92 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (75 bp):
AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTTGAACAAC
Found at i:39942986 original size:14 final size:14
Alignment explanation
Indices: 39942967--39943001 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39942957 TGAGTTGATT
39942967 TTGAAAAACAAAAA
1 TTGAAAAACAAAAA
*
39942981 TTGAAAAACAGAAA
1 TTGAAAAACAAAAA
*
39942995 TGGAAAA
1 TTGAAAA
39943002 TACCTCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.06, G:0.14, T:0.14
Consensus pattern (14 bp):
TTGAAAAACAAAAA
Found at i:39943046 original size:86 final size:83
Alignment explanation
Indices: 39942901--39943139 Score: 277
Period size: 86 Copynumber: 2.8 Consensus size: 83
39942891 TTTTTTTAAC
* * * *
39942901 AACAGAAATTGAAATTACCTCAGCGTGTTCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAT
39942966 TTTGAAAAACAAAAATTGAAA
66 TTTG-AAAACAAAAA-T-AAA
*
39942987 AACAGAAATGGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAT
* * *
39943052 TTAGAAAACAGACATAAA
66 TTTGAAAACAAAAATAAA
* * * *
39943070 AACAGAAATTGAAAGTGA-CTCAACACGTGAGCC-AAGGCTCAACTCACCT-TTCGCAATATGAG
1 AACAGAAATTGAAAAT-ACCTCAGCA--TG-TCCTGAGGCTCAACTCACCTCTT-GCAATATGAG
39943132 TTGATTTT
61 TTGATTTT
39943140 TTTGAAAGTA
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
83 23 0.17
84 4 0.03
85 42 0.31
86 65 0.49
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (83 bp):
AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAT
TTTGAAAACAAAAATAAA
Found at i:39943252 original size:233 final size:231
Alignment explanation
Indices: 39942259--39943683 Score: 1087
Period size: 233 Copynumber: 6.2 Consensus size: 231
39942249 CATGTGAACT
* * *** *
39942259 GAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
* ** *
39942324 GCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT---------T-AA-AAC-
66 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAAACATAAATAACA
* * ** *
39942377 AGAAATT-GAAATTACCTCAGCGTGTC-CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA-A
130 AG-AATTGGAAA-TACCTCAACGTGGCTC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* **
39942439 TT-TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTT
192 TTCTTGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
** *
39942478 GAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG--AAAACAGAAATTGAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
** * * * ** * **
39942541 ATGTGTCTTGGGGCTCAACTTATTTCTCGCAATATGAGTTGATTCTTTCAAAAACAT-AATAACG
66 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATT-TTGAAAAAACATAAATAAC-
* *** * *
39942605 AAAATAGAAATGGAAAATACCTCGGTGTGAC-CTGAGGCTCAACTCACCTCTCGCAATATGAGTT
129 ---A-AGAATTGG-AAATACCTCAACGTGGCTC-AAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
39942669 GA--TT-TTGAAAA-CAGAAATTGAAATTACCTCAGCGTGTCCT
188 GATTTTCTTGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
* **
39942709 AAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTG--AAAACAGAAATTGAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
* ** * **** * *
39942771 GCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT-----TTTTTTAACAAC-A
66 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAACATAAATAACAA
* * * **
39942830 GAAATT-GAAATTACCTCAGCGTGTC-CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
131 G-AATTGGAAA-TACCTCAACGTGGCTC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * * * ** *
39942893 TTTTTAACAA-CAGAAATTGAAATTACCTCAGCGTGTTCT
193 TCTTGAA-AAGCAGAAATTGAAAATACCTCAACGTGCCCC
*
39942932 GAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTGAAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG----------A---AAAAACAGAAAT
* * * * *
39942996 GGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTAGAAAAC
53 TGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-
*
39943061 AGACATAAA-AAC-AGAAATT-GAAAGTGA-CTCAACACGTGAGC-CAAGGCTCAACTCACCTTT
117 A-ACATAAATAACAAG-AATTGGAAA-T-ACCTC-A-ACGTG-GCTCAAGGCTCAACTCACCTCT
* * * **
39943121 CGCAATATGAGTTGATTTTTTTG-AAAGTAGAATTTGAAAATACCTCGGCGTGCCCC
175 CGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
39943177 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
*
39943242 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACATAAATTGAA
66 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAAACATAAA-T-AA
* **
39943306 CAAGAATTGGAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
128 CAAGAATTGGAAATACCTCAACGTGGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * **
39943371 TCTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTT
193 TCTTGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
*** *
39943410 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
*
39943475 GCGTGTCCTGAGGCTCAACTCGCCTCTAGCAATATGAGTTGATTTTG-AAAAAC-------A-AA
66 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAACATAAATAACAA
* * * ** *
39943531 -AATT-GAAATTACCTCAGCGTGTC-CTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTT
131 GAATTGGAAA-TACCTCAACGTGGCTC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGA---T
* * * * * *
39943593 TTTTTTGACAA-CAGAAATTGAAATTACCTCAGCGTGTCCT
191 TTTCTTGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
* *
39943633 GAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTG-AAAAACAAAAATT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT
39943684 AAAAGTCTTA
Statistics
Matches: 1024, Mismatches: 114, Indels: 134
0.81 0.09 0.11
Matches are distributed among these distances:
216 3 0.00
217 60 0.06
218 3 0.00
219 82 0.08
220 7 0.01
221 59 0.06
222 10 0.01
223 122 0.12
224 11 0.01
225 5 0.00
226 3 0.00
227 3 0.00
229 2 0.00
230 67 0.07
231 66 0.06
232 67 0.07
233 240 0.23
234 18 0.02
235 6 0.01
236 1 0.00
238 62 0.06
244 20 0.02
245 60 0.06
246 45 0.04
247 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (231 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCA
GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAACATAAATAACAA
GAATTGGAAATACCTCAACGTGGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCT
TGAAAAGCAGAAATTGAAAATACCTCAACGTGCCCC
Found at i:39943599 original size:149 final size:146
Alignment explanation
Indices: 39943310--39943683 Score: 538
Period size: 149 Copynumber: 2.5 Consensus size: 146
39943300 ATTGAACAAG
* * *
39943310 AATTGGAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCT
1 AATT-GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTT-T
* * * ** *
39943374 TGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
63 TGAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
39943439 TTGATTTTTTTGACAACAGA
128 TTGATTTTTTTGA-AACAGA
*
39943459 AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCGCCTCTAGCAATATGAGTTGA-TTTTGA
1 AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGA
** *
39943523 AAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTG
66 AAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
39943588 ATTTTTTTTTTGACAACAGA
131 A---TTTTTTTGA-AACAGA
39943608 AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGA
1 AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGA
39943672 AAAACAAAAATT
66 AAAACAAAAATT
39943684 AAAAGTCTTA
Statistics
Matches: 207, Mismatches: 14, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
146 61 0.29
147 2 0.01
148 4 0.02
149 140 0.68
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (146 bp):
AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGA
AAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTGAAACAGA
Found at i:39943806 original size:69 final size:71
Alignment explanation
Indices: 39943693--39943860 Score: 202
Period size: 69 Copynumber: 2.4 Consensus size: 71
39943683 TAAAAGTCTT
* * **
39943693 AACTCACTTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
1 AACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGTGCCCCG
39943756 AGGCTC
66 AGGCTC
** * * **
39943762 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAA-A-AAATTAAAAATACCTCAACGTGTCTTG
1 AACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGTGCCCCG
39943825 AGGCTC
66 AGGCTC
39943831 AACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AACTCACT-TCTCGCAATATGAGTTGATTTT
39943861 CCTTGGAAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 1 0.01
69 77 0.90
70 3 0.03
71 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (71 bp):
AACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGTGCCCCG
AGGCTC
Found at i:39970336 original size:21 final size:21
Alignment explanation
Indices: 39970296--39970336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39970286 TTTAAGATGG
*
39970296 ATGTTTTGAGCTTGTTTAATC
1 ATGTTTTGAGCTTGTATAATC
39970317 ATGTTTTGAG-TTGGTATAAT
1 ATGTTTTGAGCTT-GTATAAT
39970337 TGATGGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (21 bp):
ATGTTTTGAGCTTGTATAATC
Found at i:39972430 original size:42 final size:44
Alignment explanation
Indices: 39972322--39972486 Score: 137
Period size: 43 Copynumber: 3.8 Consensus size: 44
39972312 AACTCATACA
* * * *
39972322 ATGCCAACGTCCCAGACGA-GGTCTTACATGTAATCA--AATATTG
1 ATGCCAACGTCCCAAAC-ATGGTCTTACACGAAATCATCAA-ATCG
* * ** *
39972365 ATGTC-ACTGTCCCAAACAGGGTCTTGTACGAAATCAT-ATA-CG
1 ATGCCAAC-GTCCCAAACATGGTCTTACACGAAATCATCAAATCG
* *
39972407 ATGCTAACGTCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAACGTCCCAAACATGGTCTTACACG-AAATCATCAAATCG
*
39972451 ATGCCAACGTCCCAAACGTGGTCTTACACGAAATCA
1 ATGCCAACGTCCCAAACATGGTCTTACACGAAATCA
39972487 CATATCGGAA
Statistics
Matches: 96, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
42 26 0.27
43 40 0.42
44 30 0.31
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGCCAACGTCCCAAACATGGTCTTACACGAAATCATCAAATCG
Found at i:39972483 original size:86 final size:85
Alignment explanation
Indices: 39972317--39972486 Score: 195
Period size: 86 Copynumber: 2.0 Consensus size: 85
39972307 TCGTAAACTC
* * *
39972317 ATACAATGCCAACGTCCCAGACGAGGTCTTACATGTAATCAAATATTGATGTCACTGTCCCAAAC
1 ATACAATGCCAACGTCCCAGACGAGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAAC
**
39972382 AGGGTCTTGTACGAAATCAT
66 AGGGTCTTACACGAAATCAT
* * *
39972402 ATACGATGCTAACGTCCCAGAC-ATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCC
1 ATACAATGCCAACGTCCCAGACGA-GGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTCCC
39972464 AAAC-GTGGTCTTACACGAAATCA
62 AAACAG-GGTCTTACACGAAATCA
39972487 CATATCGGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
84 1 0.01
85 32 0.44
86 35 0.49
87 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (85 bp):
ATACAATGCCAACGTCCCAGACGAGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAAC
AGGGTCTTACACGAAATCAT
Found at i:39976119 original size:13 final size:13
Alignment explanation
Indices: 39976103--39976128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39976093 GAGTTTATAA
39976103 ATAATTAATAGAG
1 ATAATTAATAGAG
39976116 ATAATTAATAGAG
1 ATAATTAATAGAG
39976129 CAAAATCATA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
ATAATTAATAGAG
Found at i:39977968 original size:30 final size:30
Alignment explanation
Indices: 39977932--39977996 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
39977922 ACTTATTTTA
39977932 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
* *
39977962 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
39977992 TTGTT
1 TTGTT
39977997 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGGCAT
Found at i:39978149 original size:13 final size:11
Alignment explanation
Indices: 39978115--39978142 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39978105 TATATATATT
39978115 TAAAAATAATA
1 TAAAAATAATA
39978126 TAAAAATAATA
1 TAAAAATAATA
39978137 TAAAAA
1 TAAAAA
39978143 ATTAATACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:39979308 original size:13 final size:14
Alignment explanation
Indices: 39979287--39979317 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39979277 TTTAAAAAAT
39979287 AATTAAAATATACA
1 AATTAAAATATACA
39979301 AATT-AAATATACA
1 AATTAAAATATACA
39979314 AATT
1 AATT
39979318 TTGTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTAAAATATACA
Found at i:39979785 original size:14 final size:14
Alignment explanation
Indices: 39979766--39979793 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39979756 GCTACTGATT
39979766 ACAATGTTGTGTTG
1 ACAATGTTGTGTTG
39979780 ACAATGTTGTGTTG
1 ACAATGTTGTGTTG
39979794 TTAATCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (14 bp):
ACAATGTTGTGTTG
Found at i:39980045 original size:19 final size:20
Alignment explanation
Indices: 39980000--39980049 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
39979990 AAAAGAATTG
39980000 TACTATTTTTTACTGTTTTGC
1 TACTATTTTTTA-TGTTTTGC
*
39980021 TGCTATTTTTT-TGTTTT-C
1 TACTATTTTTTATGTTTTGC
39980039 TCACTATTTTT
1 T-ACTATTTTT
39980050 CTATCATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
21 10 0.38
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.66
Consensus pattern (20 bp):
TACTATTTTTTATGTTTTGC
Found at i:39981999 original size:11 final size:11
Alignment explanation
Indices: 39981983--39982007 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39981973 CCTTCCAACC
39981983 ATTATCCTAAT
1 ATTATCCTAAT
39981994 ATTATCCTAAT
1 ATTATCCTAAT
39982005 ATT
1 ATT
39982008 TTTTTGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATCCTAAT
Found at i:39985167 original size:18 final size:20
Alignment explanation
Indices: 39985130--39985169 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
39985120 ACCTAACACG
*
39985130 AATTAAATTTAAGCCATTTC
1 AATTAAATTTAAGACATTTC
39985150 AATTAAA-TTAA-ACATTTC
1 AATTAAATTTAAGACATTTC
39985168 AA
1 AA
39985170 CATCACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTAAATTTAAGACATTTC
Found at i:39995025 original size:30 final size:29
Alignment explanation
Indices: 39994984--39995043 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
39994974 CGGCTTCTTT
39994984 TCCTGCAGATAAAGTGCTTGTTGAAAACC
1 TCCTGCAGATAAAGTGCTTGTTGAAAACC
*
39995013 NTCCTGCTGATAAAGTGCTTGTTGAAAACC
1 -TCCTGCAGATAAAGTGCTTGTTGAAAACC
39995043 T
1 T
39995044 GGGGGATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.30
Consensus pattern (29 bp):
TCCTGCAGATAAAGTGCTTGTTGAAAACC
Found at i:40000336 original size:30 final size:30
Alignment explanation
Indices: 40000295--40000357 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40000285 TTTTTTTTGA
*
40000295 AAGATCCGAAACATGATCTTCAACGGTAGC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
*
40000325 AAGATCGGAAACATGATCTTCAACGGTAAC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
40000355 AAG
1 AAG
40000358 CTTGGCGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (30 bp):
AAGATCCGAAACATGATCTTCAACGGTAAC
Found at i:40000423 original size:30 final size:30
Alignment explanation
Indices: 40000382--40000438 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
40000372 TTGAAATATA
*
40000382 CGAAGCATGATCTTCAACGGTAACAAGATC
1 CGAAACATGATCTTCAACGGTAACAAGATC
*
40000412 CGAAACATGATCTTCAGCGGTAACAAG
1 CGAAACATGATCTTCAACGGTAACAAG
40000439 CTTGGCGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (30 bp):
CGAAACATGATCTTCAACGGTAACAAGATC
Found at i:40000425 original size:81 final size:81
Alignment explanation
Indices: 40000290--40000489 Score: 346
Period size: 81 Copynumber: 2.5 Consensus size: 81
40000280 TTAATTTTTT
* * * *
40000290 TTTGAAAGATCCGAAACATGATCTTCAACGGTAGCAAGATCGGAAACATGATCTTCAACGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
40000355 AAGCTTGGCGGTGAAG
66 AAGCTTGGCGGTGAAG
* *
40000371 TTTGAAATATACGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAGCGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
40000436 AAGCTTGGCGGTGAAG
66 AAGCTTGGCGGTGAAG
40000452 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
40000490 CTTGGCGGTG
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 112 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (81 bp):
TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
AAGCTTGGCGGTGAAG
Found at i:40001548 original size:39 final size:39
Alignment explanation
Indices: 40001484--40001564 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
40001474 ATAAAAGTGG
*
40001484 AATTTGACATGTGAAAAATAGTCTTA-TACTTTATATTTT
1 AATTTGACATGTGAAAAATAGTCTTATTAATTT-TATTTT
* *
40001523 AATTT-ACATGTTAAAAATTATTCTTATTAATTTTATTTT
1 AATTTGACATGTGAAAAA-TAGTCTTATTAATTTTATTTT
40001562 AAT
1 AAT
40001565 ATACTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 11 0.30
39 21 0.57
40 5 0.14
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (39 bp):
AATTTGACATGTGAAAAATAGTCTTATTAATTTTATTTT
Found at i:40007560 original size:19 final size:21
Alignment explanation
Indices: 40007538--40007582 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40007528 TTTTATGGCC
*
40007538 TTTTTAG-AAATTTG-GTTTT
1 TTTTTAGAAAATTTGAGATTT
*
40007557 TTTTTTGAAAATTTGAGATTT
1 TTTTTAGAAAATTTGAGATTT
40007578 TTTTT
1 TTTTT
40007583 GTAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.64
Consensus pattern (21 bp):
TTTTTAGAAAATTTGAGATTT
Found at i:40021739 original size:151 final size:151
Alignment explanation
Indices: 40021460--40021771 Score: 606
Period size: 151 Copynumber: 2.1 Consensus size: 151
40021450 TGAAATGTTA
40021460 AAGGTAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTT
1 AAGG-AATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTT
40021525 TGGTACTCTTATTATTAATAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAA
65 TGGTACTCTTATTATTAATAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAA
40021590 TTAGTCCTCTTACTTCTATTTC
130 TTAGTCCTCTTACTTCTATTTC
*
40021612 AATGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
1 AAGGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
40021677 GGTACTCTTATTATTAATAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
66 GGTACTCTTATTATTAATAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
40021742 TAGTCCTCTTACTTCTATTTC
131 TAGTCCTCTTACTTCTATTTC
40021763 AAGGAATTT
1 AAGGAATTT
40021772 AGTTCTACTT
Statistics
Matches: 158, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
151 155 0.98
152 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (151 bp):
AAGGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
GGTACTCTTATTATTAATAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
TAGTCCTCTTACTTCTATTTC
Found at i:40023234 original size:8 final size:8
Alignment explanation
Indices: 40023204--40023242 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
40023194 ATTGGTTTGG
40023204 TTTTTAAAA
1 TTTTT-AAA
*
40023213 TATTTAATA
1 TTTTTAA-A
40023222 TTTTTAAA
1 TTTTTAAA
40023230 TTTTTAAA
1 TTTTTAAA
40023238 TTTTT
1 TTTTT
40023243 TAAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 16 0.59
9 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTTAAA
Found at i:40023243 original size:17 final size:16
Alignment explanation
Indices: 40023204--40023258 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
40023194 ATTGGTTTGG
*
40023204 TTTTTAAAATATTTAA
1 TTTTTTAAATATTTAA
*
40023220 TATTTTTAAATTTTTAAA
1 T-TTTTTAAATATTT-AA
*
40023238 TTTTTTAAAAATTTTAA
1 TTTTTTAAATA-TTTAA
40023255 TTTT
1 TTTT
40023259 GAATTAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 25 0.78
18 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAAATATTTAA
Found at i:40023252 original size:18 final size:16
Alignment explanation
Indices: 40023204--40023258 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
40023194 ATTGGTTTGG
40023204 TTTTTAAAATATTTAAT
1 TTTTTAAAAT-TTTAAT
*
40023221 ATTTTTAAATTTTTAAAT
1 -TTTTTAAAATTTT-AAT
40023239 TTTTTAAAAATTTTAAT
1 TTTTT-AAAATTTTAAT
40023256 TTT
1 TTT
40023259 GAATTAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAATTTTAAT
Found at i:40026901 original size:28 final size:30
Alignment explanation
Indices: 40026870--40026929 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 30
40026860 GTTATTGTAG
40026870 TATTTATATATT-TAG-AATTTAG-TCTTTA
1 TATTTATAT-TTCTAGAAATTTAGATCTTTA
*
40026898 TATTTTTATTTCTAGAAATTTAGATTCTTTA
1 TATTTATATTTCTAGAAATTTAGA-TCTTTA
40026929 T
1 T
40026930 TTTTCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.07
28 11 0.41
29 7 0.26
31 7 0.26
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (30 bp):
TATTTATATTTCTAGAAATTTAGATCTTTA
Found at i:40027355 original size:21 final size:21
Alignment explanation
Indices: 40027331--40027370 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40027321 TTGTATTTGT
40027331 ATTTTTATT-TTTTAAAAAATA
1 ATTTTT-TTATTTTAAAAAATA
40027352 ATTTTTTTATTTTAAAAAA
1 ATTTTTTTATTTTAAAAAA
40027371 GTAAGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTTATTTTAAAAAATA
Found at i:40027650 original size:27 final size:25
Alignment explanation
Indices: 40027589--40027651 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
40027579 ATTTGATGAG
*
40027589 AATAATTTATTAAATAAAAATAAAAT
1 AATAATTT-TTAAATAAAAACAAAAT
* *
40027615 AATATTTTTTAAAATTAAAACAAAAT
1 AATAATTTTT-AAATAAAAACAAAAT
40027641 AATAAATTTTT
1 AAT-AATTTTT
40027652 TTGACAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 23 0.74
27 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATTTTTAAATAAAAACAAAAT
Found at i:40028035 original size:29 final size:29
Alignment explanation
Indices: 40027993--40028062 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
40027983 ATAAGTAAGT
* *
40027993 CCTTAAAGTATTTTTGT-ATCTAAAGAAGC
1 CCTTAAACTATTTTT-TAACCTAAAGAAGC
* *
40028022 CCTTAAACTTTTTTTTACACCTAAATAAGC
1 CCTTAAACTATTTTTTA-ACCTAAAGAAGC
40028052 CCTTAAACTAT
1 CCTTAAACTAT
40028063 AATGACTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 13 0.38
30 20 0.59
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (29 bp):
CCTTAAACTATTTTTTAACCTAAAGAAGC
Found at i:40045026 original size:84 final size:84
Alignment explanation
Indices: 40044874--40045027 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
40044864 GCTCTTCCTT
* * * * *
40044874 TTTTTTTCACTCAATTGAGCACTTGATCTTTCAAAATACATCAAAAAGATCCTCAAACTTCTTAA
1 TTTTTTTCACTAAATTGAGCACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTTAA
40044939 AAAAAAACAAGTAAGTACA
66 AAAAAAACAAGTAAGTACA
* * * *
40044958 TTTTTTTCACTAAATTCG-GTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAAATTTTTC
1 TTTTTTTCACTAAATT-GAGCACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTTA
40045022 AAAAAA
65 AAAAAA
40045028 GCAATTAAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 59 0.98
85 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (84 bp):
TTTTTTTCACTAAATTGAGCACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAAATTCTTAA
AAAAAAACAAGTAAGTACA
Found at i:40045197 original size:36 final size:36
Alignment explanation
Indices: 40045143--40045214 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
40045133 AATTATATTT
* *
40045143 TTTTATAAAAAACGTAAAAAATAAAAAAATGTAAAA
1 TTTTATAAAAAACATAAAAAATAAAAAAATGCAAAA
* *
40045179 TTTTATAAAAATA-ATAAAAAATTATAAAATGCAAAA
1 TTTTATAAAAA-ACATAAAAAATAAAAAAATGCAAAA
40045215 AAAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (36 bp):
TTTTATAAAAAACATAAAAAATAAAAAAATGCAAAA
Found at i:40045471 original size:183 final size:181
Alignment explanation
Indices: 40045227--40045591 Score: 439
Period size: 183 Copynumber: 2.0 Consensus size: 181
40045217 AAAAATATTT
** *
40045227 TTAACAATTAACTTTAACTATTGATTGTTAAAGTTAACGACCCCTAGTTTTTTTCAATTAAAGTC
1 TTAACAATTAACTTTAACTATTGACCGTTAAAGTTAACGACCCCTAGTTTTTTTAAATTAAAGTC
* ** * * * *
40045292 ATCGCGTGTTGCAACATAGTGTGATATGTGGCAAAAAATGAT-AATAA-AAAAATCAATAAAAGT
66 ATCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGATAAAAAATAAAAATCAATAAAAGT
* **
40045355 TATAGAAAAATTATGAAATGGTTCTTTTGGTATGATAATTTTTATAAATTTTTTC
131 TATAGAAAAATTAT-AAA--ATT-TTTTGGTACAATAATTTTTATAAATTTTTTC
* * * * * *
40045410 TTAACAATTAGCTTTAATTGTTGACCGTTAAAGTTAATGACCTCT-TTTTTTTTAAAATTAAAGT
1 TTAACAATTAACTTTAACTATTGACCGTTAAAGTTAACGACCCCTAGTTTTTTT-AAATTAAAGT
**
40045474 CATCACGTGTCACAACATAGCGTGACATGTAGTGAAAAATGATAAAAAAAATAAAAATCAATAAA
65 CATCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGAT--AAAAAATAAAAATCAATAAA
* *
40045539 AGTTATAGAAAAATTGTAAAATTTTTTGGTACAATAATTTTTATAATTTTTTT
128 AGTTATAGAAAAATTATAAAATTTTTTGGTACAATAATTTTTATAAATTTTTT
40045592 ACGAAATTTA
Statistics
Matches: 154, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
182 7 0.05
183 109 0.71
184 2 0.01
186 7 0.05
187 29 0.19
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (181 bp):
TTAACAATTAACTTTAACTATTGACCGTTAAAGTTAACGACCCCTAGTTTTTTTAAATTAAAGTC
ATCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGATAAAAAATAAAAATCAATAAAAGT
TATAGAAAAATTATAAAATTTTTTGGTACAATAATTTTTATAAATTTTTTC
Found at i:40045693 original size:28 final size:28
Alignment explanation
Indices: 40045644--40045698 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
40045634 ACTTTATAAA
* *
40045644 ATTTTATAATTTTTTTATATTTCTATAT
1 ATTTTATAATTCTTTTAGATTTCTATAT
*
40045672 ATTTTATAA-TCTTTTACGATTTTTATA
1 ATTTTATAATTCTTTTA-GATTTCTATA
40045699 AAAATTTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
ATTTTATAATTCTTTTAGATTTCTATAT
Found at i:40045909 original size:85 final size:85
Alignment explanation
Indices: 40045827--40046041 Score: 224
Period size: 85 Copynumber: 2.5 Consensus size: 85
40045817 TAATAAAATC
40045827 AGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTGATACATTTTGAAAGTTCAAG
1 AGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGT-TTTTTTGATACATTTTGAAAGTTCAAG
*
40045892 TATCC-AATTGAGT-TAAAAAAA
65 TACCCAAATT-AGTGT-AAAAAA
** * * * * *
40045913 AGTAG--TAATTACTTCTTTTTTAAAAATGTTTGAGGGTATTTTCGATGCATTTTGAAATTTCAA
1 AGGGGCTTAATTACTT-TTTTTGAAAAA-GTTTGAGGGTTTTTTTGATACATTTTGAAAGTTCAA
*
40045976 GTACCCAAATTAGTGCAAAAAA
64 GTACCCAAATTAGTGTAAAAAA
* * *
40045998 AGGGACTTAATTGCTTTTTTCGAAACAA-TTTGAGGGGTTTTTTT
1 AGGGGCTTAATTACTTTTTTTGAAA-AAGTTTGA-GGGTTTTTTT
40046042 CACCCTTAAG
Statistics
Matches: 104, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
84 9 0.09
85 53 0.51
86 32 0.31
87 10 0.10
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (85 bp):
AGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTTTTTTTGATACATTTTGAAAGTTCAAGT
ACCCAAATTAGTGTAAAAAA
Found at i:40048600 original size:15 final size:15
Alignment explanation
Indices: 40048582--40048626 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40048572 ATTTTCTAGG
*
40048582 TTTGTTTAATTTTTT
1 TTTGTTTAATTATTT
*
40048597 TTTGTCTAGATTATTT
1 TTTGTTTA-ATTATTT
*
40048613 TTTCTTTAATTATT
1 TTTGTTTAATTATT
40048627 ATTAAAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (15 bp):
TTTGTTTAATTATTT
Found at i:40051720 original size:16 final size:16
Alignment explanation
Indices: 40051696--40051726 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40051686 TTAATTGTTA
40051696 ATTACAACTCTATTTC
1 ATTACAACTCTATTTC
*
40051712 ATTATAACTCTATTT
1 ATTACAACTCTATTT
40051727 TATTCCAATA
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:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:40057322 original size:65 final size:64
Alignment explanation
Indices: 40057218--40057346 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 64
40057208 TAATTTTAAT
40057218 TGTATACAAAACTTCCCTATATGGCATTTCAATTAAACTCCACTTCCCCCCCCCCCCAACCAAAA
1 TGTATACAAAACTTCCCTATATGGCATTTCAATTAAACTCCACTT-CCCCCCCCCCCAACCAAAA
*
40057283 TGTATACAAAACTTCCCTATATGGCATTTCAATTAAACTCCACTTCCCTCCCCCCCAACCAAAA
1 TGTATACAAAACTTCCCTATATGGCATTTCAATTAAACTCCACTTCCCCCCCCCCCAACCAAAA
40057347 AAAAATTCCA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 18 0.29
65 45 0.71
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (64 bp):
TGTATACAAAACTTCCCTATATGGCATTTCAATTAAACTCCACTTCCCCCCCCCCCAACCAAAA
Found at i:40059533 original size:2 final size:2
Alignment explanation
Indices: 40059494--40059522 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40059484 CAATCAAAGA
40059494 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40059523 GTTTGTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40062049 original size:3 final size:3
Alignment explanation
Indices: 40062041--40062066 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40062031 TAATAAAGCG
40062041 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40062067 TGATCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40062422 original size:29 final size:29
Alignment explanation
Indices: 40062369--40062434 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
40062359 AAAATTTATA
*
40062369 TTTAAAAAAATATAAAAAACATT-AATTT
1 TTTAAAAAAATATAAAAAACATTAAAATT
* *
40062397 TTTAAAGAACATATAAAGAAA-GTTAAAATT
1 TTTAAA-AAAATATAAA-AAACATTAAAATT
40062427 TTTAAAAA
1 TTTAAAAA
40062435 TTTCTAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.19
29 13 0.41
30 13 0.41
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTAAAAAAATATAAAAAACATTAAAATT
Found at i:40062651 original size:21 final size:21
Alignment explanation
Indices: 40062622--40062663 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40062612 GAATAATTTC
* *
40062622 ATTTGATTTGACTCAACTTGA
1 ATTTCATTTCACTCAACTTGA
*
40062643 ATTTCATTTCACTCCACTTGA
1 ATTTCATTTCACTCAACTTGA
40062664 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTTCATTTCACTCAACTTGA
Found at i:40062899 original size:13 final size:13
Alignment explanation
Indices: 40062881--40062905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40062871 TAGGATTGAT
40062881 TTAATATTTATTA
1 TTAATATTTATTA
40062894 TTAATATTTATT
1 TTAATATTTATT
40062906 TTCAAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATATTTATTA
Found at i:40071669 original size:31 final size:31
Alignment explanation
Indices: 40071643--40071707 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
40071633 AATTTTTTGT
40071643 TCAATTTTT-TCTGTTTATATCGATTTTCAAG
1 TCAATTTTTCT-TGTTTATATCGATTTTCAAG
40071674 TCAATTTTTCTTGTTTATATCGATTTTCAAG
1 TCAATTTTTCTTGTTTATATCGATTTTCAAG
40071705 TCA
1 TCA
40071708 GTTGATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (31 bp):
TCAATTTTTCTTGTTTATATCGATTTTCAAG
Found at i:40071842 original size:82 final size:82
Alignment explanation
Indices: 40071742--40071905 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
40071732 CTAATATTTG
40071742 GATTGATTCTTTATCCAACCAATTGATTTGATTCGATTCATATAACATTAATTTTGAATCGAGAT
1 GATTGATTCTTTATCCAACCAATTGATTTGATTCGATTCATATAACATTAATTTTGAATCGAGAT
40071807 TTAAGGTTTAAGGGAAA
66 TTAAGGTTTAAGGGAAA
40071824 GATTGATTCTTTATCCAACCAATTGATTTGATTCGATTCATATAACATTAATTTTGAATCGAGAT
1 GATTGATTCTTTATCCAACCAATTGATTTGATTCGATTCATATAACATTAATTTTGAATCGAGAT
*
40071889 TTAAGGTTTATGGGAAA
66 TTAAGGTTTAAGGGAAA
40071906 TAGTTTTTTA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.40
Consensus pattern (82 bp):
GATTGATTCTTTATCCAACCAATTGATTTGATTCGATTCATATAACATTAATTTTGAATCGAGAT
TTAAGGTTTAAGGGAAA
Found at i:40079169 original size:23 final size:22
Alignment explanation
Indices: 40079126--40079183 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40079116 AAAAGGTATC
* *
40079126 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40079147 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40079170 TGCATATCATATCT
1 TACAAATCATATCT
40079184 AAGATTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40079186 original size:19 final size:19
Alignment explanation
Indices: 40079162--40079306 Score: 230
Period size: 19 Copynumber: 7.9 Consensus size: 19
40079152 AATCATATCT
40079162 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40079181 TCTAAGATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
40079199 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
40079216 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40079235 TCTAAGATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
40079253 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
40079270 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40079289 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
40079307 TGAAGATTAT
Statistics
Matches: 118, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
17 32 0.27
18 32 0.27
19 54 0.46
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40079230 original size:54 final size:54
Alignment explanation
Indices: 40079162--40079298 Score: 274
Period size: 54 Copynumber: 2.5 Consensus size: 54
40079152 AATCATATCT
40079162 TCTAAGATTGCATATCATATCTAAGATTGTAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGTAATCATATCTAAGATTGTATCATA
40079216 TCTAAGATTGCATATCATATCTAAGATTGTAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGTAATCATATCTAAGATTGTATCATA
40079270 TCTAAGATTGCATATCATATCTAAGATTG
1 TCTAAGATTGCATATCATATCTAAGATTG
40079299 CATATCATTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTGTAATCATATCTAAGATTGTATCATA
Found at i:40079462 original size:21 final size:20
Alignment explanation
Indices: 40079425--40079463 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40079415 TTGGACTTCG
**
40079425 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
40079445 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
40079464 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:40079777 original size:45 final size:45
Alignment explanation
Indices: 40079656--40079791 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 45
40079646 AGAAGGCGAT
*
40079656 ATCTGCTATCTTTGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
40079701 ATCTGCT-TCTTCAATCTGCTCCCCATATAATATAGAGATGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
40079745 ATCTGTTATCTTCGATTTGCTCTCCGTCTAATACAGAGAGGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
40079790 AT
1 AT
40079792 TTTTCATCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 37 0.49
45 39 0.51
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (45 bp):
ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:40079964 original size:78 final size:78
Alignment explanation
Indices: 40079835--40080118 Score: 478
Period size: 78 Copynumber: 3.6 Consensus size: 78
40079825 TGGAGGTTAG
40079835 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
40079900 CAATGAAGGTCAT
66 CAATGAAGGTCAT
*
40079913 ATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
40079978 CAATGAAGGTCAT
66 CAATGAAGGTCAT
* *
40079991 ATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTAGATCTGCTT
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
* *
40080056 TAATGAAGGTCAG
66 CAATGAAGGTCAT
* * * **
40080069 ATCTGCTATGTTTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
40080119 TGTTTCTTCG
Statistics
Matches: 196, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 196 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (78 bp):
ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGATCTGCTT
CAATGAAGGTCAT
Found at i:40080410 original size:78 final size:78
Alignment explanation
Indices: 40080289--40080684 Score: 783
Period size: 78 Copynumber: 5.1 Consensus size: 78
40080279 CAAAGGTTAG
*
40080289 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
1 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
40080354 CAATGAAGGTCCA
66 CAATGAAGGTCCA
40080367 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
1 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
40080432 CAATGAAGGTCCA
66 CAATGAAGGTCCA
40080445 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
1 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
40080510 CAATGAAGGTCCA
66 CAATGAAGGTCCA
40080523 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
1 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
40080588 CAATGAAGGTCCA
66 CAATGAAGGTCCA
40080601 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
1 ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
40080666 CAATGAAGGTCCA
66 CAATGAAGGTCCA
40080679 ATCTGT
1 ATCTGT
40080685 CTTGTCAACA
Statistics
Matches: 317, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 317 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (78 bp):
ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTT
CAATGAAGGTCCA
Found at i:40080928 original size:87 final size:89
Alignment explanation
Indices: 40080832--40080993 Score: 222
Period size: 89 Copynumber: 1.8 Consensus size: 89
40080822 ATAGTACAGA
* *
40080832 GATGCCAAATCATCTTAGATCTGCTTC-A-GCGTAAACA-CGTGAAAGCCAAATCTGCTATGTCT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATC-TGAAAGCCAAATCTGCTATGTCT
40080894 TCGATCTGCTCCTTGTCAACACAAG
65 TCGATCTGCTCCTTGTCAACACAAG
* * * ** *
40080919 GATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
40080984 CGATCTGCTC
66 CGATCTGCTC
40080994 TCCGTCGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 25 0.39
88 1 0.02
89 37 0.58
90 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
CGATCTGCTCCTTGTCAACACAAG
Found at i:40080941 original size:220 final size:220
Alignment explanation
Indices: 40080685--40081327 Score: 1175
Period size: 220 Copynumber: 2.9 Consensus size: 220
40080675 TCCAATCTGT
40080685 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
1 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
40080750 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
66 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
40080815 TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
131 TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
40080880 AATCTGCTATGTCTTCGATCTGCTC
196 AATCTGCTATGTCTTCGATCTGCTC
40080905 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
1 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
40080970 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
66 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
40081035 TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
131 TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
40081100 AATCTGCTATGTCTTCGATCTGCTC
196 AATCTGCTATGTCTTCGATCTGCTC
40081125 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
1 CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
*
40081190 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTTGATTTG
66 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
* * * * * * * * *
40081255 TTCTCTGACAATATAGAGATG--TAA-CATCTTGGATCCGCTTCAGCGTAAACACCTGAAGGTCA
131 TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
40081317 AATCTGCTATG
196 AATCTGCTATG
40081328 CTTTAGCTTG
Statistics
Matches: 413, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
217 44 0.11
218 2 0.00
220 367 0.89
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (220 bp):
CTTGTCAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAG
ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTG
TTCTCTGATAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
AATCTGCTATGTCTTCGATCTGCTC
Found at i:40081148 original size:87 final size:89
Alignment explanation
Indices: 40081052--40081213 Score: 222
Period size: 89 Copynumber: 1.8 Consensus size: 89
40081042 ATAGTACAGA
* *
40081052 GATGCCAAATCATCTTAGATCTGCTTC-A-GCGTAAACA-CGTGAAAGCCAAATCTGCTATGTCT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATC-TGAAAGCCAAATCTGCTATGTCT
40081114 TCGATCTGCTCCTTGTCAACACAAG
65 TCGATCTGCTCCTTGTCAACACAAG
* * * ** *
40081139 GATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
40081204 CGATCTGCTC
66 CGATCTGCTC
40081214 TCCGTCGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 25 0.39
88 1 0.02
89 37 0.58
90 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
CGATCTGCTCCTTGTCAACACAAG
Found at i:40085582 original size:47 final size:47
Alignment explanation
Indices: 40085513--40085607 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
40085503 AATTTTCACC
40085513 TCTTTCCATTCCTCTAGGGCTATATTCTCTACTACCTCTTTCTCATG
1 TCTTTCCATTCCTCTAGGGCTATATTCTCTACTACCTCTTTCTCATG
* * * *
40085560 TCTTTCCCTTCCTCTAGGGCTATATTCTCTATTGCCTGTTTCTCATG
1 TCTTTCCATTCCTCTAGGGCTATATTCTCTACTACCTCTTTCTCATG
40085607 T
1 T
40085608 GGCATGATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.13, C:0.31, G:0.11, T:0.46
Consensus pattern (47 bp):
TCTTTCCATTCCTCTAGGGCTATATTCTCTACTACCTCTTTCTCATG
Found at i:40089869 original size:22 final size:22
Alignment explanation
Indices: 40089834--40089891 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40089824 AAAAGGTATC
* *
40089834 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
40089855 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40089878 TGCATATCATATCT
1 TACAAATCATATCT
40089892 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40089894 original size:19 final size:19
Alignment explanation
Indices: 40089870--40089941 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
40089860 AATCATATCT
40089870 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40089889 TCTAAGATTGCA-AT--TA
1 TCTAAGATTGCATATCATA
40089905 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40089924 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
40089942 TGAAAATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.28
17 2 0.04
18 2 0.04
19 32 0.64
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40089939 original size:14 final size:14
Alignment explanation
Indices: 40089885--40089920 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
40089875 GATTGCATAT
40089885 CATATCTAAGATTG
1 CATATCTAAGATTG
40089899 CAATTATCTAAGATTG
1 C-A-TATCTAAGATTG
40089915 CATATC
1 CATATC
40089921 ATATCTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 2 0.10
16 13 0.65
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (14 bp):
CATATCTAAGATTG
Found at i:40090097 original size:21 final size:20
Alignment explanation
Indices: 40090060--40090098 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40090050 TTGGACTTCG
**
40090060 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
40090080 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
40090099 TCTGGGCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:40095851 original size:22 final size:22
Alignment explanation
Indices: 40095826--40095890 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
40095816 TAACTTATAT
* * *
40095826 ATTATGATTAACTTATTAATTA
1 ATTATAATTAAATCATTAATTA
*
40095848 ATTATAATTAAATCATTAATTC
1 ATTATAATTAAATCATTAATTA
40095870 ATTA-ACATT-AATC-TTAATTA
1 ATTATA-ATTAAATCATTAATTA
40095890 A
1 A
40095891 CACTTTTGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 25 0.68
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATAATTAAATCATTAATTA
Found at i:40100767 original size:47 final size:47
Alignment explanation
Indices: 40100668--40100795 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 47
40100658 AATCGATAAG
* * ** *
40100668 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCTCGGAG
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
* * * * *
40100715 CACCTATATCACGGCCCGTAGCCGAATCAAGGTAACTCCTTTCAAAA
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
**
40100762 TACCTATATCATGGCCCGTAGAAAAATCAAGGTA
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTA
40100796 TTATTCATAC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (47 bp):
TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
Found at i:40105226 original size:8 final size:8
Alignment explanation
Indices: 40105213--40105238 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40105203 TGTTACTACC
40105213 CACTTTTA
1 CACTTTTA
40105221 CACTTTTA
1 CACTTTTA
40105229 CACTTTTA
1 CACTTTTA
40105237 CA
1 CA
40105239 AACAAGTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (8 bp):
CACTTTTA
Found at i:40106712 original size:21 final size:21
Alignment explanation
Indices: 40106686--40106728 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40106676 ACATCTGAGC
40106686 ATATCTTCAAGTATCTGAATT
1 ATATCTTCAAGTATCTGAATT
40106707 ATATCTTCAAGTATCTGAATT
1 ATATCTTCAAGTATCTGAATT
40106728 A
1 A
40106729 CTCTATGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (21 bp):
ATATCTTCAAGTATCTGAATT
Found at i:40112706 original size:43 final size:43
Alignment explanation
Indices: 40112644--40112725 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
40112634 CATGTACCGA
*
40112644 ATCCATAATGAACTTGGACCACTCAACGAGCTCAGATGCTTGC
1 ATCCATAATGAAATTGGACCACTCAACGAGCTCAGATGCTTGC
*
40112687 ATCCATAAT-AAATTCGGACCACTCAACGAGCTCGGATGC
1 ATCCATAATGAAATT-GGACCACTCAACGAGCTCAGATGC
40112726 CACATATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
ATCCATAATGAAATTGGACCACTCAACGAGCTCAGATGCTTGC
Found at i:40126788 original size:6 final size:6
Alignment explanation
Indices: 40126729--40126833 Score: 72
Period size: 6 Copynumber: 17.5 Consensus size: 6
40126719 ATGGTGGATT
* * * * * *
40126729 TGTATC AGTATC AGTATC AGTATC TGTAT- TAGTATC TATATT TGCATC
1 TGTATC TGTATC TGTATC TGTATC TGTATC T-GTATC TGTATC TGTATC
* * * *
40126777 TATATC TGTATC TATATC TGTAAC TGCATC TGTAT- TCGTATC TGT-TAC
1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC T-GTATC TGTAT-C
40126825 TGTATC TGT
1 TGTATC TGT
40126834 TTGTACACAT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
5 3 0.04
6 71 0.92
7 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (6 bp):
TGTATC
Found at i:40128108 original size:6 final size:6
Alignment explanation
Indices: 40128097--40128144 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
40128087 CAAAGTGAGT
*
40128097 AAAAAG AAAAAG AAAAAG AGTAAAA- AGAAAG AAAATAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A--AAAAG AAAAAG AAAA-AG AAAAAG AAAA
40128145 TATATACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 22 0.61
7 7 0.19
8 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:40128146 original size:13 final size:12
Alignment explanation
Indices: 40128097--40128144 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
40128087 CAAAGTGAGT
40128097 AAAAAGAAAAAG
1 AAAAAGAAAAAG
40128109 AAAAAGAGTAAAA-
1 AAAAAGA--AAAAG
*
40128122 AGAAAGAAAATAG
1 AAAAAGAAAA-AG
40128135 AAAAAGAAAA
1 AAAAAGAAAA
40128145 TATATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 3 0.10
12 8 0.27
13 15 0.50
14 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:40143706 original size:33 final size:34
Alignment explanation
Indices: 40143664--40143730 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
40143654 GTATGCATTT
*
40143664 CTGATACTG-TACTGAAATGGGCTAAGGCCCACA
1 CTGATACTGTTACTGAAATAGGCTAAGGCCCACA
* *
40143697 CTGATACTGTTACTGTATTAGGCTAAGGCCCACA
1 CTGATACTGTTACTGAAATAGGCTAAGGCCCACA
40143731 TGGATATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.30
34 21 0.70
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (34 bp):
CTGATACTGTTACTGAAATAGGCTAAGGCCCACA
Found at i:40147703 original size:42 final size:42
Alignment explanation
Indices: 40147644--40147742 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
40147634 CATGCCCGTA
40147644 TGGCCAAGCCGTGTGGCTCACACGACCAATGAAACGCCCATG
1 TGGCCAAGCCGTGTGGCTCACACGACCAATGAAACGCCCATG
* * * *
40147686 TGGCCATA-CCGTGTGGCTCACACGGCTAATGATACGCCCGTG
1 TGGCCA-AGCCGTGTGGCTCACACGACCAATGAAACGCCCATG
* *
40147728 T-CCCAGGCCGTGTGG
1 TGGCCAAGCCGTGTGG
40147743 GTATTCGATG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 11 0.22
42 37 0.76
43 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.18
Consensus pattern (42 bp):
TGGCCAAGCCGTGTGGCTCACACGACCAATGAAACGCCCATG
Found at i:40156215 original size:45 final size:45
Alignment explanation
Indices: 40156142--40156257 Score: 189
Period size: 45 Copynumber: 2.6 Consensus size: 45
40156132 CGGTACTAAA
* *
40156142 CAGT-ATTTACAGCAGAGCTGCCAATATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
* *
40156186 CAGTGATTTGCAGCAAAGCTGCTAGTATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
40156231 CAGTGATTTGCAGCAGAGCTGCCAGTA
1 CAGTGATTTGCAGCAGAGCTGCCAGTA
40156258 CAGTACACTT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
44 4 0.06
45 61 0.94
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
Found at i:40156428 original size:27 final size:27
Alignment explanation
Indices: 40156395--40156602 Score: 245
Period size: 27 Copynumber: 7.7 Consensus size: 27
40156385 TATCACATAG
* *
40156395 GGGCAAAATAGTCAATTTACCATGTAA
1 GGGCAAAATAGTCATTTTACCATATAA
* * *
40156422 AGGCAAAACAGTCATTTTACCACATAA
1 GGGCAAAATAGTCATTTTACCATATAA
* *
40156449 GGGCAAAATAGTTATTTTACCATACAA
1 GGGCAAAATAGTCATTTTACCATATAA
* * *
40156476 GGGCAAAACAATCATTTTACCACATAA
1 GGGCAAAATAGTCATTTTACCATATAA
* * * **
40156503 GGGAAAAATAATTATTTTATTATATAA
1 GGGCAAAATAGTCATTTTACCATATAA
* *
40156530 GAGCAAAACAGTCATTTTACCATATAA
1 GGGCAAAATAGTCATTTTACCATATAA
*
40156557 GGGCAAAATAGTCATTTTACCACATAA
1 GGGCAAAATAGTCATTTTACCATATAA
*
40156584 GGGCAAAATAATCATTTTA
1 GGGCAAAATAGTCATTTTA
40156603 TCAATTAGGG
Statistics
Matches: 149, Mismatches: 32, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (27 bp):
GGGCAAAATAGTCATTTTACCATATAA
Found at i:40160197 original size:54 final size:54
Alignment explanation
Indices: 40160129--40160234 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
40160119 AAGATTTTTT
*
40160129 TCTATTCTTGGCTTTTACAAAGTCAAAAAATCTGATAAGTCCTTAGCTTTCTCC
1 TCTATTCTTAGCTTTTACAAAGTCAAAAAATCTGATAAGTCCTTAGCTTTCTCC
* * * * *
40160183 TCTATTTTTAGCTTTTACAAGGTCAAAAAATTTGATGAGTCCTTGGCTTTCT
1 TCTATTCTTAGCTTTTACAAAGTCAAAAAATCTGATAAGTCCTTAGCTTTCT
40160235 TCACATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (54 bp):
TCTATTCTTAGCTTTTACAAAGTCAAAAAATCTGATAAGTCCTTAGCTTTCTCC
Found at i:40160958 original size:29 final size:29
Alignment explanation
Indices: 40160926--40161079 Score: 157
Period size: 29 Copynumber: 5.3 Consensus size: 29
40160916 ATCGTAATCG
* **
40160926 TCCCTTTTCATATTTGATGGTCAAAACCA
1 TCCCTTTTCATAATTGATGGTCATCACCA
* *
40160955 TCCCTTTTCATTAATCGATGGTCGTCACCA
1 TCCCTTTTCA-TAATTGATGGTCATCACCA
*
40160985 TCCCTTTTCATAGTTGATGGTCATCACCA
1 TCCCTTTTCATAATTGATGGTCATCACCA
* * * *
40161014 TCCCTTTTCATAATCGATAGCCAT-AGCTA
1 TCCCTTTTCATAATTGATGGTCATCA-CCA
* * *
40161043 TCCCTTTTCATAATCGATAGTCGTCACCA
1 TCCCTTTTCATAATTGATGGTCATCACCA
*
40161072 TCCATTTT
1 TCCCTTTT
40161080 TTTATAGTTT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 79 0.75
30 25 0.24
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (29 bp):
TCCCTTTTCATAATTGATGGTCATCACCA
Found at i:40162529 original size:40 final size:39
Alignment explanation
Indices: 40162492--40162583 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
40162482 GCTACTCGTT
*
40162492 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
40162532 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
40162571 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40162584 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:40162563 original size:39 final size:40
Alignment explanation
Indices: 40162473--40162636 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
40162463 CGGAATTTAA
** *
40162473 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
40162513 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40162552 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40162592 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40162632 CCGGA
1 CCGGA
40162637 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40179388 original size:16 final size:16
Alignment explanation
Indices: 40179367--40179424 Score: 107
Period size: 16 Copynumber: 3.6 Consensus size: 16
40179357 AAAAACCCTA
40179367 AAAGCCCAAAGAATCC
1 AAAGCCCAAAGAATCC
40179383 AAAGCCCAAAGAATCC
1 AAAGCCCAAAGAATCC
*
40179399 AAAGCCCAAAGAATTC
1 AAAGCCCAAAGAATCC
40179415 AAAGCCCAAA
1 AAAGCCCAAA
40179425 AACCTAAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAGCCCAAAGAATCC
Found at i:40187120 original size:43 final size:41
Alignment explanation
Indices: 40187059--40187151 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 41
40187049 ATATATTGTA
*
40187059 CAATGCCAACGTCCTAGAC-GTGGTCTTAC-ATGTAATTACATAT
1 CAATGCC-ACGTCCTAGACAG-GGTCTTACTA-G-AATCACATAT
*
40187102 CAATGCCACTGTCCTAGACAGGGTCTTACTAGAGTCACATAT
1 CAATGCCAC-GTCCTAGACAGGGTCTTACTAGAATCACATAT
40187144 CAATGCCA
1 CAATGCCA
40187152 ACGTATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
42 18 0.40
43 25 0.56
44 2 0.04
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (41 bp):
CAATGCCACGTCCTAGACAGGGTCTTACTAGAATCACATAT
Found at i:40212536 original size:46 final size:46
Alignment explanation
Indices: 40212460--40212571 Score: 129
Period size: 46 Copynumber: 2.4 Consensus size: 46
40212450 ACAGGACAGA
*
40212460 AATGAGCCATGTAAGTCCATAACAGTTATATGGCTTTGGAGACAAG
1 AATGAGCCATGTAAGTCCATAACAGTTATATGGCATTGGAGACAAG
** *
40212506 AATGAGCCATGTAA-TCCCATATTA-TATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGT-CCATAACAGT-TATATGGCATTGGAGACAAG
* **
40212552 AATAATTCATGTAAGTCCAT
1 AATGAGCCATGTAAGTCCAT
40212572 GTCGAAGACA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.04
46 53 0.95
47 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
AATGAGCCATGTAAGTCCATAACAGTTATATGGCATTGGAGACAAG
Found at i:40214046 original size:46 final size:45
Alignment explanation
Indices: 40213965--40214167 Score: 154
Period size: 46 Copynumber: 4.4 Consensus size: 45
40213955 CAAGGCTTAA
* * ** * *
40213965 TATTCTTGTATTCTTGAGTCTACAACAAATTTAGGAACTTGGAACC
1 TATTC-TGTATTCTCGAGTCTACAACATATGCAGGAGCTCGGAACC
* * * * *
40214011 TATTTCTGTATTCTCGAGTCCACAACGTATGTAGGAGCTCGAAACT
1 TA-TTCTGTATTCTCGAGTCTACAACATATGCAGGAGCTCGGAACC
* * ** * *
40214057 TAATCGTGTATTCTCGAGTCTGCAATGTATGCAAGAGCTCAGAACC
1 TATTC-TGTATTCTCGAGTCTACAACATATGCAGGAGCTCGGAACC
* * * * *
40214103 TAATCTTCTATTCTCAAGTCTACAACATATGCAGGAGCTTGGAGCC
1 TATTC-TGTATTCTCGAGTCTACAACATATGCAGGAGCTCGGAACC
**
40214149 TATTCCATATTCTCGAGTC
1 TATTCTGTATTCTCGAGTC
40214168 CCGCAGCATA
Statistics
Matches: 123, Mismatches: 32, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
45 13 0.11
46 107 0.87
47 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (45 bp):
TATTCTGTATTCTCGAGTCTACAACATATGCAGGAGCTCGGAACC
Found at i:40216668 original size:54 final size:54
Alignment explanation
Indices: 40216602--40217811 Score: 1930
Period size: 54 Copynumber: 22.4 Consensus size: 54
40216592 CAATTTGTAG
* * * * *
40216602 AATTACCATTTTACCCTCGATTTATAGAATTACTGTTTCACCCTT-GATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* * * * * *
40216656 AATTACAGTTTTACCCTCGATTTATAGAATTACCATTTTACCC-TCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* * * * * *
40216710 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCC-TCGATTTATAG
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* * * * * * *
40216764 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCC-TCGATTTATAG
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* * * * *
40216818 AATTACCATTTTACCCTCGATTTATAGAATTACTGTTTCACCCTT-GATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* * * * * *
40216872 AATTACAGTTTTACCCTCGATTTATAGAATTACCATTTTACCC-TCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
40216926 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40216980 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217034 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217088 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217142 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217196 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217250 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217304 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217358 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217412 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217466 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217520 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217574 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217628 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
** * * *
40217682 AATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTA-CCTTTGATTTATAG
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAG-TTTACAA
* *
40217736 AATTACTGTTTTACCCTCAATTTACAAAATTACTATTTTACCCTTAGTTTACAA
1 AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
40217790 AATTACCGTTTTACCCTCGATT
1 AATTACCGTTTTACCCTCGATT
40217812 GTGAAATTAC
Statistics
Matches: 1110, Mismatches: 40, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
53 7 0.01
54 1095 0.99
55 8 0.01
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTTAGTTTACAA
Found at i:40217892 original size:27 final size:26
Alignment explanation
Indices: 40217801--40218050 Score: 110
Period size: 27 Copynumber: 9.2 Consensus size: 26
40217791 ATTACCGTTT
* * *
40217801 TACCCTCGATTGTGAAATTACTGAAA
1 TACCCTGGTTTGTAAAATTACTGAAA
** * **
40217827 TACCCCT-GTAAGATAGAATTACCAAAA
1 TA-CCCTGGTTTG-TAAAATTACTGAAA
*
40217854 TACCCCTAGTTTGTAAAATTACTGAAA
1 TA-CCCTGGTTTGTAAAATTACTGAAA
*
40217881 TACCACTGGTTTGTGAAATTA-TCGAAA
1 TACC-CTGGTTTGTAAAATTACT-GAAA
** **
40217908 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCT-GGTTTGTAAAATTACTGAAA
* ** *
40217935 TACCCTTGATTTACAAAATTACAGAAA
1 TACCC-TGGTTTGTAAAATTACTGAAA
* * *
40217962 TACCCTTGACTTTCTAAAAATTA-TAAAAA
1 TACCC-TG-GTTTGT-AAAATTACT-GAAA
* **
40217991 TACCATTGGTTTACAAAATTACTGAAA
1 TACC-CTGGTTTGTAAAATTACTGAAA
* * *
40218018 TACCCTTGGTTTGTAGATTTACCGAAA
1 TACCC-TGGTTTGTAAAATTACTGAAA
*
40218045 CACCCT
1 TACCCT
40218051 TGTAGGATGA
Statistics
Matches: 169, Mismatches: 41, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
26 10 0.06
27 132 0.78
28 11 0.07
29 16 0.09
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (26 bp):
TACCCTGGTTTGTAAAATTACTGAAA
Found at i:40218147 original size:27 final size:27
Alignment explanation
Indices: 40218083--40218147 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
40218073 ACCCCTAATA
*
40218083 GGTAAAAAGACCGTAAAACCCCTGTAG
1 GGTAAAATGACCGTAAAACCCCTGTAG
* * * *
40218110 GGTAAAGTGACCGTAATACCCTTGTAT
1 GGTAAAATGACCGTAAAACCCCTGTAG
40218137 GGTAAAATGAC
1 GGTAAAATGAC
40218148 GAATATGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAACCCCTGTAG
Found at i:40218879 original size:20 final size:20
Alignment explanation
Indices: 40218854--40218920 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
40218844 GATATGATAT
*
40218854 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
40218874 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
40218894 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
40218914 ACATGAT
1 ACATGAT
40218921 GTATTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:40219048 original size:52 final size:51
Alignment explanation
Indices: 40218970--40219105 Score: 233
Period size: 52 Copynumber: 2.7 Consensus size: 51
40218960 GAGGAAGTGC
40218970 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
40219022 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
40219073 AAAAGGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
40219106 AGGCCTCCAG
Statistics
Matches: 83, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 8 0.10
51 25 0.30
52 36 0.43
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:40219067 original size:25 final size:26
Alignment explanation
Indices: 40218970--40219105 Score: 199
Period size: 26 Copynumber: 5.3 Consensus size: 26
40218960 GAGGAAGTGC
40218970 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40218996 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40219022 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40219048 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40219073 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
40219096 AAAAGAGGCT
1 AAAAG-GGCT
40219106 AGGCCTCCAG
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 31 0.31
26 58 0.57
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40219303 original size:42 final size:42
Alignment explanation
Indices: 40219238--40219329 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
40219228 TAGTCTCCCC
* * ** *
40219238 AAATGGGCTTGCATATATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
40219280 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
40219322 AAATGGGC
1 AAATGGGC
40219330 CTATGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:40219431 original size:31 final size:31
Alignment explanation
Indices: 40219353--40219423 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
40219343 CGTTTACAGT
40219353 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
40219384 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
40219415 AAAGGCTTC
1 AAAGGCTTC
40219424 AACCCAGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:40221191 original size:2 final size:2
Alignment explanation
Indices: 40221186--40221212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40221176 AACTTAAAAA
40221186 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
40221213 TTGGATAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.