Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 213 of 228
Found at i:62272556 original size:39 final size:39
Alignment explanation
Indices: 62272502--62272579 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
62272492 ATAAGTCGCC
*
62272502 GGCACTCGGGGATGCGTAGGTTATCTCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
62272541 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
62272580 ATCGGAGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
Found at i:62277005 original size:12 final size:12
Alignment explanation
Indices: 62276988--62277014 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62276978 GTACACTTAA
62276988 AAATATTAAAAC
1 AAATATTAAAAC
62277000 AAATATTAAAAC
1 AAATATTAAAAC
62277012 AAA
1 AAA
62277015 AAACAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:62277223 original size:25 final size:26
Alignment explanation
Indices: 62277172--62277224 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
62277162 TGCACAAAAA
62277172 AACAACACCCAAACAACAAAAATAGC
1 AACAACACCCAAACAACAAAAATAGC
*
62277198 AACAACACCACCAA-AA-AAAAATAGC
1 AACAACACC-CAAACAACAAAAATAGC
62277223 AA
1 AA
62277225 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 11 0.44
26 11 0.44
27 3 0.12
ACGTcount: A:0.64, C:0.28, G:0.04, T:0.04
Consensus pattern (26 bp):
AACAACACCCAAACAACAAAAATAGC
Found at i:62279122 original size:21 final size:21
Alignment explanation
Indices: 62279098--62279159 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 21
62279088 AATTTAATTT
62279098 TTTATTTTAATATTATATATA
1 TTTATTTTAATATTATATATA
*
62279119 TTTAATGTGTTATTATTA-ATA-A
1 TTT-AT-T-TTAATATTATATATA
*
62279141 TTAATTTTAA-ATTATATAT
1 TTTATTTTAATATTATATAT
62279160 TTCATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 1 0.03
21 5 0.15
22 5 0.15
23 4 0.12
24 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTATTTTAATATTATATATA
Found at i:62281875 original size:14 final size:14
Alignment explanation
Indices: 62281856--62281887 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
62281846 TAAAATCTTC
*
62281856 GATTCCAACTACAG
1 GATTCCAACTAAAG
62281870 GATTCCAACTAAAG
1 GATTCCAACTAAAG
62281884 GATT
1 GATT
62281888 TCTCCACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (14 bp):
GATTCCAACTAAAG
Found at i:62287176 original size:14 final size:14
Alignment explanation
Indices: 62287157--62287187 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
62287147 TTCTAGTTTG
62287157 TTTTGTTCTAATAT
1 TTTTGTTCTAATAT
*
62287171 TTTTGTTGTAATAT
1 TTTTGTTCTAATAT
62287185 TTT
1 TTT
62287188 AGTTTATGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (14 bp):
TTTTGTTCTAATAT
Found at i:62292418 original size:15 final size:15
Alignment explanation
Indices: 62292398--62292454 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
62292388 TCCTCACCCC
62292398 TTTTTTTAGCTTTGA
1 TTTTTTTAGCTTTGA
* *
62292413 TTTTTTTAGTTTTCAAA
1 TTTTTTTAGCTTT--GA
62292430 TTTTTTTTTTAGCTTTGA
1 ---TTTTTTTAGCTTTGA
62292448 TTTTTTT
1 TTTTTTT
62292455 GAGTTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
15 19 0.58
17 1 0.03
18 1 0.03
20 12 0.36
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.72
Consensus pattern (15 bp):
TTTTTTTAGCTTTGA
Found at i:62292441 original size:35 final size:36
Alignment explanation
Indices: 62292398--62292471 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 36
62292388 TCCTCACCCC
62292398 TTTTTTTAGCTTTGATTTTTTT-AGTTTTCAAATTT
1 TTTTTTTAGCTTTGATTTTTTTGAGTTTTCAAATTT
62292433 TTTTTTTAGCTTTGATTTTTTTGAGTTTTCAAATTT
1 TTTTTTTAGCTTTGATTTTTTTGAGTTTTCAAATTT
62292469 TTT
1 TTT
62292472 AGGGTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.69
Consensus pattern (36 bp):
TTTTTTTAGCTTTGATTTTTTTGAGTTTTCAAATTT
Found at i:62292453 original size:36 final size:35
Alignment explanation
Indices: 62292398--62292471 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
62292388 TCCTCACCCC
*
62292398 TTTTTTTAGCTTTGATTTTTTTAGTTTTCAAATTT
1 TTTTTTTAGCTTTGATTTTTTGAGTTTTCAAATTT
62292433 TTTTTTTAGCTTTGATTTTTTTGAGTTTTCAAATTT
1 TTTTTTTAGCTTTGA-TTTTTTGAGTTTTCAAATTT
62292469 TTT
1 TTT
62292472 AGGGTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 15 0.41
36 22 0.59
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.69
Consensus pattern (35 bp):
TTTTTTTAGCTTTGATTTTTTGAGTTTTCAAATTT
Found at i:62292662 original size:15 final size:15
Alignment explanation
Indices: 62292617--62292662 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
62292607 AAGTTGTGGA
62292617 TTTAATC-TATATTT
1 TTTAATCTTATATTT
62292631 TTTAAT-TTGAT-TATT
1 TTTAATCTT-ATAT-TT
62292646 TTTAATCTTATATTT
1 TTTAATCTTATATTT
62292661 TT
1 TT
62292663 CAAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 8 0.30
15 16 0.59
16 3 0.11
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTAATCTTATATTT
Found at i:62308562 original size:39 final size:39
Alignment explanation
Indices: 62308519--62308600 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
62308509 TTGAGGAAGG
*
62308519 ATTATTGTAAATTCTAAACATTATATCAA-AAAAGTAAAA
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAA-TAAAA
* *
62308558 ATTATGGTAAATTTTAAACATTATATTAAGAAAATAAAA
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
62308597 ATTA
1 ATTA
62308601 AGAGAGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 35 0.90
40 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (39 bp):
ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
Found at i:62310921 original size:21 final size:22
Alignment explanation
Indices: 62310879--62310921 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
62310869 TCACGTTAAC
** *
62310879 AAATAATTAAAAACTTATAATA
1 AAATAATTAAAAACAAAAAATA
62310901 AAAT-ATTAAAAACAAAAAATA
1 AAATAATTAAAAACAAAAAATA
62310922 TATAAAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAATTAAAAACAAAAAATA
Found at i:62310937 original size:18 final size:16
Alignment explanation
Indices: 62310898--62310947 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
62310888 AAAACTTATA
62310898 ATAAAATATTAAAAAC
1 ATAAAATATTAAAAAC
* *
62310914 AAAAAATATATAAAATTC
1 ATAAAATAT-TAAAA-AC
*
62310932 ATAAAATTTTAAAAAC
1 ATAAAATATTAAAAAC
62310948 TTAGCATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 9 0.33
17 10 0.37
18 8 0.30
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAATATTAAAAAC
Found at i:62317554 original size:29 final size:28
Alignment explanation
Indices: 62317492--62317556 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
62317482 ATAAAATTGC
* *
62317492 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
62317520 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
62317550 TAAAATA
1 TAAAATA
62317557 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:62319210 original size:44 final size:43
Alignment explanation
Indices: 62319147--62319530 Score: 242
Period size: 44 Copynumber: 9.0 Consensus size: 43
62319137 CATTTAATCC
*
62319147 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* * *
62319191 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTTGATCT
* * * * *
62319237 GTTCCACTGTAATTTCAGGGAGATAAGACCTAATAC---GATGC-
1 GCTCCACTGTAATCTCAGGGAGATAAGA-TTACTTCTTTGAT-CT
* ** * * *
62319278 ACTTTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
*
62319317 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* * * *
62319361 GCTCCGCTGTAATCTCAAGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTTGATCT
* * * ** ** *
62319407 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGATACGATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
* * * * *
62319448 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
62319487 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
62319531 ACTTCACTTG
Statistics
Matches: 260, Mismatches: 53, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
36 1 0.00
38 1 0.00
39 53 0.20
40 5 0.02
41 54 0.21
42 1 0.00
44 72 0.28
45 2 0.01
46 65 0.25
47 6 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
Found at i:62319290 original size:170 final size:169
Alignment explanation
Indices: 62319021--62319530 Score: 849
Period size: 170 Copynumber: 3.0 Consensus size: 169
62319011 GCTTCAATCA
* * *
62319021 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTATAATCTCAAG
1 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTATAATCTCAGG
* ** * * *
62319086 GAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCATTTAATCCGCTC
66 GAGATAAGACCTGATACGATC-ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTC
*
62319151 CACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT
130 CACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
* *
62319191 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTGTAATTTCAGG
1 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTATAATCTCAGG
* *
62319256 GAGATAAGACCTAATACGATGCACTTTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTC
66 GAGATAAGACCTGATACGAT-CACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTC
*
62319321 CACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCC
130 CACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
*
62319361 GCTCCGCTGTAATCTCAAGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTATAATCTCAGG
1 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTATAATCTCAGG
62319426 GAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTC
66 GAGATAAGACCTGATACGAT-CACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTC
62319491 CACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
130 CACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
62319531 ACTTCACTTG
Statistics
Matches: 317, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
170 316 1.00
171 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (169 bp):
GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTATAATCTCAGG
GAGATAAGACCTGATACGATCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCC
ACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
Found at i:62331111 original size:11 final size:10
Alignment explanation
Indices: 62331089--62331119 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
62331079 CTTGATGTCG
62331089 AAAATTAAAA
1 AAAATTAAAA
*
62331099 AAACTTAAAA
1 AAAATTAAAA
62331109 AAAATTAAAA
1 AAAATTAAAA
62331119 A
1 A
62331120 TACGATCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:62332136 original size:29 final size:28
Alignment explanation
Indices: 62332074--62332138 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
62332064 ATAAAATTGC
* *
62332074 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
62332102 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
62332132 TAAAATA
1 TAAAATA
62332139 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:62333618 original size:12 final size:12
Alignment explanation
Indices: 62333601--62333627 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62333591 AATAAATCAT
62333601 ATATGTATATTA
1 ATATGTATATTA
62333613 ATATGTATATTA
1 ATATGTATATTA
62333625 ATA
1 ATA
62333628 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:62333969 original size:21 final size:21
Alignment explanation
Indices: 62333945--62334000 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
62333935 CACCATTATT
* * *
62333945 TCTAATTTCACTGCTATAGTA
1 TCTAATCTCACCGCTACAGTA
62333966 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
62333987 ACTAATCTCACCGC
1 TCTAATCTCACCGC
62334001 CACCGCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:62334828 original size:23 final size:23
Alignment explanation
Indices: 62334771--62334815 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
62334761 CATATAATCA
62334771 AATCAAACTAAAAATGATAAATG
1 AATCAAACTAAAAATGATAAATG
62334794 AATCAAACTAAAAATGATAAAT
1 AATCAAACTAAAAATGATAAAT
62334816 TATAGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAAACTAAAAATGATAAATG
Found at i:62336255 original size:14 final size:14
Alignment explanation
Indices: 62336231--62336264 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
62336221 TTTATTTTCC
*
62336231 CCCTCTTTTTCTCT
1 CCCTCTCTTTCTCT
*
62336245 CTCTCTCTTTCTCT
1 CCCTCTCTTTCTCT
62336259 CCCTCT
1 CCCTCT
62336265 TCAGTTTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
CCCTCTCTTTCTCT
Found at i:62347564 original size:42 final size:42
Alignment explanation
Indices: 62347468--62347570 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
62347458 TTTTTGGAAC
* *
62347468 CTTGGTCAAAATGGCTATGGCACTAGTCAAAATAATTTTTCT
1 CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
* *
62347510 -TCTGGTCAAAATTGCTATGG-ATTTGGTCAAAATAATTTTGCT
1 CT-TGGTCAAAATTGCTATGGCA-CTAGTCAAAATAATTTTGCT
*
62347552 CTTGGTCAAAATTGTTATG
1 CTTGGTCAAAATTGCTATG
62347571 CTGATGGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (42 bp):
CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
Found at i:62347572 original size:21 final size:20
Alignment explanation
Indices: 62347512--62347572 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
62347502 ATTTTTCTTC
* *
62347512 TGGTCAAAATTGCTATGGATT
1 TGGTCAAAATTGTTAT-GCTT
** *
62347533 TGGTCAAAATAATTTTGCTCT
1 TGGTCAAAATTGTTATGCT-T
62347554 TGGTCAAAATTGTTATGCT
1 TGGTCAAAATTGTTATGCT
62347573 GATGGATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGTCAAAATTGTTATGCTT
Found at i:62358354 original size:14 final size:14
Alignment explanation
Indices: 62358333--62358364 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
62358323 TGGTATGGGT
62358333 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
62358346 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
62358360 TTATA
1 TTATA
62358365 AGCAAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:62358522 original size:24 final size:25
Alignment explanation
Indices: 62358495--62358542 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
62358485 AGAAGAAAGT
62358495 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
62358519 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
62358543 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:62358863 original size:28 final size:28
Alignment explanation
Indices: 62358803--62358858 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
62358793 TTAATTTCAA
*
62358803 ATTTTGTTGTATATATGTACATACATAC
1 ATTTTGTTGTATATATATACATACATAC
*
62358831 ATTTTG-T-TATATATATACATACGTAC
1 ATTTTGTTGTATATATATACATACATAC
62358857 AT
1 AT
62358859 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
27 1 0.04
28 6 0.23
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (28 bp):
ATTTTGTTGTATATATATACATACATAC
Found at i:62359862 original size:21 final size:21
Alignment explanation
Indices: 62359838--62359878 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62359828 TAACGCATTG
62359838 GATATGA-CATTTTGTTTTCTC
1 GATATGAGCATTTT-TTTTCTC
*
62359859 GATATGAGGATTTTTTTTCT
1 GATATGAGCATTTTTTTTCT
62359879 AAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (21 bp):
GATATGAGCATTTTTTTTCTC
Found at i:62362199 original size:22 final size:22
Alignment explanation
Indices: 62362148--62362193 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
62362138 TAGTTTAAAC
**
62362148 TTTAAATTCCTTTATCCTTTAT
1 TTTAAATTTATTTATCCTTTAT
62362170 TTTAAATTTATTTAT-CTTTAT
1 TTTAAATTTATTTATCCTTTAT
62362191 TTT
1 TTT
62362194 TGAATTCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAAATTTATTTATCCTTTAT
Found at i:62362868 original size:40 final size:41
Alignment explanation
Indices: 62362801--62362882 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
62362791 AAATGTGAAG
* * * *
62362801 CTGCCGACTATTTGGCGGATTGAAGACATGTGGATTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGATTGAATT
62362842 CTGCCGAATATTT-ACGGATTAAAGACATGTAGATTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGATTGAATT
62362882 C
1 C
62362883 GACAATTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 25 0.68
41 12 0.32
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (41 bp):
CTGCCGAATATTTGACGGATTAAAGACATGTAGATTGAATT
Found at i:62366351 original size:18 final size:19
Alignment explanation
Indices: 62366324--62366361 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
62366314 GGAAGCAAGC
*
62366324 AATGACTGAAGA-AATCAG
1 AATGACTGAAAAGAATCAG
*
62366342 AATGATTGAAAAGAATCAG
1 AATGACTGAAAAGAATCAG
62366361 A
1 A
62366362 CCTGGAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.18
Consensus pattern (19 bp):
AATGACTGAAAAGAATCAG
Found at i:62369827 original size:73 final size:73
Alignment explanation
Indices: 62369745--62369930 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
62369735 ACAACTTGAC
62369745 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
62369810 CACTAACA
66 CACTAACA
62369818 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
62369883 CACTAACA
66 CACTAACA
*
62369891 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
62369931 AATAATAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:62369939 original size:3 final size:3
Alignment explanation
Indices: 62369931--62369962 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
62369921 ATTACATCCA
62369931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62369963 AACATGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62374299 original size:73 final size:73
Alignment explanation
Indices: 62374180--62374365 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
62374170 ACAACTTGAC
62374180 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
62374245 CACTAACA
66 CACTAACA
62374253 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
62374318 CACTAACA
66 CACTAACA
*
62374326 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
62374366 AATAATAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:62374374 original size:3 final size:3
Alignment explanation
Indices: 62374366--62374403 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
62374356 ATTACATCCA
62374366 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62374404 AACATGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:62378943 original size:31 final size:31
Alignment explanation
Indices: 62378905--62378982 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
62378895 ACTATAAAAA
62378905 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
* *
62378936 TAGTCACTTTTGTTTGTCTTAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
*
62378967 TAGTCACTTATGTTTG
1 TAGTCACTTTTGTTTG
62378983 AAATGTTACG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGCCTCAGGTTACATTT
Found at i:62381411 original size:18 final size:18
Alignment explanation
Indices: 62381388--62381422 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
62381378 TTACCAACTC
62381388 CATTCTCCAAATTACCAT
1 CATTCTCCAAATTACCAT
62381406 CATTCTCCAAATTACCA
1 CATTCTCCAAATTACCA
62381423 CCAAGTCCGA
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:0.34, G:0.00, T:0.31
Consensus pattern (18 bp):
CATTCTCCAAATTACCAT
Found at i:62381921 original size:18 final size:19
Alignment explanation
Indices: 62381886--62381922 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62381876 AGCAATAAGG
62381886 AGCGCCGCAACAAGCCCTC
1 AGCGCCGCAACAAGCCCTC
62381905 AGCGCCGCAAC-AGCCCTC
1 AGCGCCGCAACAAGCCCTC
62381923 GCCTCCAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.24, C:0.49, G:0.22, T:0.05
Consensus pattern (19 bp):
AGCGCCGCAACAAGCCCTC
Found at i:62383009 original size:15 final size:15
Alignment explanation
Indices: 62382986--62383018 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62382976 TGCATTGTTT
62382986 TATACATATGTTTTA
1 TATACATATGTTTTA
*
62383001 TATATATATGTTTTA
1 TATACATATGTTTTA
62383016 TAT
1 TAT
62383019 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TATACATATGTTTTA
Found at i:62384027 original size:71 final size:71
Alignment explanation
Indices: 62383934--62384085 Score: 286
Period size: 71 Copynumber: 2.1 Consensus size: 71
62383924 AAAGGATCGG
62383934 TGGCGACTCCAGTTTTTGTTTTTAAGTCGACAACTAAATTTTTTGTTTTCAAAAAACCGGTTTCG
1 TGGCGACTCCAGTTTTTGTTTTTAAGTCGACAACTAAATTTTTTGTTTTCAAAAAACCGGTTTCG
*
62383999 ACAGCT
66 ACAACT
*
62384005 TGGCGACTCCAGTTTTTGTTTTTAAGTCGACAACTAAATTTTTTGTTTTCAAAAAACTGGTTTCG
1 TGGCGACTCCAGTTTTTGTTTTTAAGTCGACAACTAAATTTTTTGTTTTCAAAAAACCGGTTTCG
62384070 ACAACT
66 ACAACT
62384076 TGGCGACTCC
1 TGGCGACTCC
62384086 GCTGGGGACG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (71 bp):
TGGCGACTCCAGTTTTTGTTTTTAAGTCGACAACTAAATTTTTTGTTTTCAAAAAACCGGTTTCG
ACAACT
Found at i:62384229 original size:6 final size:6
Alignment explanation
Indices: 62384218--62384244 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62384208 TGTTGGCTAC
62384218 TTTGCA TTTGCA TTTGCA TTTGCA TTT
1 TTTGCA TTTGCA TTTGCA TTTGCA TTT
62384245 TTGCATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGCA
Found at i:62390467 original size:51 final size:51
Alignment explanation
Indices: 62390391--62390491 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
62390381 GGCTTCAAAA
62390391 GGGTGCCTTTGTTTACTGTTGGCTGAAT-TTAGGTATCATTCATATTCTCAT
1 GGGTGCCTTTGTTTACTGTTGGCTGAATGTT-GGTATCATTCATATTCTCAT
* * *
62390442 GGGTGTCTTTGTTTGCTTTTGGCTGAATGTTGGTATCATTCATATTCTCA
1 GGGTGCCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCA
62390492 AGGCTGTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (51 bp):
GGGTGCCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCAT
Found at i:62393145 original size:3 final size:3
Alignment explanation
Indices: 62393137--62393165 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62393127 ATCACATGTT
62393137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62393166 TGGATGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:62393205 original size:16 final size:16
Alignment explanation
Indices: 62393181--62393222 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
62393171 GTAATGATGT
*
62393181 AACTTAGTTGTATTCC
1 AACTAAGTTGTATTCC
62393197 AACTAAGTTTGTATTCC
1 AACTAAG-TTGTATTCC
62393214 AACTAAGTT
1 AACTAAGTT
62393223 TGTTAGTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (16 bp):
AACTAAGTTGTATTCC
Found at i:62393210 original size:17 final size:17
Alignment explanation
Indices: 62393188--62393225 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
62393178 TGTAACTTAG
62393188 TTGTATTCCAACTAAGT
1 TTGTATTCCAACTAAGT
62393205 TTGTATTCCAACTAAGT
1 TTGTATTCCAACTAAGT
62393222 TTGT
1 TTGT
62393226 TAGTGGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (17 bp):
TTGTATTCCAACTAAGT
Found at i:62401670 original size:27 final size:28
Alignment explanation
Indices: 62401616--62401669 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
62401606 AGGTCTGAAG
*
62401616 TTAAATAAATGAATGATTAAATTAAAAT
1 TTAAATAAATGAATGATTAAAATAAAAT
*
62401644 TTAAAT-AATGAATTATATAAAATAAA
1 TTAAATAAATGAATGAT-TAAAATAAA
62401670 TAAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
TTAAATAAATGAATGATTAAAATAAAAT
Found at i:62402050 original size:3 final size:3
Alignment explanation
Indices: 62402042--62402091 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
62402032 GTCAAAAAAG
62402042 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62402090 AA
1 AA
62402092 AACATTTCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:62405225 original size:119 final size:119
Alignment explanation
Indices: 62405014--62405254 Score: 473
Period size: 119 Copynumber: 2.0 Consensus size: 119
62405004 ACTTTTTCTT
62405014 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGAAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGAAAATTTATGCTCGAAATAGTTGACATA
62405079 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
*
62405133 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGAAAATTTATGCTCGAAATAGTTGACATA
62405198 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
62405252 CCA
1 CCA
62405255 CCCTCATTTG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (119 bp):
CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGAAAATTTATGCTCGAAATAGTTGACATA
GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
Found at i:62411138 original size:23 final size:23
Alignment explanation
Indices: 62411094--62411138 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
62411084 TCTTCGATTG
*
62411094 CAATTTTACTAAAAAGTTTAAAC
1 CAATTTTACTAAAAAGTGTAAAC
*
62411117 CAATGTTTATTAAAAAG-GTAAA
1 CAAT-TTTACTAAAAAGTGTAAA
62411139 AGTACCATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (23 bp):
CAATTTTACTAAAAAGTGTAAAC
Found at i:62423092 original size:18 final size:19
Alignment explanation
Indices: 62423059--62423096 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
62423049 AGACTCCAGG
*
62423059 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
62423078 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
62423096 T
1 T
62423097 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:62428786 original size:4 final size:4
Alignment explanation
Indices: 62428777--62428814 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
62428767 ACAAGCTGTT
* *
62428777 TTTA TTTA TTTA TTTA TCTA TTCA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
62428815 ACCTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:62428917 original size:17 final size:16
Alignment explanation
Indices: 62428865--62428924 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 16
62428855 TTTATGCATT
*
62428865 TTTTTATTATTGTCATTA
1 TTTTT-TTATT-TTATTA
62428883 TTGTTTTTA-TTTAGTTA
1 TT-TTTTTATTTTA-TTA
62428900 TTTTTGTTATTTTATTA
1 TTTTT-TTATTTTATTA
62428917 TTTCTTTT
1 TTT-TTTT
62428925 TGATATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.14
17 17 0.47
18 11 0.31
19 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTTTATTTTATTA
Found at i:62428926 original size:21 final size:20
Alignment explanation
Indices: 62428866--62428933 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
62428856 TTATGCATTT
*
62428866 TTTTATTATTGTCATTATTGT-
1 TTTTATTATT-TC-TTTTTGTA
* *
62428887 TTTTATTTAGTTATTTTTGTTA
1 TTTTA-TTATTTCTTTTTG-TA
62428909 TTTTATTATTTCTTTTTGATA
1 TTTTATTATTTCTTTTTG-TA
62428930 TTTT
1 TTTT
62428934 CATGTCACGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.13
21 24 0.63
22 9 0.24
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTATTATTTCTTTTTGTA
Found at i:62430948 original size:4 final size:4
Alignment explanation
Indices: 62430939--62431000 Score: 58
Period size: 4 Copynumber: 15.8 Consensus size: 4
62430929 TTTTTAAGTT
* * *
62430939 TTTA TTTA -TT- TTTA TTTA TTTA TTTTA TTTA TTTGT TTTC TTTA TTTG
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT-A TTTA TTTA TTTA
62430987 TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTT
62431001 TATAAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
3 7 0.15
4 34 0.71
5 7 0.15
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:62430966 original size:13 final size:13
Alignment explanation
Indices: 62430939--62431003 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
62430929 TTTTTAAGTT
62430939 TTTATTTATTTTTA
1 TTTATTTA-TTTTA
62430953 TTTATTTATTTTA
1 TTTATTTATTTTA
* *
62430966 TTTATTTGTTTTC
1 TTTATTTATTTTA
*
62430979 TTTATTT-GTTTA
1 TTTATTTATTTTA
62430991 -TTATTTATTTTA
1 TTTATTTATTTTA
62431003 T
1 T
62431004 AAAATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
11 6 0.14
12 7 0.16
13 23 0.52
14 8 0.18
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:62431097 original size:34 final size:35
Alignment explanation
Indices: 62431030--62431103 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 35
62431020 ATTTGAAATG
* * *
62431030 TTTTATAATATTATCTTTTACAATTTTAAATATAT
1 TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
*
62431065 TTTTTTAAAATTATTTTTTA-AAATTTAAATATAT
1 TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
62431099 TTTTT
1 TTTTT
62431104 AATAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
Found at i:62431105 original size:13 final size:14
Alignment explanation
Indices: 62431053--62431089 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
62431043 TCTTTTACAA
62431053 TTTT-AAATATATTT
1 TTTTAAAAT-TATTT
62431067 TTTTAAAATTA-TT
1 TTTTAAAATTATTT
62431080 TTTTAAAATT
1 TTTTAAAATT
62431090 TAAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.55
14 6 0.27
15 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:62431194 original size:22 final size:22
Alignment explanation
Indices: 62431159--62431226 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
62431149 TTATTATTTG
62431159 TTTTATAATA-TTTAAATGTAT
1 TTTTATAATATTTTAAATGTAT
* *
62431180 ATTTTA-AATATTTTAAATTTGT
1 -TTTTATAATATTTTAAATGTAT
*
62431202 TTTTATAATTTTTTAAA--TAT
1 TTTTATAATATTTTAAATGTAT
62431222 TTTTA
1 TTTTA
62431227 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.17
21 9 0.22
22 24 0.60
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTTATAATATTTTAAATGTAT
Found at i:62431205 original size:21 final size:22
Alignment explanation
Indices: 62431154--62431219 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
62431144 CAAAATTATT
62431154 ATTTG-TTTTATAATA-TTTAA
1 ATTTGTTTTTATAATATTTTAA
* *
62431174 ATGTATATTTTA-AATATTTTAA
1 ATTTGT-TTTTATAATATTTTAA
*
62431196 ATTTGTTTTTATAATTTTTTAA
1 ATTTGTTTTTATAATATTTTAA
62431218 AT
1 AT
62431220 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 3 0.08
21 9 0.24
22 25 0.68
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
ATTTGTTTTTATAATATTTTAA
Found at i:62431212 original size:122 final size:122
Alignment explanation
Indices: 62431079--62431324 Score: 281
Period size: 122 Copynumber: 2.0 Consensus size: 122
62431069 TTAAAATTAT
62431079 TTTTTAAAA-TTTAAATATATTTTTTAA-TAAATAAAACAT-TTAAATATTTTAAAGATATGACC
1 TTTTTAAAATTTTAAA-ATA-TTTTTAATTAAATAAAACATATT--AT-TTTTAAAGATATGACC
62431141 TTTCAAA-ATTATTATTTGTTTTATA-ATA-TTTAAATGTATATTTTAAATATT-TTAAATTTG
61 TTTCAAATA-TATTATTTGTTTT-TACATATTTTAAATGTATATTTTAAATATTCTTAAATTTG
* * *** * *
62431201 TTTTTATAATTTTTTAAATATTTTTAATTTTTTTAAAATATATTATTTTTAAAGATATGATCTTT
1 TTTTTA-AAATTTTAAAATATTTTTAA-TTAAATAAAACATATTATTTTTAAAGATATGACCTTT
*
62431266 CAAATATATTATTTGTTTTTACGATATTTTAAATGTATATTTTAAATATTCTTTAATTT
64 CAAATATATTATTTGTTTTTAC-ATATTTTAAATGTATATTTTAAATATTCTTAAATTT
62431325 TAAATATAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
121 2 0.02
122 48 0.45
123 11 0.10
124 36 0.34
125 9 0.08
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (122 bp):
TTTTTAAAATTTTAAAATATTTTTAATTAAATAAAACATATTATTTTTAAAGATATGACCTTTCA
AATATATTATTTGTTTTTACATATTTTAAATGTATATTTTAAATATTCTTAAATTTG
Found at i:62431250 original size:19 final size:19
Alignment explanation
Indices: 62431210--62431250 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
62431200 GTTTTTATAA
*
62431210 TTTTTTAAATATTTTTAAT
1 TTTTTTAAATATTATTAAT
62431229 TTTTTTAAA-ATATATT-AT
1 TTTTTTAAATAT-TATTAAT
62431247 TTTT
1 TTTT
62431251 AAAGATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTAAATATTATTAAT
Found at i:62431258 original size:15 final size:15
Alignment explanation
Indices: 62431230--62431279 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
62431220 ATTTTTAATT
62431230 TTTTTAAAATATATTA
1 TTTTT-AAATATATTA
* *
62431246 TTTTTAAAGATATGA
1 TTTTTAAATATATTA
*
62431261 TCTTTCAAATATATTA
1 T-TTTTAAATATATTA
62431277 TTT
1 TTT
62431280 GTTTTTACGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (15 bp):
TTTTTAAATATATTA
Found at i:62431339 original size:30 final size:28
Alignment explanation
Indices: 62431291--62431369 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
62431281 TTTTTACGAT
* * *
62431291 ATTTTAAATGTATATTTTAAATATTCTTTA
1 ATTTTAAATATAT-TTTTAAA-ATTATTAA
62431321 ATTTTAAATATAATTTTTATAAATTATTAA
1 ATTTTAAATAT-ATTTTTA-AAATTATTAA
62431351 ATTTTAAA-ATATTTTTAAA
1 ATTTTAAATATATTTTTAAA
62431370 GATATTCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 2 0.05
30 29 0.66
31 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATATTTTTAAAATTATTAA
Found at i:62431354 original size:124 final size:122
Alignment explanation
Indices: 62431125--62431355 Score: 317
Period size: 124 Copynumber: 1.9 Consensus size: 122
62431115 CATTTAAATA
62431125 TTTTAAAGATATGACCTTTCAAAATTATTATTTGTTTTATAATATTTAAATGTATATTTTAAATA
1 TTTTAAAGATATGACCTTTCAAAATTATTATTTGTTTTATAATATTTAAATGTATATTTTAAATA
*** * *
62431190 TTTTAAATTTGTTTTTATAATTTTTTAAATATTTTTAATTTTTTTAAAATATATTAT
66 TTTTAAATTTGTAAATATAATTTTTTAAATATATTAAATTTTTTTAAAATATATTAT
*
62431247 TTTTAAAGATATGATCTTTC-AAATATATTATTTGTTTT-TACGATATTTTAAATGTATATTTTA
1 TTTTAAAGATATGACCTTTCAAAAT-TATTATTTGTTTTATA--ATA-TTTAAATGTATATTTTA
*
62431310 AATATTCTTTAATTT-TAAATATAATTTTTATAAAT-TATTAAATTTT
62 AATATT-TTAAATTTGTAAATATAATTTTT-TAAATATATTAAATTTT
62431356 AAAATATTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
121 6 0.06
122 32 0.33
123 3 0.03
124 43 0.45
125 12 0.12
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (122 bp):
TTTTAAAGATATGACCTTTCAAAATTATTATTTGTTTTATAATATTTAAATGTATATTTTAAATA
TTTTAAATTTGTAAATATAATTTTTTAAATATATTAAATTTTTTTAAAATATATTAT
Found at i:62431406 original size:21 final size:20
Alignment explanation
Indices: 62431353--62431406 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
62431343 ATTATTAAAT
62431353 TTTAAAATATTTTTAAAGATA
1 TTTAAAAT-TTTTTAAAGATA
* **
62431374 TTCAAAATTTTTTTAAATTTTA
1 TTTAAAA-TTTTTTAAA-GATA
62431396 TTTAAAATTTT
1 TTTAAAATTTT
62431407 AAAATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAAAATTTTTTAAAGATA
Found at i:62435509 original size:28 final size:30
Alignment explanation
Indices: 62435477--62435532 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
62435467 CAAATGGGGA
62435477 TTAAAT-TGAGAAATATG-AAAA-GTATGTG
1 TTAAATATGAGAAAT-TGTAAAATGTATGTG
*
62435505 TTAAATATGTGAAATTGTAAAATGTATG
1 TTAAATATGAGAAATTGTAAAATGTATG
62435533 GGATTCTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 11 0.46
30 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.36
Consensus pattern (30 bp):
TTAAATATGAGAAATTGTAAAATGTATGTG
Found at i:62436104 original size:25 final size:25
Alignment explanation
Indices: 62436076--62436138 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
62436066 TACCAATTTG
62436076 CAGCTCATATGAGCTTACCG-TTATT
1 CAGCTCATATGAGCTTACCGTTTA-T
* * *
62436101 CAGCTCAAAAGAGTTTACCGTTTAT
1 CAGCTCATATGAGCTTACCGTTTAT
*
62436126 C-GCTCGTATGAGC
1 CAGCTCATATGAGC
62436139 ATACATGTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 3 0.10
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (25 bp):
CAGCTCATATGAGCTTACCGTTTAT
Found at i:62440367 original size:21 final size:20
Alignment explanation
Indices: 62440321--62440371 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
62440311 GTTATAGTAT
**
62440321 ATATTTTTAATTTTTAATTT
1 ATATTTTTAATTTTTAATAC
* *
62440341 AAATTTTTACTTTTTTAATAC
1 ATATTTTTA-ATTTTTAATAC
62440362 ATATTTTTAA
1 ATATTTTTAA
62440372 AAAGTCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTAATTTTTAATAC
Found at i:62440516 original size:12 final size:13
Alignment explanation
Indices: 62440492--62440532 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
62440482 AAATTTTTTG
62440492 AATATATTT-AAA
1 AATATATTTAAAA
62440504 AATA-ATTTAAAA
1 AATATATTTAAAA
*
62440516 AATCATAATTAAAA
1 AAT-ATATTTAAAA
62440530 AAT
1 AAT
62440533 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 1 0.04
14 10 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATATTTAAAA
Found at i:62440548 original size:10 final size:10
Alignment explanation
Indices: 62440495--62440558 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 10
62440485 TTTTTTGAAT
62440495 ATATTTAAAA
1 ATATTTAAAA
62440505 ATAATTTAAAAA
1 AT-ATTT-AAAA
62440517 ATCATAATTAAAA
1 AT-AT--TTAAAA
*
62440530 A-ATTAAAAA
1 ATATTTAAAA
62440539 ATATTT-AAA
1 ATATTTAAAA
62440548 ATATTCTAAAA
1 ATATT-TAAAA
62440559 CAAGTAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
9 14 0.32
10 6 0.14
11 9 0.20
12 8 0.18
13 5 0.11
14 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:62440669 original size:22 final size:21
Alignment explanation
Indices: 62440641--62440711 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
62440631 TTAAAAAAAT
62440641 AATTTAAAAGATATATATTTAA
1 AATTTAAAA-ATATATATTTAA
62440663 AATTTAAAAA-ATTATATTATAAA
1 AATTTAAAAATA-TATATT-T-AA
* *
62440686 ACATTT-CAAATATACATTTAA
1 A-ATTTAAAAATATATATTTAA
62440707 AATTT
1 AATTT
62440712 TATAAAACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 5 0.12
21 10 0.24
22 11 0.26
23 11 0.26
24 5 0.12
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (21 bp):
AATTTAAAAATATATATTTAA
Found at i:62440680 original size:21 final size:23
Alignment explanation
Indices: 62440641--62440686 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
62440631 TTAAAAAAAT
*
62440641 AATTTAAAAGATATATATT-TAA
1 AATTTAAAAAATATATATTATAA
62440663 AATTTAAAAAAT-TATATTATAA
1 AATTTAAAAAATATATATTATAA
62440685 AA
1 AA
62440687 CATTTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTTAAAAAATATATATTATAA
Found at i:62453555 original size:18 final size:20
Alignment explanation
Indices: 62453518--62453555 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
62453508 ATGTTGAATC
62453518 TTTGAGATTTCTGATAATTT
1 TTTGAGATTTCTGATAATTT
*
62453538 TTTGAG-TTT-TGATTATTT
1 TTTGAGATTTCTGATAATTT
62453556 AAATAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.61
Consensus pattern (20 bp):
TTTGAGATTTCTGATAATTT
Found at i:62456386 original size:10 final size:11
Alignment explanation
Indices: 62456360--62456385 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62456350 AGAAAATAAA
62456360 AAAAATATTTT
1 AAAAATATTTT
62456371 AAAAATATTTT
1 AAAAATATTTT
62456382 AAAA
1 AAAA
62456386 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62471971 original size:3 final size:3
Alignment explanation
Indices: 62471906--62471953 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
62471896 CTAGCTTTTC
62471906 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62471954 TATACTCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:62472022 original size:21 final size:22
Alignment explanation
Indices: 62471998--62472038 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
62471988 ATTAAATATA
62471998 TATGTCTTA-CTATAT-TATTAT
1 TATGT-TTATCTATATCTATTAT
62472019 TATGTTTATCTATATCTATT
1 TATGTTTATCTATATCTATT
62472039 TATTTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.59
Consensus pattern (22 bp):
TATGTTTATCTATATCTATTAT
Found at i:62472138 original size:43 final size:43
Alignment explanation
Indices: 62472072--62472153 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
62472062 CATACATACA
* *
62472072 TATATTTTATAACTCATACATATACATACATATATATATCTTT
1 TATATTTTATAACTCATAAATATACATACATATACATATCTTT
* * *
62472115 TATATTTTATAATTTCA-AAATATATATATATATACATAT
1 TATATTTTATAA-CTCATAAATATACATACATATACATAT
62472154 ACATTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 30 0.91
44 3 0.09
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (43 bp):
TATATTTTATAACTCATAAATATACATACATATACATATCTTT
Found at i:62482651 original size:70 final size:67
Alignment explanation
Indices: 62482515--62482651 Score: 175
Period size: 70 Copynumber: 2.0 Consensus size: 67
62482505 CTACATAAAC
* * * * * *
62482515 AATATAATGGTTTTGACTTTTAACTTAATAAGTAAACATTTATTAAAACGATATAGTTTTGTCTT
1 AATATAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACAACATAGTTTTGCCTT
62482580 TT
66 TT
* *
62482582 AATATAATGGTTTTGATTTTTAACTTTAAAAAAAATAAACATTTATCAAAACAACGTAGTTTTGC
1 AATATAATGGTTTTGACTTTTAAC-TT--AAAAAATAAACATTTATCAAAACAACATAGTTTTGC
62482647 CTTTT
63 CTTTT
62482652 GTTATTAGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
67 23 0.39
68 2 0.03
70 34 0.58
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (67 bp):
AATATAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACAACATAGTTTTGCCTT
TT
Found at i:62485012 original size:30 final size:30
Alignment explanation
Indices: 62484978--62485084 Score: 178
Period size: 30 Copynumber: 3.6 Consensus size: 30
62484968 CCAATATCTC
62484978 GATACCCATATCTTTGACTTTCTAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
* *
62485008 GATACCCATACCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
62485038 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
62485068 GATACTCATATCTTTGA
1 GATACCCATATCTTTGA
62485085 TTTTTCATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCTAATATTT
Found at i:62489710 original size:30 final size:30
Alignment explanation
Indices: 62489659--62489752 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
62489649 TTTTATTATG
*
62489659 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
62489690 CCAATATTTGATATCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
62489720 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62489750 CCA
1 CCA
62489753 TAAATATGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 49 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:62489714 original size:15 final size:15
Alignment explanation
Indices: 62489669--62489746 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
62489659 CCAATATCTC
*
62489669 GATACCCATATCTTT
1 GATATCCATATCTTT
* *
62489684 GACTTTCCA-ATATTT
1 GA-TATCCATATCTTT
62489699 GATATCCATATCTTT
1 GATATCCATATCTTT
* * *
62489714 GACTTTCTAT-TATTT
1 GA-TATCCATATCTTT
*
62489729 GATACCCATATCTTT
1 GATATCCATATCTTT
62489744 GAT
1 GAT
62489747 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (15 bp):
GATATCCATATCTTT
Found at i:62491681 original size:29 final size:27
Alignment explanation
Indices: 62491629--62491683 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
62491619 ATTTGAGAGA
**
62491629 TTTTTTTCCATTAAATGTTTAATTCTT
1 TTTTTTTCCATTAAATGTGGAATTCTT
62491656 TTTTTTTCCCGATTAAATGTGGAATTCT
1 TTTTTTT-CC-ATTAAATGTGGAATTCT
62491684 AATAGCTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 2 0.08
29 15 0.62
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTTTTTCCATTAAATGTGGAATTCTT
Found at i:62494332 original size:17 final size:17
Alignment explanation
Indices: 62494312--62494350 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
62494302 TTATTATTAT
*
62494312 TATATATATTTTATATA
1 TATACATATTTTATATA
*
62494329 TATACATATTTTTTATA
1 TATACATATTTTATATA
62494346 TATAC
1 TATAC
62494351 TTACGTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TATACATATTTTATATA
Found at i:62495357 original size:108 final size:109
Alignment explanation
Indices: 62495068--62495469 Score: 650
Period size: 109 Copynumber: 3.7 Consensus size: 109
62495058 TAAAAAAGGG
* * *
62495068 AAACATTTC-AAAATAAGGCAATATTTTGCTTTTGGAAATTCGAGGAACGTGCCTTAAGGTACTG
1 AAACTTTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
62495132 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
*
62495176 AAACTTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAACTTTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
62495241 GGTTTCGATTTCTCGTTCGACCAAAT-GACTTAATATCCTTTTCAA
66 GGTTTCGATTTCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AA
*
62495286 AAA-TTTTC-AAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAACTTTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
62495349 GGTCTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
* * * * *
62495393 AAACTTTTCAAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAACCTGCCCTAAGGTGCTG
1 AAACTTTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
62495458 GGTTTCGATTTC
66 GGTTTCGATTTC
62495470 ACGGTTAACC
Statistics
Matches: 274, Mismatches: 14, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
107 5 0.02
108 105 0.38
109 159 0.58
110 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
AAACTTTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
Found at i:62495449 original size:217 final size:217
Alignment explanation
Indices: 62495073--62495469 Score: 722
Period size: 217 Copynumber: 1.8 Consensus size: 217
62495063 AAGGGAAACA
* * *
62495073 TTTCAAAATAAGGCAATATTTTGCTTTTGGAAATTCGAGGAACGTGCCTTAAGGTACTGGGTTTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTCTC
62495138 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCAATGTTT
66 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCAATGTTT
* *
62495203 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATG
131 TGCGTTTGGAAATTCGAGAAACCTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATG
62495268 ACTTAATATCCTTTTCAAAAAT
196 ACTTAATATCCTTTTCAAAAAT
*
62495290 TTTCAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTCTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTCTC
*
62495355 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGTAATGTTT
66 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCAATGTTT
*
62495420 TGCGTTTGGAAATTCGAGAAACCTGCCCTAAGGTGCTGGGTTTCGATTTC
131 TGCGTTTGGAAATTCGAGAAACCTGCCCTAAGGTACTGGGTTTCGATTTC
62495470 ACGGTTAACC
Statistics
Matches: 172, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 172 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (217 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTCTC
GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCAATGTTT
TGCGTTTGGAAATTCGAGAAACCTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATG
ACTTAATATCCTTTTCAAAAAT
Found at i:62499197 original size:6 final size:6
Alignment explanation
Indices: 62499188--62499227 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
62499178 CAAAAATAGG
*
62499188 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAG AGAAAA AG
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA AG
62499228 GAGAGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 21 0.70
7 6 0.20
8 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:62499201 original size:10 final size:10
Alignment explanation
Indices: 62499188--62499225 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
62499178 CAAAAATAGG
62499188 AGAAAAAGAA
1 AGAAAAAGAA
62499198 AGAAGAAA-AA
1 AGAA-AAAGAA
62499208 AGAAAAAGAA
1 AGAAAAAGAA
62499218 AGAGAAAA
1 AGA-AAAA
62499226 AGGAGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.12
10 15 0.60
11 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:62499213 original size:20 final size:19
Alignment explanation
Indices: 62499188--62499226 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
62499178 CAAAAATAGG
62499188 AGAAAAAGAAAGAAGAAAAA
1 AGAAAAAGAAAG-AGAAAAA
62499208 AGAAAAAGAAAGAGAAAAA
1 AGAAAAAGAAAGAGAAAAA
62499227 GGAGAGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAGAGAAAAA
Found at i:62501617 original size:87 final size:87
Alignment explanation
Indices: 62501508--62501841 Score: 257
Period size: 87 Copynumber: 3.8 Consensus size: 87
62501498 TAAAATAAAT
* * * * *
62501508 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATTTCCCT-ATGATTACA
1 GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGCATCAGGTCTTATTTCCCTGA-GATTACA
*
62501572 GTGGAACAGACCAAAGAATTTCA
65 GTGGAACAGACTAAAGAATTTCA
* * * * * * *
62501595 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCACTGAGATT
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGCAGATTGCA-TCAG--GTCTTATTTCCCTGAGATT
** ** * **
62501659 ACAGT-GAAGTGGGTTAA-AA-TGAA
62 ACAGTGGAACAGACTAAAGAATTTCA
* * *
62501682 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATTGCGTCAGGTCTTATTTCCCTGAGATTACA
1 -GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGCATCAGGTCTTATTTCCCTGAGATTACA
*
62501747 GTGGAACAGACTGAAGAATTTCA
65 GTGGAACAGACTAAAGAATTTCA
* ** * * * *
62501770 GATCTTATCTCCATG-AGATTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATT
1 GATCTTATCTCCCTGAAG-TTACAGCAGAGCAGATTGCATC-AG--GTCTTATTTCCCTGAGATT
62501834 ACAGTGGA
62 ACAGTGGA
62501842 GCGGATTAAA
Statistics
Matches: 186, Mismatches: 47, Indels: 25
0.72 0.18 0.10
Matches are distributed among these distances:
85 20 0.11
86 11 0.06
87 65 0.35
88 38 0.20
89 8 0.04
90 43 0.23
91 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGCATCAGGTCTTATTTCCCTGAGATTACAG
TGGAACAGACTAAAGAATTTCA
Found at i:62501655 original size:44 final size:43
Alignment explanation
Indices: 62501596--62502235 Score: 334
Period size: 44 Copynumber: 14.8 Consensus size: 43
62501586 AGAATTTCAG
*
62501596 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAG-A
* * * ** * * * * *
62501640 ATCCTATCTCACTGAGATTACAGTGAAGTGGGTTAAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGT-TAGA
* ** * * *
62501684 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATTG-CGTCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTTAGA
* * * *
62501725 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAG-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG---TT-AGA
* *
62501771 ATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAG-A
* * * * *
62501815 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGT-TAGA
** * * * * * *
62501859 ATCTTATCTCTTTGA-AGTTAAAGTAGAGTAGATCG-TGTCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTTAGA
* * *
62501900 ATTTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGTTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAG-A
* * ** * * * *
62501944 ATCCTATCTCCCTGAGATTACAGTGAAGTGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGT-TAGA
* * * * * * *
62501988 ATCTTATCTCTCT-AAAGTTACAGTAGAGAAGATCGTA-TCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTTAGA
* ** *
62502029 GTCTTATCTCTTTGAGATTACAGCGGAGCAGATTGAAGTTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAG-A
* ** * * * *
62502073 ATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGT-TAGA
* * * * * *
62502117 ATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCGTA-TCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTTAGA
* * * *
62502158 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAG-A
* * *
62502202 ATCCTATCTCACTGAGATTACAGTGGAGCGGATT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
62502236 AAAACAAAGG
Statistics
Matches: 437, Mismatches: 131, Indels: 56
0.70 0.21 0.09
Matches are distributed among these distances:
41 104 0.24
42 25 0.06
43 10 0.02
44 254 0.58
45 9 0.02
46 35 0.08
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTTAGA
Found at i:62501717 original size:88 final size:88
Alignment explanation
Indices: 62501595--62502180 Score: 311
Period size: 85 Copynumber: 6.8 Consensus size: 88
62501585 AAGAATTTCA
* * * *
62501595 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCACTGAGATTA
1 GATCTTATCTCTCTGAGATTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATTA
* * *
62501660 CAGTGAAGTGGGTTAAAATGAAG
66 CAGTGAAGAGGATTAAAATAAAG
* * * * *
62501683 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATTG-CGTCAG--GTCTTATTTCCCTGAGATT
1 GATCTTATCTCTCTGAGA-TTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATT
* * **
62501744 ACAGTGGAACA-GACTGAAGAATTTCA-
65 ACAGT-GAAGAGGA-TTAA-AA-TAAAG
** *
62501770 GATCTTATCTC-CATGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATT
1 GATCTTATCTCTC-TGAGATTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATT
* *
62501834 ACAGTGGAGCGGATTAAAATAAAG
65 ACAGTGAAGAGGATTAAAATAAAG
* * * * * * * * *
62501858 GATCTTATCTCTTTGA-AGTTAAAGTAGAGTAGATCG-TGTCAG--ATTTTATCTCCTTGAGATT
1 GATCTTATCTCTCTGAGA-TTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATT
* * * * *
62501919 ACAGCGGAGCA-GATTGAAGT-TAG
65 ACAGTGAAG-AGGATTAAAATAAAG
* * * * ** * * * * * *
62501942 TAATCCTATCTCCCTGAGATTACAG-TGAAGTGGATTAAAATAAAG-GATCTTATCTCTCT-AAA
1 -GATCTTATCTCTCTGAGATTACAGCAG-AGCAGATTGAAGT-TAGTAATCTTATCTCCCTGAGA
* *** *
62502004 GTTACAGT-AGAGAAGA-TCGTAT-CAG
63 -TTACAGTGA-AGAGGATTAAAATAAAG
* * *
62502029 G-TCTTATCTCTTTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCTCTGAGATTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATTA
* *
62502093 CAGTGGAGTGGATTAAAATAAAG
66 CAGTGAAGAGGATTAAAATAAAG
* * * * * *
62502116 GATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCGTA-TCAG--GTCTTATCTCCCTGAGATT
1 GATCTTATCTCTCTGAGA-TTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATT
62502177 ACAG
65 ACAG
62502181 CGGAGCAGAT
Statistics
Matches: 369, Mismatches: 97, Indels: 67
0.69 0.18 0.13
Matches are distributed among these distances:
84 5 0.01
85 147 0.40
86 15 0.04
87 58 0.16
88 115 0.31
89 5 0.01
90 24 0.07
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (88 bp):
GATCTTATCTCTCTGAGATTACAGCAGAGCAGATTGAAGTTAGTAATCTTATCTCCCTGAGATTA
CAGTGAAGAGGATTAAAATAAAG
Found at i:62501776 original size:175 final size:175
Alignment explanation
Indices: 62501485--62501966 Score: 659
Period size: 175 Copynumber: 2.8 Consensus size: 175
62501475 CCATCGGTTG
* **
62501485 CAGTGAAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAG
**
62501550 GTCTTATTTCCCT-ATGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGAT
66 GTCTTATTTCCCTGA-GATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGAT
*
62501614 TACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCACTGAGATTA
130 TACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTGAGATTA
* * * * *
62501660 CAGTGAAGTGGGTTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATTGCGTCAG
1 CAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAG
*
62501725 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCATGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATT
* * *
62501790 ACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTGAGATTA
* * * *
62501835 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTAAAGTAGAGTAGATCGTGTCAG
1 CAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAG
* * * * * * * *
62501900 ATTTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAG---TT-AGTAATCCTATCTCCCTGAGA
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAG--ATCTTATCTCCCTGAGA
62501961 TTACAG
129 TTACAG
62501967 TGAAGTGGAT
Statistics
Matches: 271, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
171 2 0.01
172 2 0.01
173 21 0.08
175 245 0.90
176 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (175 bp):
CAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCGTCAG
GTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATT
ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTGAGATTA
Found at i:62501793 original size:46 final size:46
Alignment explanation
Indices: 62501720--62501841 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 46
62501710 AGTAGATTGC
* *
62501720 GTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGA-A
1 GTCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGATA
* * * * *
62501765 TTTCAGATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTA
1 -GTCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGATA
62501812 GT-A-ATCTTATCTCCCTGAGATTACAGTGGA
1 GTCAGATCTTATCTCCCTGAGATTACAGTGGA
62501842 GCGGATTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 26 0.39
45 1 0.02
46 38 0.58
47 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (46 bp):
GTCAGATCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGATA
Found at i:62501928 original size:129 final size:129
Alignment explanation
Indices: 62501767--62502344 Score: 850
Period size: 129 Copynumber: 4.5 Consensus size: 129
62501757 CTGAAGAATT
* * * *
62501767 TCAGATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
1 TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * * *
62501832 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTAAAGTAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * *
62501896 TCAGATTTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
62501961 TTACAGTGAAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* *
62502025 TCAGGTCTTATCTCTTTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
62502090 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * *
62502154 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATCCTATCTCACTGAGA
1 TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
62502219 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * * * * * * * * * *
62502283 TCAGGTTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTG
1 TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTG
62502345 GTTGGCAGTG
Statistics
Matches: 409, Mismatches: 40, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 409 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (129 bp):
TCAGGTCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
Found at i:62504153 original size:17 final size:17
Alignment explanation
Indices: 62504128--62504166 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
62504118 TAATTGCTCT
*
62504128 TATATATATTTTATATA
1 TATACATATTTTATATA
*
62504145 TATACATATTTTTTATA
1 TATACATATTTTATATA
62504162 TATAC
1 TATAC
62504167 TTACGTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TATACATATTTTATATA
Found at i:62505854 original size:87 final size:87
Alignment explanation
Indices: 62505708--62505883 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
62505698 AAGTACTAGT
62505708 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGACAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGACAACACTGCTAGGTTGAAGTTTCGAGTA
* *
62505773 ATGTTTTTAATGGCTCCTTGAG
66 ATGTTCTTAACGGCTCCTTGAG
*
62505795 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGACAACACTGCTAGGTTGAAGTTTCGAGTA
62505860 ATGTTCTTAACGGCTCCTTGAG
66 ATGTTCTTAACGGCTCCTTGAG
62505882 TC
1 TC
62505884 CCACCACTGT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (87 bp):
TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGACAACACTGCTAGGTTGAAGTTTCGAGTA
ATGTTCTTAACGGCTCCTTGAG
Found at i:62507956 original size:34 final size:32
Alignment explanation
Indices: 62507876--62507956 Score: 74
Period size: 34 Copynumber: 2.4 Consensus size: 32
62507866 ATGTTCATTA
** *
62507876 AAATAAATAAACATATATATTATTTTTATATAT
1 AAATAAATAAA-ATATATATTAAATGTATATAT
* *
62507909 AAA-ATAGTGAAATATAAGTATTAAATGTATATAT
1 AAATA-AATAAAATAT-A-TATTAAATGTATATAT
62507943 AAATAAATAAAATA
1 AAATAAATAAAATA
62507957 AACACACTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
32 5 0.14
33 8 0.22
34 23 0.62
35 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (32 bp):
AAATAAATAAAATATATATTAAATGTATATAT
Found at i:62518022 original size:19 final size:22
Alignment explanation
Indices: 62517985--62518030 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
62517975 ATGCCCATAT
62517985 TTATTTTATCTAAATAAAATTA
1 TTATTTTATCTAAATAAAATTA
62518007 TTATTTT-T-TAAA-AAAATTA
1 TTATTTTATCTAAATAAAATTA
62518026 TTATT
1 TTATT
62518031 AGTAACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 1 0.04
22 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTTTATCTAAATAAAATTA
Found at i:62519149 original size:16 final size:17
Alignment explanation
Indices: 62519128--62519162 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
62519118 GACATGAAAT
62519128 TAATAAAATAAATA-AA
1 TAATAAAATAAATATAA
*
62519144 TAATAATATAAATATAA
1 TAATAAAATAAATATAA
62519161 TA
1 TA
62519163 GCATTCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAATAAATATAA
Found at i:62521252 original size:21 final size:22
Alignment explanation
Indices: 62521228--62521269 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
62521218 TTATATCACA
62521228 TCAGCATTTTCATCCT-AAATT
1 TCAGCATTTTCATCCTGAAATT
62521249 TCAGCATTTTCATCCTGAAAT
1 TCAGCATTTTCATCCTGAAAT
62521270 AAATCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (22 bp):
TCAGCATTTTCATCCTGAAATT
Found at i:62527018 original size:48 final size:48
Alignment explanation
Indices: 62526961--62527092 Score: 135
Period size: 48 Copynumber: 2.7 Consensus size: 48
62526951 TTGGGTGCTA
* *
62526961 GCCTGTCAATGGTCGGCACCAGTA-ATG-AAAAAAAAAATTTAGGCGCT-
1 GCCTATCAATGGTCGGCACCAGTATACGAAAAAAAAAAATTT--GCGCTG
* * *
62527008 GCCTTATCAATTGTCAGCACCAGTATACGAAAAAAAAAAATTTGTGCTG
1 GCC-TATCAATGGTCGGCACCAGTATACGAAAAAAAAAAATTTGCGCTG
* **
62527057 GCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAA
1 GCCTATCAATGGTCGGCACCAGTA-TACGAAAAAAA
62527093 TTGTTTTGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.04
48 38 0.54
49 16 0.23
50 13 0.19
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (48 bp):
GCCTATCAATGGTCGGCACCAGTATACGAAAAAAAAAAATTTGCGCTG
Found at i:62527190 original size:90 final size:87
Alignment explanation
Indices: 62527024--62527199 Score: 217
Period size: 90 Copynumber: 2.0 Consensus size: 87
62527014 TCAATTGTCA
* * * *
62527024 GCACCAGTATACGAAAAAAAAAAATTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACGAAA
1 GCACCAGCATACGAAAAAAAAAAATTTGTGCTGGCCTATCAATGGCCGACACCACCAGTACGAAA
*** *
62527089 AAAATTGTTTTGGGTGTTGGCCG
66 AAAAAAATTTT-GGTGCTGGCCG
** * *
62527112 GCACCAGCAGTACGAAAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGACACCACCAGTATGA
1 GCACCAGCA-TACGAAAAAAAAAAATT-TGTGCTGGCCTATCAATGGCCGACACCACCAGTACGA
62527177 AAAAAAAAATTTTGGTGCTGGCC
64 AAAAAAAAATTTTGGTGCTGGCC
62527200 TGTCAATGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
88 8 0.11
89 24 0.32
90 42 0.57
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (87 bp):
GCACCAGCATACGAAAAAAAAAAATTTGTGCTGGCCTATCAATGGCCGACACCACCAGTACGAAA
AAAAAAATTTTGGTGCTGGCCG
Found at i:62527268 original size:50 final size:50
Alignment explanation
Indices: 62526941--62527336 Score: 266
Period size: 50 Copynumber: 8.4 Consensus size: 50
62526931 TAAAAAAAAC
* * * * *
62526941 AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGTCGGCACCAGTA--ATGA
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
* * * * * * *
62526989 AAAAAAAAATTTAGGCGCT-GCCTTATCAATTGTCAGCACCAGTA-TACGAA
1 AAAAAAAAATTTAGGTGCTGGCC-TGTCAATGGCCGGCACCAGCAGTATG-A
* * *
62527039 AAAAAAAAATTT--GTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG-
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
** * *
62527086 --AAAAAAA-TT--GTTTTGG-GTGT---TGGCCGGCACCAGCAGTACGA
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
* * * * * *
62527127 AAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGACACCACCAGTATGA
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
* * *
62527177 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGTCCGGTACCAGCAGTATGA
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
* * * *
62527227 AAAAAAAAATTTGGGTGCTAGCCTGTGAATGGCCGGCA-C--CAGT-T-T
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
* * ** *
62527272 AAAAAAAAA-TT-GGTGTTGGCCTGTCAATGACCGGCACCAATA-TACG-
1 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
62527318 AAAAAAAAATTTAGGTGCT
1 AAAAAAAAATTTAGGTGCT
62527337 AGACTTCTAA
Statistics
Matches: 278, Mismatches: 48, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
40 18 0.06
43 30 0.11
44 12 0.04
45 17 0.06
46 16 0.06
47 11 0.04
48 59 0.21
49 10 0.04
50 105 0.38
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (50 bp):
AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCAGCAGTATGA
Found at i:62530481 original size:30 final size:32
Alignment explanation
Indices: 62530450--62530511 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
62530440 TTGTCGGCGG
62530450 TGGTTGAGGGTGAACAGCGACGGTCGTCGGTGA
1 TGGTTGAGGGTGAACAGCGACGGTCGTC-GTGA
**
62530483 TGGTTGAGGGTGAACAGCGGTGGTCGTCG
1 TGGTTGAGGGTGAACAGCGACGGTCGTCG
62530512 AAGTTGCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.16, C:0.15, G:0.47, T:0.23
Consensus pattern (32 bp):
TGGTTGAGGGTGAACAGCGACGGTCGTCGTGA
Found at i:62531256 original size:22 final size:22
Alignment explanation
Indices: 62531228--62531294 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
62531218 TCATTTAAAA
62531228 TATTTTTTTTTCAATTTCAATT
1 TATTTTTTTTTCAATTTCAATT
*
62531250 TATTTTTTTCTCAA-TTC-ATT
1 TATTTTTTTTTCAATTTCAATT
*
62531270 TATATTATTTTTT-AATTTAAATT
1 TAT-TT-TTTTTTCAATTTCAATT
62531293 TA
1 TA
62531295 ACTTTTTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 20 0.53
23 5 0.13
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTTTTTTTCAATTTCAATT
Found at i:62531270 original size:20 final size:22
Alignment explanation
Indices: 62531228--62531303 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
62531218 TCATTTAAAA
*
62531228 TATTTTTTTTTCAATTTCAATT
1 TATTTTTTTCTCAATTTCAATT
62531250 TATTTTTTTCTCAA-TTC-ATT
1 TATTTTTTTCTCAATTTCAATT
* *
62531270 TATATTATTTT-TTAATTTAAATT
1 TAT-TT-TTTTCTCAATTTCAATT
**
62531293 TAACTTTTTCT
1 TATTTTTTTCT
62531304 GCACTTCATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.14
21 12 0.27
22 21 0.48
23 5 0.11
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTTTTTCTCAATTTCAATT
Found at i:62531301 original size:44 final size:44
Alignment explanation
Indices: 62531227--62531347 Score: 111
Period size: 44 Copynumber: 2.7 Consensus size: 44
62531217 TTCATTTAAA
* * *
62531227 ATATTTTTTTTTCAATTTCAATTTATTTTTTTCT-CAATTCATTT
1 ATATTATTTTTTCAATTTAAATTTA-CTTTTTCTGCAATTCATTT
*
62531271 ATATTATTTTTT-AATTTAAATTTAACTTTTTCTGCACTTCATTT
1 ATATTATTTTTTCAATTTAAATTT-ACTTTTTCTGCAATTCATTT
* * ** *
62531315 AAATTTTCTATTTTCAATGCAAATTTATTTTTT
1 ATATTAT-T-TTTTCAATTTAAATTTACTTTTT
62531348 TCTTATTTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
43 17 0.27
44 26 0.41
45 1 0.02
46 10 0.16
47 9 0.14
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.61
Consensus pattern (44 bp):
ATATTATTTTTTCAATTTAAATTTACTTTTTCTGCAATTCATTT
Found at i:62531404 original size:91 final size:90
Alignment explanation
Indices: 62531246--62531410 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
62531236 TTTCAATTTC
* *
62531246 AATTTATTTTTTTCTCAATTCATTTATATTATTTTTTAATTTAAATTTAACTTTTTCTGCACTTC
1 AATTTATTTTTTTCTCAATTCATTTATATTATTTTCTAATTTAAATTAAACTTTTTCTGCACTTC
62531311 ATTTAAATTTTCTATTTTCAATGCA
66 ATTTAAATTTTCTATTTTCAATGCA
* * * * *
62531336 AATTTATTTTTTTCTTATTTCATTTTATATTAAATTTTCTATTTTCAATTCAAATTTTTTCT-C-
1 AATTTATTTTTTTCTCAATTCA-TTTATATT--ATTTTCTAATTTAAATT-AAACTTTTTCTGCA
62531399 C-TCATTTAAATT
62 CTTCATTTAAATT
62531411 AAAAATTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
90 20 0.31
91 19 0.30
92 1 0.02
93 15 0.23
94 9 0.14
ACGTcount: A:0.27, C:0.12, G:0.01, T:0.59
Consensus pattern (90 bp):
AATTTATTTTTTTCTCAATTCATTTATATTATTTTCTAATTTAAATTAAACTTTTTCTGCACTTC
ATTTAAATTTTCTATTTTCAATGCA
Found at i:62534651 original size:49 final size:49
Alignment explanation
Indices: 62534485--62534841 Score: 303
Period size: 49 Copynumber: 7.2 Consensus size: 49
62534475 CCGGCCTAAA
*** * * *
62534485 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGGCTAACACTC
1 AAAATTT-TTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* **
62534535 -AAATTTTTTTTCGTA-TACT-GTGTAGGCCATTGACAGGCCAGCACCCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCA-CCC
* * * *
62534582 AAAAATTCTTTTCGTACTGTTGGTGCCGGCCATTAACAGGCCAGCACCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* * *
62534631 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGCAAGCACCTAT
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACC--C
* * * **
62534682 AAAATTTTTTTTCGTACTGCTGGTGTCGGCCATTAACAAGCCAGCATGCAAA
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCA--C-CC
* * * *
62534734 AAAAATTTTTTT-GT-CTGGTGGTGCCGACCATTGACAGGCCAGCACCT
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* * * * * *
62534781 AAATTTTTTTTTCGTA-TACTGATGCCGGCTATTAACAAGGCCAACACCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGAC-AGGCCAGCACCC
**
62534830 AATTTTTTTTTT
1 AAAATTTTTTTT
62534842 GTTTTTTAAA
Statistics
Matches: 249, Mismatches: 46, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
46 18 0.07
47 15 0.06
48 39 0.16
49 76 0.31
50 46 0.18
51 43 0.17
52 11 0.04
53 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (49 bp):
AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
Found at i:62534765 original size:150 final size:145
Alignment explanation
Indices: 62534485--62534796 Score: 360
Period size: 150 Copynumber: 2.1 Consensus size: 145
62534475 CCGGCCTAAA
* * *
62534485 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGGCTAACACTCAAATTTTTTTTCGTA
1 AAAATTT-TTTTTCGTACTGCTGGTGCCAGCCATTGACAGGCTAACACTAAAATTTTTTTTCGTA
* * *** * *
62534550 TACTGTGTAGGCCATTGACAGGCCAGCACCCCAAAAATTCTTTTCGTACTGTTGGTGCCGGCCAT
65 TACTGTGTAGGCCATTAACAAGCCAGCACAAAAAAAATTCTTTTCGTACTGGTGGTGCCGACCAT
62534615 TAACAGGCCAGCACCC
130 TAACAGGCCAGCACCC
* *
62534631 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGC-AAGCACCTATAAAATTTTTTTTC
1 AAAATTTTTTTTCGTACTGCTGGTGCCAGCCATTGACAGGCTAA-CA-C--TAAAATTTTTTTTC
* * *
62534695 GTACTGCTGGTGTCGGCCATTAACAAGCCAGCATGCAAAAAAAATT-TTTTTGT-CTGGTGGTGC
62 GTA-TACT-GTGTAGGCCATTAACAAGCCAGCA--CAAAAAAAATTCTTTTCGTACTGGTGGTGC
* *
62534758 CGACCATTGACAGGCCAGCACCT
123 CGACCATTAACAGGCCAGCACCC
*
62534781 AAATTTTTTTTTCGTA
1 AAAATTTTTTTTCGTA
62534797 TACTGATGCC
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
144 2 0.01
145 32 0.23
146 8 0.06
148 16 0.11
149 3 0.02
150 65 0.46
151 6 0.04
152 8 0.06
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (145 bp):
AAAATTTTTTTTCGTACTGCTGGTGCCAGCCATTGACAGGCTAACACTAAAATTTTTTTTCGTAT
ACTGTGTAGGCCATTAACAAGCCAGCACAAAAAAAATTCTTTTCGTACTGGTGGTGCCGACCATT
AACAGGCCAGCACCC
Found at i:62536309 original size:42 final size:42
Alignment explanation
Indices: 62536250--62536335 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
62536240 CTGTCCTCTA
62536250 TAATCATTTCCAACCATTTATATATATGAATATATCCAAAAC
1 TAATCATTTCCAACCATTTATATATATGAATATATCCAAAAC
62536292 TAATCATTTCCAACCATTTATATATATGAATATATCCAAAAC
1 TAATCATTTCCAACCATTTATATATATGAATATATCCAAAAC
62536334 TA
1 TA
62536336 TCTCTACGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (42 bp):
TAATCATTTCCAACCATTTATATATATGAATATATCCAAAAC
Found at i:62537337 original size:18 final size:19
Alignment explanation
Indices: 62537291--62537341 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
62537281 TTTCTCATAC
* * *
62537291 AAAATGATTAAAAAATCAT
1 AAAATCATTAAAAAAACAG
*
62537310 AAAATCATTAAAAAAAGAG
1 AAAATCATTAAAAAAACAG
62537329 AAAAT-ATTAAAAA
1 AAAATCATTAAAAA
62537342 TATTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAATCATTAAAAAAACAG
Found at i:62537358 original size:23 final size:23
Alignment explanation
Indices: 62537332--62537380 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
62537322 AAAAGAGAAA
62537332 ATATTAAAAATATTAAAATTGAT
1 ATATTAAAAATATTAAAATTGAT
62537355 ATATTAAAAATATTAAAATTGAT
1 ATATTAAAAATATTAAAATTGAT
62537378 ATA
1 ATA
62537381 AACTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
ATATTAAAAATATTAAAATTGAT
Found at i:62537388 original size:20 final size:22
Alignment explanation
Indices: 62537331--62537394 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 22
62537321 AAAAAGAGAA
62537331 AATATTAAAAATATTAAAATTG
1 AATATTAAAAATATTAAAATTG
62537353 ATATATTAAAAATATTAAAATTG
1 A-ATATTAAAAATATTAAAATTG
**
62537376 -ATA-TAAACTTATTAAAATT
1 AATATTAAAAATATTAAAATT
62537395 AAAAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.36
21 3 0.08
22 1 0.03
23 21 0.54
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (22 bp):
AATATTAAAAATATTAAAATTG
Found at i:62537410 original size:27 final size:27
Alignment explanation
Indices: 62537380--62537441 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
62537370 AAATTGATAT
* *
62537380 AAACTTATTAAAATTAAAAAAATATAA-
1 AAACTAATGAAAATT-AAAAAATATAAC
* *
62537407 AAACTAATGAATATTATAAAATATAAC
1 AAACTAATGAAAATTAAAAAATATAAC
62537434 AAACTAAT
1 AAACTAAT
62537442 AAATTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (27 bp):
AAACTAATGAAAATTAAAAAATATAAC
Found at i:62538031 original size:9 final size:9
Alignment explanation
Indices: 62538017--62538051 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
62538007 TCAATTAAAT
62538017 AAAAAATTA
1 AAAAAATTA
62538026 AAAAAATTA
1 AAAAAATTA
62538035 AAAAGAA-TA
1 AAAA-AATTA
62538044 AAAAAATT
1 AAAAAATT
62538052 GGTTCAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 20 0.83
10 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:62538246 original size:22 final size:23
Alignment explanation
Indices: 62538216--62538268 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
62538206 TAATACTTTT
*
62538216 TATGATTTTTAT-AGAATTAT-AA
1 TATG-TTTTTATAAAAATTATAAA
*
62538238 TATGTTTTTATAAAAATTTTAAA
1 TATGTTTTTATAAAAATTATAAA
62538261 TATGTTTT
1 TATGTTTT
62538269 ATTAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (23 bp):
TATGTTTTTATAAAAATTATAAA
Found at i:62538375 original size:21 final size:20
Alignment explanation
Indices: 62538327--62538380 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
62538317 TTAATATTTA
62538327 ATAATTTTTAT-ATCTCTTG
1 ATAATTTTTATGATCTCTTG
* * *
62538346 ATTATTTTTATGATCTTTTTT
1 ATAATTTTTATGATC-TCTTG
62538367 ATAATTTTTATGAT
1 ATAATTTTTATGAT
62538381 AATTTTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.34
20 3 0.10
21 16 0.55
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (20 bp):
ATAATTTTTATGATCTCTTG
Found at i:62538386 original size:21 final size:20
Alignment explanation
Indices: 62538349--62538395 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
62538339 TCTCTTGATT
**
62538349 ATTTTTATGATCTTTTTTATA
1 ATTTTTATGAT-AATTTTATA
*
62538370 ATTTTTATGATAATTTTATG
1 ATTTTTATGATAATTTTATA
62538390 ATTTTT
1 ATTTTT
62538396 TAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (20 bp):
ATTTTTATGATAATTTTATA
Found at i:62538387 original size:11 final size:12
Alignment explanation
Indices: 62538344--62538391 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
62538334 TTATATCTCT
*
62538344 TGATTATTTTTA
1 TGATAATTTTTA
*
62538356 TGAT-CTTTTT-
1 TGATAATTTTTA
62538366 T-ATAATTTTTA
1 TGATAATTTTTA
62538377 TGATAA-TTTTA
1 TGATAATTTTTA
62538388 TGAT
1 TGAT
62538392 TTTTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 15 0.48
12 8 0.26
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (12 bp):
TGATAATTTTTA
Done.