Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold287
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: 1864789
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 140151 characters in sequence are not A, C, G, or T
File 3 of 7
Found at i:525493 original size:23 final size:23
Alignment explanation
Indices: 525446--525492 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
525436 GGGGGAGAAC
*
525446 AACTCAACTAAGGAGAACAGCAA
1 AACTCAACTAAGGAGAACAACAA
525469 AACTCAACTAA-GAGAACAACAA
1 AACTCAACTAAGGAGAACAACAA
525491 AA
1 AA
525493 ATAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (23 bp):
AACTCAACTAAGGAGAACAACAA
Found at i:536085 original size:7 final size:7
Alignment explanation
Indices: 536073--536297 Score: 56
Period size: 7 Copynumber: 31.9 Consensus size: 7
536063 GTTTAAAATC
536073 AAACCTT
1 AAACCTT
536080 AAACCTT
1 AAACCTT
* *
536087 AAATCAT
1 AAACCTT
*
536094 AATCCTT
1 AAACCTT
* *
536101 AAGCCCAT
1 AA-ACCTT
*
536109 AAACCCT
1 AAACCTT
536116 AAA-CTAT
1 AAACCT-T
*
536123 AAACTTT
1 AAACCTT
*
536130 AAACCAT
1 AAACCTT
*
536137 AAACCCT
1 AAACCTT
* *
536144 AATCCCCT
1 AA-ACCTT
* *
536152 AATCCCCT
1 AA-ACCTT
536160 -AACCTTT
1 AAACC-TT
*
536167 AAACCAT
1 AAACCTT
*
536174 AAACATT
1 AAACCTT
*
536181 AAACCCT
1 AAACCTT
*
536188 AAACCCT
1 AAACCTT
* *
536195 AAATCAT
1 AAACCTT
536202 AAACAC-T
1 AAAC-CTT
536209 AAA-CTAT
1 AAACCT-T
536216 AAACC-T
1 AAACCTT
536222 ACAACC-T
1 A-AACCTT
*
536229 AAACCGT
1 AAACCTT
536236 AAACAC-T
1 AAAC-CTT
*
536243 AAATTCTT
1 AAA-CCTT
536251 -AACAC-T
1 AAAC-CTT
* *
536257 AAATCAT
1 AAACCTT
536264 AAATCC-T
1 AAA-CCTT
536271 AAACCTT
1 AAACCTT
*
536278 AAACCTC
1 AAACCTT
536285 AAACCTT
1 AAACCTT
536292 AAACCT
1 AAACCT
536298 ACACCCTAAA
Statistics
Matches: 167, Mismatches: 31, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
5 1 0.01
6 13 0.08
7 126 0.75
8 27 0.16
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (7 bp):
AAACCTT
Found at i:536124 original size:29 final size:28
Alignment explanation
Indices: 536073--536145 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
536063 GTTTAAAATC
* * *
536073 AAACCTTAAACCTTAAATCATAATCCTT
1 AAACCATAAACCCTAAATCATAAACCTT
* *
536101 AAGCCCATAAACCCTAAA-CTATAAACTTT
1 AA-ACCATAAACCCTAAATC-ATAAACCTT
536130 AAACCATAAACCCTAA
1 AAACCATAAACCCTAA
536146 TCCCCTAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (28 bp):
AAACCATAAACCCTAAATCATAAACCTT
Found at i:536126 original size:14 final size:14
Alignment explanation
Indices: 536073--536310 Score: 69
Period size: 14 Copynumber: 16.9 Consensus size: 14
536063 GTTTAAAATC
* *
536073 AAACCTTAAACCTT
1 AAACCATAAACCCT
* * *
536087 AAATCATAATCCTT
1 AAACCATAAACCCT
*
536101 AAGCCCATAAACCCT
1 AA-ACCATAAACCCT
* **
536116 AAACTATAAACTTT
1 AAACCATAAACCCT
536130 AAACCATAAACCCT
1 AAACCATAAACCCT
* * *
536144 AATCCCCTAATCCCCT
1 AA-ACCATAA-ACCCT
* *
536160 -AACCTTTAAACCAT
1 AAACC-ATAAACCCT
536174 AAA-CATTAAACCCT
1 AAACCA-TAAACCCT
* * *
536188 AAACCCTAAATCAT
1 AAACCATAAACCCT
**
536202 AAA-CACTAAACTAT
1 AAACCA-TAAACCCT
536216 AAACC-TACAA-CCT
1 AAACCATA-AACCCT
* *
536229 AAACCGTAAACACT
1 AAACCATAAACCCT
* * *
536243 AAATTC-TTAACACT
1 AAA-CCATAAACCCT
* *
536257 AAATCATAAATCCT
1 AAACCATAAACCCT
*
536271 AAACCTTAAA-CCT
1 AAACCATAAACCCT
*
536284 CAAACCTTAAA-CCT
1 -AAACCATAAACCCT
* *
536298 ACACCCTAAACCC
1 AAACCATAAACCC
536311 CAAATATATA
Statistics
Matches: 167, Mismatches: 41, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
13 24 0.14
14 115 0.69
15 24 0.14
16 4 0.02
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:536239 original size:48 final size:49
Alignment explanation
Indices: 536173--536282 Score: 129
Period size: 48 Copynumber: 2.3 Consensus size: 49
536163 CTTTAAACCA
* *
536173 TAAACATTAAACCCTAAACCCTAAA-TCATAAACACTAAA-CTATAAA-CC
1 TAAACCTTAAACCCTAAACACTAAATTC-TAAACACTAAATC-ATAAATCC
* *
536221 TACAACC-TAAACCGTAAACACTAAATTCTTAACACTAAATCATAAATCC
1 TA-AACCTTAAACCCTAAACACTAAATTCTAAACACTAAATCATAAATCC
536270 TAAACCTTAAACC
1 TAAACCTTAAACC
536283 TCAAACCTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
48 37 0.70
49 16 0.30
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (49 bp):
TAAACCTTAAACCCTAAACACTAAATTCTAAACACTAAATCATAAATCC
Found at i:536305 original size:7 final size:7
Alignment explanation
Indices: 536108--536310 Score: 74
Period size: 7 Copynumber: 29.0 Consensus size: 7
536098 CTTAAGCCCA
536108 TAAACCC
1 TAAACCC
**
536115 TAAACTA
1 TAAACCC
**
536122 TAAACTT
1 TAAACCC
*
536129 TAAACCA
1 TAAACCC
536136 TAAACCC
1 TAAACCC
*
536143 TAATCCCC
1 TAA-ACCC
*
536151 TAATCCCC
1 TAA-ACCC
*
536159 T-AACCTT
1 TAAACC-C
*
536166 TAAACCA
1 TAAACCC
**
536173 TAAACAT
1 TAAACCC
536180 TAAACCC
1 TAAACCC
536187 TAAACCC
1 TAAACCC
* *
536194 TAAATCA
1 TAAACCC
*
536201 TAAACAC
1 TAAACCC
**
536208 TAAACTA
1 TAAACCC
536215 TAAA-CC
1 TAAACCC
536221 TACAA-CC
1 TA-AACCC
*
536228 TAAACCG
1 TAAACCC
*
536235 TAAACAC
1 TAAACCC
**
536242 TAAATTC
1 TAAACCC
* *
536249 TTAACAC
1 TAAACCC
* *
536256 TAAATCA
1 TAAACCC
*
536263 TAAATCC
1 TAAACCC
*
536270 TAAACCT
1 TAAACCC
536277 TAAA-CC
1 TAAACCC
*
536283 TCAAACCT
1 T-AAACCC
536291 TAAA-CC
1 TAAACCC
*
536297 TACACCC
1 TAAACCC
536304 TAAACCC
1 TAAACCC
536311 CAAATATATA
Statistics
Matches: 145, Mismatches: 43, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
6 12 0.08
7 115 0.79
8 18 0.12
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:536569 original size:7 final size:7
Alignment explanation
Indices: 536557--536690 Score: 58
Period size: 7 Copynumber: 18.7 Consensus size: 7
536547 ACTAATTAAT
536557 CTAAACC
1 CTAAACC
536564 CTAAACC
1 CTAAACC
536571 TCT-AACC
1 -CTAAACC
* *
536578 CTTATCC
1 CTAAACC
536585 CTTAAACC
1 C-TAAACC
**
536593 CTAAATT
1 CTAAACC
*
536600 ATAAACC
1 CTAAACC
*
536607 ATAAACC
1 CTAAACC
*
536614 ATAAACCC
1 CTAAA-CC
536622 CT-AACC
1 CTAAACC
*
536628 CTTAAATC
1 C-TAAACC
*
536636 TTAAACC
1 CTAAACC
*
536643 C-CAACC
1 CTAAACC
*
536649 ATTAAACC
1 -CTAAACC
*
536657 ATAAACC
1 CTAAACC
*
536664 ATAAACC
1 CTAAACC
*
536671 CATAATCC
1 C-TAAACC
536679 CTAAACC
1 CTAAACC
*
536686 TTAAA
1 CTAAA
536691 ATAGTAACTC
Statistics
Matches: 97, Mismatches: 21, Indels: 18
0.71 0.15 0.13
Matches are distributed among these distances:
6 9 0.09
7 65 0.67
8 23 0.24
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:536606 original size:14 final size:14
Alignment explanation
Indices: 536601--536739 Score: 70
Period size: 14 Copynumber: 9.7 Consensus size: 14
536591 CCCTAAATTA
*
536601 TAAACCATAAACCA
1 TAAACCATAAACCC
*
536615 TAAACCCCT-AACCC
1 TAAA-CCATAAACCC
* *
536629 TTAAATCTTAAACCC
1 -TAAACCATAAACCC
* *
536644 -CAACCATTAAACCA
1 TAAACCA-TAAACCC
536658 TAAACCATAAACCC
1 TAAACCATAAACCC
* * *
536672 ATAATCCCTAAACCT
1 -TAAACCATAAACCC
536687 TAAA--ATAGTAACTCC
1 TAAACCATA--AAC-CC
* *
536702 TAAATCTTAAACCC
1 TAAACCATAAACCC
* *
536716 TAAACCATATACCT
1 TAAACCATAAACCC
536730 TAAACCATAA
1 TAAACCATAA
536740 TAATAGTATT
Statistics
Matches: 92, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
12 2 0.02
13 3 0.03
14 49 0.53
15 36 0.39
17 2 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:536612 original size:50 final size:49
Alignment explanation
Indices: 536558--536690 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 49
536548 CTAATTAATC
* * ** *
536558 TAAACCCTAAACCTCTAACCCTTATCCCTTAAACCCTAA-ATTATAAACCA
1 TAAACCATAAACCCCTAACCCTTAAACCTTAAACCCCAACA-T-TAAACCA
*
536608 TAAACCATAAACCCCTAACCCTTAAATCTTAAACCCCAACCATTAAACCA
1 TAAACCATAAACCCCTAACCCTTAAACCTTAAACCCCAA-CATTAAACCA
*
536658 TAAACCATAAACCCATAATCCC-TAAACCTTAAA
1 TAAACCATAAACCCCTAA-CCCTTAAACCTTAAA
536691 ATAGTAACTC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 67 0.93
51 4 0.06
52 1 0.01
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.23
Consensus pattern (49 bp):
TAAACCATAAACCCCTAACCCTTAAACCTTAAACCCCAACATTAAACCA
Found at i:536627 original size:21 final size:20
Alignment explanation
Indices: 536603--536663 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
536593 CTAAATTATA
536603 AACCATAAACCATAAACCCC
1 AACCATAAACCATAAACCCC
* * *
536623 TAACCCTTAAATCTTAAACCCC
1 -AA-CCATAAACCATAAACCCC
536645 AACCATTAAACCATAAACC
1 AACCA-TAAACCATAAACC
536664 ATAAACCCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 15 0.47
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (20 bp):
AACCATAAACCATAAACCCC
Found at i:536658 original size:8 final size:7
Alignment explanation
Indices: 536645--536739 Score: 50
Period size: 7 Copynumber: 13.1 Consensus size: 7
536635 CTTAAACCCC
536645 AACCATTA
1 AACCA-TA
536653 AACCATA
1 AACCATA
536660 AACCATA
1 AACCATA
536667 AACCCATA
1 AA-CCATA
* *
536675 ATCCCTA
1 AACCATA
*
536682 AACCTTA
1 AACCATA
536689 AA--ATA
1 AACCATA
*
536694 GTAACTCCTA
1 --AAC-CATA
* *
536704 AATCTTA
1 AACCATA
*
536711 AACCCTA
1 AACCATA
536718 AACCATA
1 AACCATA
* *
536725 TACCTTA
1 AACCATA
536732 AACCATA
1 AACCATA
536739 A
1 A
536740 TAATAGTATT
Statistics
Matches: 66, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
5 2 0.03
7 49 0.74
8 13 0.20
10 2 0.03
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.23
Consensus pattern (7 bp):
AACCATA
Found at i:536683 original size:15 final size:15
Alignment explanation
Indices: 536600--536685 Score: 56
Period size: 15 Copynumber: 5.9 Consensus size: 15
536590 ACCCTAAATT
536600 ATAAACCATAAA-CC
1 ATAAACCATAAACCC
*
536614 ATAAACCCCT-AACCC
1 ATAAA-CCATAAACCC
* * *
536629 TTAAATCTTAAACCC
1 ATAAACCATAAACCC
*
536644 --CAACCATTAAA-CC
1 ATAAACCA-TAAACCC
536657 ATAAACCATAAACCC
1 ATAAACCATAAACCC
* *
536672 ATAATCCCTAAACC
1 ATAAACCATAAACC
536686 TTAAAATAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
13 5 0.09
14 17 0.31
15 33 0.60
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAACCATAAACCC
Found at i:537182 original size:23 final size:23
Alignment explanation
Indices: 537156--537199 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
537146 AAAGCGTCGC
*
537156 TAATGGTCAACCTATAGCGGCAT
1 TAATGCTCAACCTATAGCGGCAT
* *
537179 TAATGCTCTATCTATAGCGGC
1 TAATGCTCAACCTATAGCGGC
537200 GTTTTTTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (23 bp):
TAATGCTCAACCTATAGCGGCAT
Found at i:540469 original size:20 final size:20
Alignment explanation
Indices: 540444--540517 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
540434 GTCACTTACC
*
540444 CACACGCCCGTGTGGAGAAG
1 CACACGCCCGTGTGGACAAG
540464 CACACGCCCGTGTGGACAAG
1 CACACGCCCGTGTGGACAAG
*
540484 CACACGCCTGTGTGGACAAG
1 CACACGCCCGTGTGGACAAG
*
540504 CAAACGCCCGTGTG
1 CACACGCCCGTGTG
540518 AAGACCATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.24, C:0.32, G:0.31, T:0.12
Consensus pattern (20 bp):
CACACGCCCGTGTGGACAAG
Found at i:541881 original size:77 final size:78
Alignment explanation
Indices: 541791--541948 Score: 309
Period size: 77 Copynumber: 2.0 Consensus size: 78
541781 TAATTAGCCT
541791 AATTAAATTACACAAAACCACCTAAATGCTTACTTACCATTATTCAATAAAAA-TTCAACTCTTG
1 AATTAAATTACACAAAACCACCTAAATGCTTACTTACCATTATTCAATAAAAAGTTCAACTCTTG
541855 TACATATAATATC
66 TACATATAATATC
541868 AATTAAATTACACAAAACCACCTAAATGCTTACTTACCATTATTCAATAAAAAGTTCAACTCTTG
1 AATTAAATTACACAAAACCACCTAAATGCTTACTTACCATTATTCAATAAAAAGTTCAACTCTTG
541933 TACATATAATATC
66 TACATATAATATC
541946 AAT
1 AAT
541949 CTTGCAAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 53 0.66
78 27 0.34
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (78 bp):
AATTAAATTACACAAAACCACCTAAATGCTTACTTACCATTATTCAATAAAAAGTTCAACTCTTG
TACATATAATATC
Found at i:543188 original size:14 final size:15
Alignment explanation
Indices: 543162--543190 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
543152 TAAAATCTTT
543162 AAAATAAATTTTTTG
1 AAAATAAATTTTTTG
543177 AAAATAAATTTTTT
1 AAAATAAATTTTTT
543191 AATTTTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AAAATAAATTTTTTG
Found at i:545928 original size:15 final size:14
Alignment explanation
Indices: 545886--545942 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
545876 ATTTAACTTA
545886 AGGGTTAAGGTTTT
1 AGGGTTAAGGTTTT
** *
545900 AAAGTTAAGTTTTT
1 AGGGTTAAGGTTTT
545914 AGGGTTTAAGGTTTTT
1 AGGG-TTAAGG-TTTT
* *
545930 AGGTTTAGGGTTT
1 AGGGTTAAGGTTT
545943 GTGGTTTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 16 0.48
15 10 0.30
16 7 0.21
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
AGGGTTAAGGTTTT
Found at i:545936 original size:22 final size:22
Alignment explanation
Indices: 545911--545965 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
545901 AAGTTAAGTT
*
545911 TTTAGGGTTTAAGGTTTTTAGG
1 TTTAGGGTTTAAGGTTTTTAAG
**
545933 TTTAGGGTTTGTGGTTTTTAAG
1 TTTAGGGTTTAAGGTTTTTAAG
545955 TTTAGGGTTTA
1 TTTAGGGTTTA
545966 GGGCTTGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (22 bp):
TTTAGGGTTTAAGGTTTTTAAG
Found at i:545948 original size:29 final size:27
Alignment explanation
Indices: 545927--546021 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 27
545917 GTTTAAGGTT
*
545927 TTTA-GGTTTAGGGTTTGTGGTTTTTAAG
1 TTTAGGGTTTAGGGCTTGTGG--TTTAAG
545955 TTTAGGGTTTAGGGCTTGTGGTTTTTAAG
1 TTTAGGGTTTAGGGCTTGTGG--TTTAAG
* *
545984 TTTAGGGTTTAGGGTTTAGGGGTTTTAAG
1 TTTAGGGTTTAGGGCTT-GTGG-TTTAAG
*
546013 TTAAGGGTT
1 TTTAGGGTT
546022 AGCGTTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
28 4 0.07
29 54 0.89
30 3 0.05
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.48
Consensus pattern (27 bp):
TTTAGGGTTTAGGGCTTGTGGTTTAAG
Found at i:546066 original size:21 final size:21
Alignment explanation
Indices: 545994--546066 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
545984 TTTAGGGTTT
*
545994 AGGGTTTAGGGGTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTA
* *
546016 AGGGTTAGCGTTTTTAATTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
546037 AGGGGTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
546058 AGGGTTAGG
1 AGGGTTAGG
546067 ATTAGGGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.23, C:0.01, G:0.36, T:0.40
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:546384 original size:21 final size:21
Alignment explanation
Indices: 546345--546385 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
546335 TTGTCCAGCT
**
546345 TCCGGCGGCGATTGTGGTTCC
1 TCCGGCGGCGATTCAGGTTCC
*
546366 TCCGGCGGGGATTCAGGTTC
1 TCCGGCGGCGATTCAGGTTC
546386 TTCTAGTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.27, G:0.39, T:0.27
Consensus pattern (21 bp):
TCCGGCGGCGATTCAGGTTCC
Found at i:546670 original size:18 final size:18
Alignment explanation
Indices: 546647--546686 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
546637 GACTCGTTAA
*
546647 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGTT
546665 AGGATACATAAAAGGGTT
1 AGGATACATAAAAGGGTT
546683 AGGA
1 AGGA
546687 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATAAAAGGGTT
Found at i:547347 original size:7 final size:7
Alignment explanation
Indices: 547337--547372 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
547327 TTATATACAT
547337 AATACTA
1 AATACTA
547344 AATACTA
1 AATACTA
547351 AATACTA
1 AATACTA
547358 AATACTA
1 AATACTA
547365 AATACTA
1 AATACTA
547372 A
1 A
547373 TTACCAATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:549222 original size:9 final size:9
Alignment explanation
Indices: 549210--549237 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
549200 TTTTATTACA
549210 ACAATTAAT
1 ACAATTAAT
549219 ACAATTAAT
1 ACAATTAAT
549228 ACAATTAAT
1 ACAATTAAT
549237 A
1 A
549238 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:549260 original size:68 final size:68
Alignment explanation
Indices: 549151--549457 Score: 591
Period size: 68 Copynumber: 4.5 Consensus size: 68
549141 GGCCAGGCCC
549151 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
549216 AAT
66 AAT
549219 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
549284 AAT
66 AAT
549287 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
549352 AAT
66 AAT
549355 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
549420 AAT
66 AAT
*
549423 ACAATT-A-ACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAA
549458 CAATTAATTT
Statistics
Matches: 238, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
66 27 0.11
67 1 0.00
68 210 0.88
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:549290 original size:9 final size:9
Alignment explanation
Indices: 549278--549305 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
549268 TTTTATTACA
549278 ACAATTAAT
1 ACAATTAAT
549287 ACAATTAAT
1 ACAATTAAT
549296 ACAATTAAT
1 ACAATTAAT
549305 A
1 A
549306 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:549358 original size:9 final size:9
Alignment explanation
Indices: 549346--549373 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
549336 TTTTATTACA
549346 ACAATTAAT
1 ACAATTAAT
549355 ACAATTAAT
1 ACAATTAAT
549364 ACAATTAAT
1 ACAATTAAT
549373 A
1 A
549374 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:549467 original size:16 final size:16
Alignment explanation
Indices: 549446--549487 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
549436 AATAATTTGA
*
549446 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
549462 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
549478 TAGTTTTAAT
1 TAATTTTAAT
549488 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:549471 original size:22 final size:23
Alignment explanation
Indices: 549461--549516 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
549451 TTACTAACAA
* * *
549461 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
549483 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
549506 TTAATTTTAAT
1 TTAATTTTAAT
549517 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:550355 original size:3 final size:3
Alignment explanation
Indices: 550347--550381 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
550337 TATGCTTTTA
* *
550347 ATT ATT ATT ATT GTT ATT ATT ATT ATT ACT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
550382 AAAGCTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:551362 original size:22 final size:22
Alignment explanation
Indices: 551337--551379 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
551327 AATGATAAAT
* *
551337 TTAAAAATTTAGAATTTAAAAG
1 TTAAAAATATAGAATTGAAAAG
551359 TTAAAAATATAGAATTGAAAA
1 TTAAAAATATAGAATTGAAAA
551380 AAAATAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (22 bp):
TTAAAAATATAGAATTGAAAAG
Found at i:552157 original size:12 final size:11
Alignment explanation
Indices: 552127--552169 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
552117 TACCCTCCCT
552127 CTTTTCCTTT-
1 CTTTTCCTTTC
*
552137 CTTTCCCTTTCC
1 CTTTTCCTTT-C
552149 CTTTTCCTTTC
1 CTTTTCCTTTC
552160 CTTTCTCCTT
1 CTTT-TCCTT
552170 CTTTCTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
11 5 0.18
12 14 0.50
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (11 bp):
CTTTTCCTTTC
Found at i:553439 original size:19 final size:20
Alignment explanation
Indices: 553403--553440 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
553393 GGCGAAAAGT
**
553403 ATTGATATTTGATCACAAAA
1 ATTGATATTTGAAAACAAAA
553423 ATTGAT-TTTGAAAACAAA
1 ATTGATATTTGAAAACAAA
553441 CAGAATGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (20 bp):
ATTGATATTTGAAAACAAAA
Found at i:554217 original size:18 final size:18
Alignment explanation
Indices: 554191--554229 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
554181 TATTTTTTAA
*
554191 TTATATTTAAAGTGAATT
1 TTATATTTAAAGTAAATT
* *
554209 TTATTTTTAAATTAAATT
1 TTATATTTAAAGTAAATT
554227 TTA
1 TTA
554230 CATATGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTATATTTAAAGTAAATT
Found at i:554257 original size:3 final size:3
Alignment explanation
Indices: 554249--554286 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
554239 TTCTTGTCTT
554249 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
554287 NNNNNNNNNN
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:558085 original size:40 final size:40
Alignment explanation
Indices: 558035--558238 Score: 149
Period size: 40 Copynumber: 5.0 Consensus size: 40
558025 TGCTAAGAAG
* *
558035 AGTACAAAAGTACTATTAGGAGCACCGTTGTGCTATCAGA
1 AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATCAGA
* * ** *
558075 AGTATGAAAGTACTGTCAGGAGCATTGTTGTGCTATCAGG
1 AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATCAGA
* * * * * * *
558115 AGTACGAAAGTACTGTCAGAAGCATCATTATGATATCAAAGG
1 AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATC--AGA
* * ** **** * *
558157 AGTATGAAAGTACTGTCAAAAGCACTAAAGTGC-AACTAGG
1 AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATC-AGA
*
558197 AGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATCAGA
1 AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATCAGA
558237 AG
1 AG
558239 CACTTATTCA
Statistics
Matches: 129, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 97 0.75
41 4 0.03
42 28 0.22
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (40 bp):
AGTACGAAAGTACTATCAGGAGCACCGTTGTGCTATCAGA
Found at i:558234 original size:82 final size:81
Alignment explanation
Indices: 558034--558238 Score: 227
Period size: 82 Copynumber: 2.5 Consensus size: 81
558024 GTGCTAAGAA
* * * **
558034 GAGTACAAAAGTACTATTAGGAGCACCGTTGTGCTATC-AGAAGTATGAAAGTACTGTCAGGAGC
1 GAGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATCAAGAAGTATGAAAGTACTGTCAAAAGC
* *** *
558098 ATTGTTGTGCTATCAG
66 ACTAAAGTGCAATCAG
* * * * * *
558114 GAGTACGAAAGTACTGTCAGAAGCATCATTATGATATCAAAGGAGTATGAAAGTACTGTCAAAAG
1 GAGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATC-AAGAAGTATGAAAGTACTGTCAAAAG
558179 CACTAAAGTGCAA-CTAG
65 CACTAAAGTGCAATC-AG
558196 GAGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATC-AGAAG
1 GAGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATCAAGAAG
558239 CACTTATTCA
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
80 34 0.34
81 1 0.01
82 65 0.65
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (81 bp):
GAGTACGAAAGTACTGTCAGGAGCACCGTTGTGCTATCAAGAAGTATGAAAGTACTGTCAAAAGC
ACTAAAGTGCAATCAG
Found at i:561787 original size:38 final size:38
Alignment explanation
Indices: 561683--562159 Score: 539
Period size: 38 Copynumber: 12.6 Consensus size: 38
561673 ATAGTTAGAA
* *
561683 CAACCGAACACACCAAATAGAAGCTCATAAGAGCTGATC
1 CAACCGAA-ACGCCAAACAGAAGCTCATAAGAGCTGATC
* * *
561722 CAACTGAACACACCAAACAGAAGCTCATAAGAACTGATC
1 CAACCGAA-ACGCCAAACAGAAGCTCATAAGAGCTGATC
* * * * *
561761 CAACTGAAACACCAAATAGAAACTCATAAGAGCTAATC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
*
561799 CAACC-AAATCGCCAAACAGAAGCTCATAAGAGATGATC
1 CAACCGAAA-CGCCAAACAGAAGCTCATAAGAGCTGATC
* *
561837 CAACCGAAACGCCAAATAGAAGCTCATAAGAGTTGATC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* * *
561875 CAACAGAATCGCCAAACAGAAGCTCATAAGAGCTGATG
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* *
561913 CAACTG-AA-GCCAAACAGAAGCTCATAATAGCTGATC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* * * * *
561949 CAACAGGATCGCCAAATAGAAGCTCATAAGAGCTTATC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* * * *
561987 CAACCAAAACGCCAAACAAAAGTTCATAAGGGCTGATC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* *
562025 CAACC-AAATAGTCAAACAGAAGCTCATAAGAGCTGATC
1 CAACCGAAA-CGCCAAACAGAAGCTCATAAGAGCTGATC
* * * *
562063 CAACCGAATCGCCAAATAGAAGCTCATAAGAGCTAATA
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
* * * * *
562101 CAATCGAATCACCAAATAGAAGCTCATAAGAGCTGGTC
1 CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
*
562139 CAACCGAAACTCCAAACAGAA
1 CAACCGAAACGCCAAACAGAA
562160 AGTATAACAT
Statistics
Matches: 374, Mismatches: 58, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
36 31 0.08
37 8 0.02
38 286 0.76
39 49 0.13
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (38 bp):
CAACCGAAACGCCAAACAGAAGCTCATAAGAGCTGATC
Found at i:562026 original size:188 final size:189
Alignment explanation
Indices: 561695--562160 Score: 614
Period size: 188 Copynumber: 2.5 Consensus size: 189
561685 ACCGAACACA
* *
561695 CCAAATAGAAGCTCATAAGAGCTGATCCAACTGAACACACCAAACAGAAGCTCATAAGAACTGAT
1 CCAAATAGAAGCTCATAAGAGCTGATACAACTG-A-ACACCAAACAGAAGCTCATAAGAGCTGAT
* * *
561760 CCAACTGAAACACCAAATAGAAACTCATAAGAGCTAATCCAACCAAATCGCCAAACAGAAGCTCA
64 CCAACAGAAACACCAAATAGAAACTCATAAGAGCTAATCCAACCAAAACGCCAAACAAAAGCTCA
* * *
561825 TAAGAGATGATCCAACCGAAA-CGCCAAATAGAAGCTCATAAGAGTTGATCCAACAGAATCG
129 TAAGAGATGATCCAACC-AAATAGCCAAACAGAAGCTCATAAGAGCTGATCCAACAGAATCG
* * * *
561886 CCAAACAGAAGCTCATAAGAGCTGATGCAACTGAA-GCCAAACAGAAGCTCATAATAGCTGATCC
1 CCAAATAGAAGCTCATAAGAGCTGATACAACTGAACACCAAACAGAAGCTCATAAGAGCTGATCC
* * * * * *
561950 AACAGGATCGCCAAATAGAAGCTCATAAGAGCTTATCCAACCAAAACGCCAAACAAAAGTTCATA
66 AACAGAAACACCAAATAGAAACTCATAAGAGCTAATCCAACCAAAACGCCAAACAAAAGCTCATA
* * * *
562015 AGGGCTGATCCAACCAAATAGTCAAACAGAAGCTCATAAGAGCTGATCCAACCGAATCG
131 AGAGATGATCCAACCAAATAGCCAAACAGAAGCTCATAAGAGCTGATCCAACAGAATCG
* * *
562074 CCAAATAGAAGCTCATAAGAGCTAATACAA-TCGAATCACCAAATAGAAGCTCATAAGAGCTGGT
1 CCAAATAGAAGCTCATAAGAGCTGATACAACT-GAA-CACCAAACAGAAGCTCATAAGAGCTGAT
* * *
562138 CCAACCGAAACTCCAAACAGAAA
64 CCAACAGAAACACCAAATAGAAA
562161 GTATAACATG
Statistics
Matches: 237, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
187 4 0.02
188 160 0.68
189 1 0.00
190 41 0.17
191 31 0.13
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (189 bp):
CCAAATAGAAGCTCATAAGAGCTGATACAACTGAACACCAAACAGAAGCTCATAAGAGCTGATCC
AACAGAAACACCAAATAGAAACTCATAAGAGCTAATCCAACCAAAACGCCAAACAAAAGCTCATA
AGAGATGATCCAACCAAATAGCCAAACAGAAGCTCATAAGAGCTGATCCAACAGAATCG
Found at i:566153 original size:15 final size:15
Alignment explanation
Indices: 566133--566163 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
566123 AACTCATATG
566133 TAAGTGTAAGAATGA
1 TAAGTGTAAGAATGA
566148 TAAGTGTAAGAATGA
1 TAAGTGTAAGAATGA
566163 T
1 T
566164 TTCCTGTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
TAAGTGTAAGAATGA
Found at i:567361 original size:61 final size:57
Alignment explanation
Indices: 567219--567363 Score: 175
Period size: 61 Copynumber: 2.5 Consensus size: 57
567209 TTATTATTTC
* * *
567219 ATATTTTATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATT
1 ATATTTAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAATT
* * *
567277 GTATTTAACAATAATTATGTTAAAATATGATTAAATTATTTATTATTACTTTTATTAAATT
1 ATATTTAATAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAATT
567338 ATATTTAATAATAAATT-TATTAAAAT
1 ATATTTAATAAT-AATTATATTAAAAT
567364 TTAATAATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
57 13 0.18
58 19 0.26
59 2 0.03
60 5 0.07
61 30 0.41
62 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
ATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAATT
Found at i:568241 original size:21 final size:21
Alignment explanation
Indices: 568217--568258 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
568207 TTGGATAAAA
*
568217 TTTTCAAATAATTTTATAATTT
1 TTTTCAAA-AATTTAATAATTT
*
568239 TTTTTAAAAATTTAATAATT
1 TTTTCAAAAATTTAATAATT
568259 AAACCGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTCAAAAATTTAATAATTT
Found at i:571604 original size:11 final size:11
Alignment explanation
Indices: 571588--571622 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
571578 TATAACATTA
571588 ATATTTTTATT
1 ATATTTTTATT
571599 ATATTTTTATT
1 ATATTTTTATT
571610 GATA-TTTTATT
1 -ATATTTTTATT
571621 AT
1 AT
571623 GAAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 18 0.78
12 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATATTTTTATT
Found at i:581758 original size:11 final size:11
Alignment explanation
Indices: 581742--581776 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
581732 TATAACATTA
581742 ATATTTTTATT
1 ATATTTTTATT
581753 ATATTTTTATT
1 ATATTTTTATT
581764 GATA-TTTTATT
1 -ATATTTTTATT
581775 AT
1 AT
581777 GAAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 18 0.78
12 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATATTTTTATT
Found at i:582136 original size:41 final size:42
Alignment explanation
Indices: 582090--582172 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
582080 ATGAAGAAGA
582090 AATGAAGAAATTCTTGACAAAGGAGGTAAG-TTCATACTAAC
1 AATGAAGAAATTCTTGACAAAGGAGGTAAGTTTCATACTAAC
582131 AATGAAGAAATTCTTGACAAAGGAGGTAAGTTTCATACTAAC
1 AATGAAGAAATTCTTGACAAAGGAGGTAAGTTTCATACTAAC
582173 CCTACTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 30 0.73
42 11 0.27
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.25
Consensus pattern (42 bp):
AATGAAGAAATTCTTGACAAAGGAGGTAAGTTTCATACTAAC
Found at i:583267 original size:20 final size:18
Alignment explanation
Indices: 583220--583268 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
583210 CAAGATAAAC
583220 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
583237 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
583257 ATTAAATTAATA
1 ATTAAATTAATA
583269 AATACTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:583311 original size:33 final size:34
Alignment explanation
Indices: 583267--583330 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
583257 ATTAAATTAA
*
583267 TAAATACTATTAAGATAAGTATT-TTATTTAATAT
1 TAAATACTATTAAAATAA-TATTATTATTTAATAT
*
583301 TAAAT-CTATTAAAATAATATTATTTTTTAA
1 TAAATACTATTAAAATAATATTATTATTTAA
583331 CAATTAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 18 0.67
34 5 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TAAATACTATTAAAATAATATTATTATTTAATAT
Found at i:585402 original size:14 final size:14
Alignment explanation
Indices: 585383--585411 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
585373 ATACTATGGC
585383 TCCACGACCTAGGA
1 TCCACGACCTAGGA
585397 TCCACGACCTAGGA
1 TCCACGACCTAGGA
585411 T
1 T
585412 GAATACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (14 bp):
TCCACGACCTAGGA
Found at i:588924 original size:39 final size:39
Alignment explanation
Indices: 588859--589038 Score: 261
Period size: 39 Copynumber: 4.6 Consensus size: 39
588849 GGTATTCACT
* * * **
588859 TTTAAGCATATACCACATTACACATATAATCATGTAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
588898 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
588937 TTTAGGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
588976 TTCAAGCATATATCACAATACTCATATAATCACATTACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
589015 TTCAAGCATAGATCATAATACTCA
1 TTTAAGCATATATCACAATACTCA
589039 AAAACATGTT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 130 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:589029 original size:22 final size:21
Alignment explanation
Indices: 588962--589029 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
588952 CAATACTCAT
*
588962 ATAATCACATAACATTCAAGC
1 ATAATCACATTACATTCAAGC
* *
588983 ATATATCACAATAC--TC-A-T
1 ATA-ATCACATTACATTCAAGC
589001 ATAATCACATTACATTCAAGC
1 ATAATCACATTACATTCAAGC
589022 ATAGATCA
1 ATA-ATCA
589030 TAATACTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 3 0.08
20 3 0.08
21 6 0.17
22 12 0.33
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (21 bp):
ATAATCACATTACATTCAAGC
Found at i:592977 original size:35 final size:34
Alignment explanation
Indices: 592919--593066 Score: 154
Period size: 35 Copynumber: 4.2 Consensus size: 34
592909 ATCCAACCAA
* ** *
592919 AAACACACTAGATGCTCAAAAGAGCTAATCCATCTG
1 AAACACACCA-ATGCTCGTAAGAGCTAATCCCTC-G
592955 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
1 AAACACACCAATGCTCGTAAGAGCTAATCCCT-CG
* * * *
592990 AAGCACACCAATGCTTGTAAGAACTAATCCCTACA
1 AAACACACCAATGCTCGTAAGAGCTAATCCCT-CG
*
593025 AAACACACCAATGCTC-TAAAGAGGTAATCCCTTCG
1 AAACACACCAATGCTCGT-AAGAGCTAATCCC-TCG
593060 AAACACA
1 AAACACA
593067 TTAAAACAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.01
35 83 0.87
36 11 0.12
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (34 bp):
AAACACACCAATGCTCGTAAGAGCTAATCCCTCG
Found at i:598441 original size:4 final size:4
Alignment explanation
Indices: 598432--598499 Score: 70
Period size: 4 Copynumber: 17.5 Consensus size: 4
598422 CTGTATGGGG
* *
598432 AAGA AAGA AAGA AAGA CA-A AAGA AAGA AAGA AAGA AGGGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA
* *
598479 AA-A AGGA AAGA AAAA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AA
598500 AAAAATAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 7 0.13
4 42 0.81
5 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:598455 original size:15 final size:15
Alignment explanation
Indices: 598438--598495 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
598428 GGGGAAGAAA
598438 GAAAGAAAGACAAAA-
1 GAAAGAAAGA-AAAAG
598453 GAAAGAAAGAAAGAAGG
1 GAAAGAAAGAAA-AA-G
598470 GAAA-AAAGAAAAAG
1 GAAAGAAAGAAAAAG
598484 GAAAGAAA-AAAA
1 GAAAGAAAGAAAA
598496 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.28
15 17 0.44
16 7 0.18
17 4 0.10
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAAG
Found at i:598462 original size:23 final size:23
Alignment explanation
Indices: 598432--598502 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
598422 CTGTATGGGG
*
598432 AAGAAAGAAAGAAAGACAAAAGA
1 AAGAAAGAAAGAAAGAAAAAAGA
*
598455 AAGAAAGAAAGAAGGGAAAAAAGAAA
1 AAGAAAGAAAGAA-AGAAAAAAG--A
*
598481 AAGGAAAGAAAAAAAGAAAAAA
1 AA-GAAAGAAAGAAAGAAAAAA
598503 AATAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
26 10 0.25
27 10 0.25
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAAGAAAGAAAAAAGA
Found at i:598478 original size:31 final size:32
Alignment explanation
Indices: 598438--598498 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
598428 GGGGAAGAAA
*
598438 GAAAGAAAGACAAAA-GAAAGAAAGAAAGAAGG
1 GAAAGAAAGA-AAAAGGAAAGAAAAAAAGAAGG
598470 GAAA-AAAGAAAAAGGAAAGAAAAAAAGAA
1 GAAAGAAAGAAAAAGGAAAGAAAAAAAGAA
598499 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 19 0.70
32 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.25, T:0.00
Consensus pattern (32 bp):
GAAAGAAAGAAAAAGGAAAGAAAAAAAGAAGG
Found at i:598504 original size:23 final size:22
Alignment explanation
Indices: 598439--598504 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 22
598429 GGGAAGAAAG
*
598439 AAAGAAAG-ACAAAAGAAAGAAA
1 AAAGAAAGAAAAAAAGAAA-AAA
* *
598461 GAAAGAAGGGAAAAAAG---AAA
1 -AAAGAAAGAAAAAAAGAAAAAA
*
598481 AAGGAAAGAAAAAAAGAAAAAA
1 AAAGAAAGAAAAAAAGAAAAAA
598503 AA
1 AA
598505 TAAATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
19 13 0.38
20 3 0.09
22 5 0.15
23 7 0.21
24 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAAAAAGAAAAAA
Found at i:599023 original size:18 final size:20
Alignment explanation
Indices: 599002--599040 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
598992 TATTATTGCA
599002 TATTTT-TAATTAT-TTTTT
1 TATTTTGTAATTATGTTTTT
*
599020 TATTTTGTATTTATGTTTTT
1 TATTTTGTAATTATGTTTTT
599040 T
1 T
599041 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TATTTTGTAATTATGTTTTT
Found at i:599393 original size:17 final size:18
Alignment explanation
Indices: 599373--599419 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
599363 AAACTAATCG
599373 TGTTTCAAAAATTT-TCC
1 TGTTTCAAAAATTTCTCC
*
599390 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCC
*
599408 TGTTTAAAAAAT
1 TGTTTCAAAAAT
599420 AATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCC
Found at i:599418 original size:18 final size:17
Alignment explanation
Indices: 599370--599419 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
599360 AAAAAACTAA
*
599370 TCGTGTTTCAAAAATTT
1 TCGTGTTTAAAAAATTT
* **
599387 TCCTGTTTTCAAAATTT
1 TCGTGTTTAAAAAATTT
599404 CTCGTGTTTAAAAAAT
1 -TCGTGTTTAAAAAAT
599420 AATAATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (17 bp):
TCGTGTTTAAAAAATTT
Found at i:599510 original size:21 final size:20
Alignment explanation
Indices: 599483--599564 Score: 89
Period size: 21 Copynumber: 4.1 Consensus size: 20
599473 GTAATTTATC
599483 AAAATTTTTGTGTTTTCAAA
1 AAAATTTTTGTGTTTTCAAA
*
599503 ATAAATTTTTGTATTTT---A
1 A-AAATTTTTGTGTTTTCAAA
* *
599521 AAAATGTTCGTGTTTTCAAA
1 AAAATTTTTGTGTTTTCAAA
599541 AAGAATTTCTTGTGTTTTCAAA
1 AA-AATTT-TTGTGTTTTCAAA
599563 AA
1 AA
599565 TTCCCATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.24
18 2 0.04
20 4 0.08
21 18 0.36
22 14 0.28
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (20 bp):
AAAATTTTTGTGTTTTCAAA
Found at i:599534 original size:38 final size:40
Alignment explanation
Indices: 599483--599565 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
599473 GTAATTTATC
* *
599483 AAAATTTTTGTGTTTTCAAAATA-AATTT-TTGTATTTT-A
1 AAAATGTTCGTGTTTTCAAAA-AGAATTTCTTGTATTTTCA
*
599521 AAAATGTTCGTGTTTTCAAAAAGAATTTCTTGTGTTTTCA
1 AAAATGTTCGTGTTTTCAAAAAGAATTTCTTGTATTTTCA
599561 AAAAT
1 AAAAT
599566 TCCCATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 1 0.03
38 24 0.62
39 8 0.21
40 6 0.15
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (40 bp):
AAAATGTTCGTGTTTTCAAAAAGAATTTCTTGTATTTTCA
Found at i:599594 original size:18 final size:18
Alignment explanation
Indices: 599483--599922 Score: 284
Period size: 17 Copynumber: 24.2 Consensus size: 18
599473 GTAATTTATC
*
599483 AAAATTTTTGTGTTTTCAAA
1 AAAATTTTCGTGTTTTC--A
* *
599503 ATAAATTTTTGTATTTT-A
1 A-AAATTTTCGTGTTTTCA
*
599521 AAAATGTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTC--A
*
599541 AAGAATTTCTTGTGTTTTCA
1 AA-AATTT-TCGTGTTTTCA
** * *
599561 AAAATTCCCAT-ATTTCA
1 AAAATTTTCGTGTTTTCA
*
599578 AAAATTTTCTTGTTTTCAGAAAAA
1 AAAATTTTCGTGTTTTC------A
*
599602 AAAATTTCCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
* * *
599619 TAAATTTCCGCGTTTTCA
1 AAAATTTTCGTGTTTTCA
599637 AAAA-TTTCG-GTATTTCA
1 AAAATTTTCGTGT-TTTCA
599654 AAAATTTTCGTGTTTTC-
1 AAAATTTTCGTGTTTTCA
** *
599671 AAAA-TTTC-TGGTGGTAA
1 AAAATTTTCGT-GTTTTCA
*
599688 AAAAATTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTC--A
599708 GAAAATTTT-GTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
**
599725 AAAATCCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
599743 AAAA-TTCCGGTGTTTT-A
1 AAAATTTTC-GTGTTTTCA
599760 AAAATTTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
599778 AAAAATTT-GTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
599794 AAAATTTTCATGTTTTCAA
1 AAAATTTTCGTGTTTTC-A
**
599813 AAAATTCCCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
599830 AAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
599848 AAAATTTTCGTGTTTTTA
1 AAAATTTTCGTGTTTTCA
* * *
599866 AGAATTTTCGTG-TCTCT
1 AAAATTTTCGTGTTTTCA
*
599883 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
599900 AAAATTTTTCGTGTTTTGA
1 AAAA-TTTTCGTGTTTTCA
599919 AAAA
1 AAAA
599923 AAATAATTAT
Statistics
Matches: 332, Mismatches: 52, Indels: 73
0.73 0.11 0.16
Matches are distributed among these distances:
15 1 0.00
16 27 0.08
17 115 0.35
18 99 0.30
19 30 0.09
20 11 0.03
21 25 0.08
22 9 0.03
24 15 0.05
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:599640 original size:35 final size:35
Alignment explanation
Indices: 599601--599922 Score: 257
Period size: 35 Copynumber: 9.1 Consensus size: 35
599591 TTTCAGAAAA
* *
599601 AAAAATTTCCGTGTTTTATAAATTTCCGCGTTTTC
1 AAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTC
* * * *
599636 AAAAATTTCGGTATTTCAAAAATTTTCGTGTTTTC
1 AAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTC
* * **
599671 -AAAATTTCTGGTGGTAAAAAAATTT-CGTGTTTTC
1 AAAAATTTC-CGTGTTTTAAAAATTTCCGTGTTTTC
* * *
599705 AAAGAAAATTT-TGTGTTTCAAAAA-TCCTCGTGTTTTC
1 --A-AAAATTTCCGTGTTTTAAAAATTTC-CGTGTTTTC
*
599742 AAAAA-TTCCGGTGTTTTAAAAATTTTCGTGTTTTC
1 AAAAATTTCC-GTGTTTTAAAAATTTCCGTGTTTTC
* * *
599777 AAAAAATTT--GTGTTTCAAAAATTTTCATGTTTTC
1 -AAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTC
*
599811 AAAAAATTCCCGTGTTTTAAAAATTTCCGTGTTTTC
1 -AAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTC
* * * *
599847 AAAAATTTTCGTGTTTTTAAGAATTTTCGTG-TCTC
1 AAAAATTTCCGTG-TTTTAAAAATTTCCGTGTTTTC
* * *
599882 TAAAA-TTCTCGTGTTTTAAAAATTTTTCGTGTTTTG
1 AAAAATTTC-CGTGTTTTAAAAA-TTTCCGTGTTTTC
599918 AAAAA
1 AAAAA
599923 AAATAATTAT
Statistics
Matches: 233, Mismatches: 36, Indels: 35
0.77 0.12 0.12
Matches are distributed among these distances:
33 2 0.01
34 62 0.27
35 93 0.40
36 58 0.25
37 11 0.05
38 7 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (35 bp):
AAAAATTTCCGTGTTTTAAAAATTTCCGTGTTTTC
Found at i:599691 original size:34 final size:35
Alignment explanation
Indices: 599573--599963 Score: 267
Period size: 34 Copynumber: 10.9 Consensus size: 35
599563 AATTCCCATA
* *
599573 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTGTTTTC-----AAAAAA-TTCTGTG
* * * * * * *
599614 TTTTATAAATTTCCGCGTTTTCAAAAATTTCGGTA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATTCTGTG
*
599649 TTTCAAAAATTTTCGTGTTTTC-AAAATTTCTG-G
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATTCTGTG
* * * *
599682 TGGTAAAAAAATTTCGTGTTTTCAAAGAAAATTTTGTG
1 T-TTCAAAAATTTTCGTGTTTTC-AA-AAAATTCTGTG
** *
599720 TTTCAAAAATCCTCGTGTTTTC-AAAAATTCCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATT-CTGTG
*
599755 TTTTAAAAATTTTCGTGTTTTCAAAAAATT-TGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATTCTGTG
* *
599789 TTTCAAAAATTTTCATGTTTTCAAAAAATTCCCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATT-CTGTG
* * *
599825 TTTTAAAAATTTCCGTGTTTTC-AAAAATTTTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATTCT-GTG
* * * *
599860 TTTTTAAGAATTTTCGTG-TCTC-TAAAATTCTCGTG
1 -TTTCAAAAATTTTCGTGTTTTCAAAAAATTCT-GTG
* * ** *
599895 TTTTAAAAATTTTTCGTGTTTTGAAAAAAAATAAT-TA
1 TTTCAAAAA-TTTTCGTGTTTT--CAAAAAATTCTGTG
* *
599932 TTTCAAAAATCTTCGTGTTTTAAAAAAATTCT
1 TTTCAAAAATTTTCGTGTTTTCAAAAAATTCT
599964 CGTATTTTAA
Statistics
Matches: 280, Mismatches: 54, Indels: 39
0.75 0.14 0.10
Matches are distributed among these distances:
33 1 0.00
34 81 0.29
35 78 0.28
36 63 0.22
37 32 0.11
38 2 0.01
39 6 0.02
41 17 0.06
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAATTCTGTG
Found at i:599725 original size:19 final size:20
Alignment explanation
Indices: 599689--599863 Score: 74
Period size: 18 Copynumber: 9.8 Consensus size: 20
599679 TGGTGGTAAA
599689 AAAATTTCGTGTTTTCAAAG
1 AAAATTTCGTGTTTTCAAAG
*
599709 AAAATTTTGTG-TTTC--A-
1 AAAATTTCGTGTTTTCAAAG
*
599725 AAAATCCTCGTGTTTTC--A-
1 AAAAT-TTCGTGTTTTCAAAG
*
599743 AAAATTCCGGTGTTTT--AA-
1 AAAATTTC-GTGTTTTCAAAG
*
599761 AAATTTTCGTGTTTTC-AA-
1 AAAATTTCGTGTTTTCAAAG
599779 AAAATTT-GTG-TTTC-AA-
1 AAAATTTCGTGTTTTCAAAG
* *
599795 AAATTTTCATGTTTTC-AA-
1 AAAATTTCGTGTTTTCAAAG
*
599813 AAAATTCCCGTGTTTT---A-
1 AAAATT-TCGTGTTTTCAAAG
599830 AAAATTTCCGTGTTTTC-AA-
1 AAAATTT-CGTGTTTTCAAAG
*
599849 AAATTTTCGTGTTTT
1 AAAATTTCGTGTTTT
599864 TAAGAATTTT
Statistics
Matches: 129, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
16 17 0.13
17 33 0.26
18 51 0.40
19 18 0.14
20 10 0.08
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (20 bp):
AAAATTTCGTGTTTTCAAAG
Found at i:599763 original size:106 final size:105
Alignment explanation
Indices: 599630--599958 Score: 321
Period size: 106 Copynumber: 3.1 Consensus size: 105
599620 AAATTTCCGC
* * * * *
599630 GTTTTCAAAAATTTCGGTATTTCAAAAATTTTCGTGTTTTCAAAATTTCTGGTGGTAAAAAAATT
1 GTTTTCAAAAATTTCGGTGTTTTAAAAATTTTCGTGTTTTCAAAAATTCTGGTGTTAAAAAATTT
* *
599695 TCGTGTTTTCAAAGAAAATTTTGTGTTTCAAAAATCCTCGT
66 TCGTGTTTTCAAA-AAAATTATGTGTTTCAAAAATCTTCGT
* *
599736 GTTTTCAAAAATTCCGGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATT-T-GTGTTTCAAAAAT
1 GTTTTCAAAAATTTCGGTGTTTTAAAAATTTTCGTGTTTTC-AAAAATTCTGGTG-TTAAAAAAT
* ** *
599799 TTTCATGTTTTC-AAAAAATTCCCGTGTTTTAAAAAT-TTCCGT
64 TTTCGTGTTTTCAAAAAAATT-ATGTGTTTCAAAAATCTT-CGT
* * * *
599841 GTTTTCAAAAATTTTC-GTGTTTTTAAGAATTTTCGTG-TCTCTAAAATTCTCGTGTTTTAAAAA
1 GTTTTCAAAAA-TTTCGGTG-TTTTAAAAATTTTCGTGTTTTCAAAAATTCT-G-GTGTTAAAAA
* * * *
599904 TTTTTCGTGTTTTGAAAAAAAATAAT-TATTTCAAAAATCTTCGT
62 ATTTTCGTGTTTT-CAAAAAAATTATGTGTTTCAAAAATCTTCGT
*
599948 GTTTTAAAAAA
1 GTTTTCAAAAA
599959 ATTCTCGTAT
Statistics
Matches: 183, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
104 13 0.07
105 38 0.21
106 75 0.41
107 46 0.25
108 4 0.02
109 7 0.04
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (105 bp):
GTTTTCAAAAATTTCGGTGTTTTAAAAATTTTCGTGTTTTCAAAAATTCTGGTGTTAAAAAATTT
TCGTGTTTTCAAAAAAATTATGTGTTTCAAAAATCTTCGT
Found at i:599909 original size:53 final size:53
Alignment explanation
Indices: 599516--599923 Score: 279
Period size: 53 Copynumber: 7.5 Consensus size: 53
599506 AATTTTTGTA
* * * *
599516 TTTT-AAAAATGTTCGTGTTTTCAAAAAGAATTTCTTGTGTTTTCAAAAATTCCCAT-
1 TTTTCAAAAATTTTCGTGTTTTC-AAAA-AATTT-TCGTG-TTTCAAAAATT-TCGTG
* * * * * *
599572 ATTTCAAAAATTTTCTTGTTTTCAGAAAAAAAAATTTCCGTGTTTTATAAATTTCCGCG
1 TTTTCAAAAATTTTCGTGTTTTC-----AAAAAATTTTCGTGTTTCAAAAATTT-CGTG
599631 TTTTCAAAAA-TTTCG-GTATTTC-AAAAATTTTCGTGTTTTC-AAAATTTC-TGG
1 TTTTCAAAAATTTTCGTGT-TTTCAAAAAATTTTCGTG-TTTCAAAAATTTCGT-G
** * * *
599682 TGGTAAAAAAATTTCGTGTTTTCAAAGAAAATTTT-GTGTTTCAAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTGTTTTC-AA-AAAATTTTCGTGTTTCAAAAAT-TTCGTG
*
599737 TTTTCAAAAA-TTCCGGTGTTTT--AAAAATTTTCGTGTTTTCAAAAAATTT-GTG
1 TTTTCAAAAATTTTC-GTGTTTTCAAAAAATTTTCGTG-TTTC-AAAAATTTCGTG
* ** *
599789 -TTTCAAAAATTTTCATGTTTTCAAAAAATTCCCGTGTTTTAAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTT-CGTG
* * * *
599842 TTTTCAAAAATTTTCGTGTTTT-TAAGAATTTTCGTGTCTCTAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATT-TCGTG
*
599895 TTTT-AAAAATTTTTCGTGTTTTGAAAAAA
1 TTTTCAAAAA-TTTTCGTGTTTTCAAAAAA
599924 AATAATTATT
Statistics
Matches: 281, Mismatches: 40, Indels: 64
0.73 0.10 0.17
Matches are distributed among these distances:
51 40 0.14
52 45 0.16
53 66 0.23
54 43 0.15
55 25 0.09
56 4 0.01
57 18 0.06
58 18 0.06
59 12 0.04
60 5 0.02
61 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTTCGTG
Found at i:603641 original size:9 final size:9
Alignment explanation
Indices: 603629--603653 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
603619 TGAACTCAAT
603629 GAAAGGATG
1 GAAAGGATG
603638 GAAAGGATG
1 GAAAGGATG
603647 GAAAGGA
1 GAAAGGA
603654 CCCAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (9 bp):
GAAAGGATG
Found at i:612001 original size:74 final size:74
Alignment explanation
Indices: 611672--612447 Score: 1047
Period size: 74 Copynumber: 10.4 Consensus size: 74
611662 TCAAGAATTA
* * * * *
611672 TATTTTCAATTTTTGTTTTTAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTT
*
611737 ATC-CTGAGA
66 A-CGCTGAGG
* *
611746 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGGCTCGGGT
1 TATTTTTAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGT
*
611811 CATC-CTGAGG
65 TA-CGCTGAGG
* * * *
611821 TATTTTTCAATTTCTGTTTTTCAAAAAAAATTAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
1 TATTTTT-AATTTCTGTTTTTC--AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGG
611886 GTTACGCTGAGG
63 GTTACGCTGAGG
* * *
611898 TATTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGT
*
611963 TACACTGAGG
65 TACGCTGAGG
*
611973 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGTT
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTT
612038 ACGCTGAGG
66 ACGCTGAGG
** * * * *
612047 TATTTTTAATTTCCATTTTTCAAACAATCAACTCATAATGCGAGAGGTGAGTTGAGCCACGAGTT
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTT
612112 ACGCTGAGG
66 ACGCTGAGG
*
612121 TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTG-TTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGG
612186 TTACGCTGAGG
64 TTACGCTGAGG
* *
612197 TATTTTTAATTTCTATTTTTTAAAAAATCAACTCATAATGCGA-AAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAA-GTGAGTTGAGCCTCGGGT
612261 TACGCTGAGG
65 TACGCTGAGG
*
612271 TATTTTTAATTT-TCGTTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGG
1 TATTTTTAATTTCT-G-TTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGG
* *
612335 GTTACCCTGTGG
63 GTTACGCTGAGG
* * *** * * *
612347 TGTTTTTAATTTCTATTTTTTTTAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTC
1 TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTT
612412 ACGCTGAGG
66 ACGCTGAGG
* *
612421 TATTTTCAATTTTTGTTTTTCAAAAAA
1 TATTTTTAATTTCTGTTTTTCAAAAAA
612448 AAAGAAAGAA
Statistics
Matches: 629, Mismatches: 61, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
73 3 0.00
74 276 0.44
75 146 0.23
76 148 0.24
77 56 0.09
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (74 bp):
TATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTT
ACGCTGAGG
Found at i:612215 original size:150 final size:149
Alignment explanation
Indices: 611672--612795 Score: 1165
Period size: 150 Copynumber: 7.4 Consensus size: 149
611662 TCAAGAATTA
* * * *
611672 TATTTTCAATTTTTGTTTTT-AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGT
* * *
611736 CATC-CTGAGATATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTT
66 TA-CGCTGAGGTATTTTTAATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTT
* *
611800 GAGGCTCGGGTCATC-CTGAGG
129 GAGCCTCGGGTTA-CGCTGAGG
* * ** *
611821 TATTTTTCAATTTCTGTTTTTCAAAAAAAATTAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
1 TATTTTT-AATTTCTGTTTTTC-AAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGG
* ** * *
611886 GTTACGCTGAGGTATTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGT
64 GTTACGCTGAGGTATTTTTAATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGT
*
611951 TGAGCCTCGGGTTACACTGAGG
128 TGAGCCTCGGGTTACGCTGAGG
611973 TATTTTTAATTTCTGTTTTTC-AAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGT
* *
612037 TACGCTGAGGTATTTTTAATTTCCATTTTTCAAACAATCAACTCATAATGCGAGAGGTGAGTTGA
66 TACGCTGAGGTATTTTTAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
* *
612102 GCCACGAGTTACGCTGAGG
131 GCCTCGGGTTACGCTGAGG
612121 TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTG-TTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGG
* *
612186 TTACGCTGAGGTATTTTTAATTTCTATTTTTTAAAAAATCAACTCATAATGCGAAAGGTGAGTTG
65 TTACGCTGAGGTATTTTTAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTG
612251 AGCCTCGGGTTACGCTGAGG
130 AGCCTCGGGTTACGCTGAGG
612271 TATTTTTAATTT-TCGTTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGG
1 TATTTTTAATTTCT-G-TTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGG
* * * *** *
612335 GTTACCCTGTGGTGTTTTTAATTTCTATTTTTTTTAAAATCAACTCATAATGCGAGAGGTGGGTT
64 GTTACGCTGAGGTATTTTTAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTT
*
612400 GAGCCTCGGGTCACGCTGAGG
129 GAGCCTCGGGTTACGCTGAGG
* * *** * * ** * * * * *
612421 TATTTTCAATTTTTGTTTTTCAAAAAAA--AAGAAAGAAAAAAAGAAATCAACTCATAATGCGAG
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATACGAGAAGT-GAGT--TGA-GC--C
** * * * * * *
612484 AGGTAGGTTGA-GCCTCGGGTCACGCTGAGGTGTTTTCAATT-TCTGTTTTTAAAAAAAAAATAA
60 TCG--GGTT-ACG-CT---G--A-GGT-A--T-TTTTAATTTCTAT-TTTTCAAAA----AATCA
*
612547 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
106 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGG
* * * * * *
612591 TATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTTATAATGCGAGAGGTGGGTTGAGCCTCGAG
1 TATTTTTAATTTCTGTTTTTC-AAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGG
* * * *
612656 TTACGCTAAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTT
65 TTACGCTGAGGTATTTTTAATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTT
* *
612721 GAGCCTCGAGTCACGCTGAGG
129 GAGCCTCGGGTTACGCTGAGG
* * * **
612742 TATTTTCAATATCTATTTTTC--AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATAC-GAGAAGTGAGTTGA
612796 ACTTCGGATC
Statistics
Matches: 831, Mismatches: 103, Indels: 83
0.82 0.10 0.08
Matches are distributed among these distances:
147 12 0.01
148 90 0.11
149 91 0.11
150 287 0.35
151 85 0.10
152 121 0.15
153 1 0.00
154 10 0.01
155 11 0.01
156 3 0.00
157 1 0.00
158 2 0.00
159 2 0.00
162 2 0.00
164 3 0.00
165 7 0.01
166 14 0.02
167 1 0.00
169 2 0.00
170 69 0.08
171 7 0.01
172 1 0.00
173 9 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (149 bp):
TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGT
TACGCTGAGGTATTTTTAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
GCCTCGGGTTACGCTGAGG
Found at i:612531 original size:93 final size:93
Alignment explanation
Indices: 612371--612543 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
612361 ATTTTTTTTA
* *
612371 AAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTTTG
1 AAATCAACTCATAATGCGAGAGGTAGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
*
612436 TTTTTCAAAAAAAAAGAAAGAAAAAAAG
66 TTTTTAAAAAAAAAAGAAAGAAAAAAAG
*
612464 AAATCAACTCATAATGCGAGAGGTAGGTTGAGCCTCGGGTCACGCTGAGGTGTTTTCAATTTCTG
1 AAATCAACTCATAATGCGAGAGGTAGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
612529 TTTTTAAAAAAAAAA
66 TTTTTAAAAAAAAAA
612544 TAAACTCATA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (93 bp):
AAATCAACTCATAATGCGAGAGGTAGGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
TTTTTAAAAAAAAAAGAAAGAAAAAAAG
Found at i:612662 original size:76 final size:76
Alignment explanation
Indices: 612458--612765 Score: 467
Period size: 76 Copynumber: 4.0 Consensus size: 76
612448 AAAGAAAGAA
* *
612458 AAAAAGAAATCAACTCATAATGCGAGAGGT-AGGTTGAGCCTCGGGTCACGCTGAGGTGTTTTCA
1 AAAAA-AAATCAACTCATAATGCGAGAGGTGA-GTTGAGCCTCGAGTCACGCTGAGGTATTTTCA
*
612522 ATTTCTGTTTTTAA
64 ATTTCTGTTTTT-C
* *
612536 AAAAAAAATAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAAT
1 AAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
612601 TTCTGTTTTTC
66 TTCTGTTTTTC
* * * *
612612 AAAAAAAATCAACTTATAATGCGAGAGGTGGGTTGAGCCTCGAGTTACGCTAAGGTATTTTCAAT
1 AAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
*
612677 TTATGTTTTTC
66 TTCTGTTTTTC
612688 -AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
1 AAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
* *
612752 ATCTATTTTTC
66 TTCTGTTTTTC
612763 AAA
1 AAA
612766 GGTCAACTCA
Statistics
Matches: 211, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
75 68 0.32
76 71 0.34
77 66 0.31
78 6 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (76 bp):
AAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
TTCTGTTTTTC
Found at i:612729 original size:75 final size:75
Alignment explanation
Indices: 612459--612795 Score: 457
Period size: 75 Copynumber: 4.5 Consensus size: 75
612449 AAGAAAGAAA
* *
612459 AAAAGAAATCAACTCATAATGCGAGAGGT-AGGTTGAGCCTCGGGTCACGCTGAGGTGTTTTCAA
1 AAAA-AAATCAACTCATAATGCGAGAGGTGA-GTTGAGCCTCGAGTCACGCTGAGGTATTTTCAA
*
612523 TTTCTGTTTTTAAA
64 TTTCTGTTTTT--C
* *
612537 AAAAAAATAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATT
612602 TCTGTTTTTC
66 TCTGTTTTTC
* * * *
612612 AAAAAAAATCAACTTATAATGCGAGAGGTGGGTTGAGCCTCGAGTTACGCTAAGGTATTTTCAAT
1 -AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAAT
*
612677 TTATGTTTTTC
65 TTCTGTTTTTC
*
612688 AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATA
1 AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATT
*
612753 TCTATTTTTC
66 TCTGTTTTTC
** *
612763 --AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 AAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
612796 ACTTCGGATC
Statistics
Matches: 236, Mismatches: 20, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
72 1 0.00
73 28 0.12
75 68 0.29
76 68 0.29
77 66 0.28
78 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (75 bp):
AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATT
TCTGTTTTTC
Found at i:613204 original size:29 final size:29
Alignment explanation
Indices: 613119--613205 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 29
613109 ACTAAAAAAT
*
613119 AAATTACATTTTAACCCTCGAATTTTCTAG
1 AAATTACATTTTAACCC-CGAATTTTTTAG
** *
613149 AAATTACATTTTGGCCTC-ATATTTTTTTA-
1 AAATTACATTTTAACCCCGA-A-TTTTTTAG
* *
613178 AAATTACATTTTTACCCCGAATGTTTTA
1 AAATTACATTTTAACCCCGAATTTTTTA
613206 CGTCTTCTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
28 7 0.15
29 18 0.39
30 21 0.46
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (29 bp):
AAATTACATTTTAACCCCGAATTTTTTAG
Found at i:613548 original size:32 final size:33
Alignment explanation
Indices: 613486--613549 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
613476 AAAAAAAAAC
*
613486 AAAAACAAAGAGAAAAAGCAACAAGCAAAAGAG
1 AAAAACAAAGAGAAAAAGCAACAAGAAAAAGAG
* *
613519 AAAAA-AAAG-GAAAGAGCAAAGAAGAAAAAGA
1 AAAAACAAAGAGAAAAAGC-AACAAGAAAAAGA
613550 AAAGGGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.26
32 15 0.56
33 5 0.19
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (33 bp):
AAAAACAAAGAGAAAAAGCAACAAGAAAAAGAG
Found at i:613668 original size:4 final size:4
Alignment explanation
Indices: 613659--613694 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
613649 CTGAACGGGG
613659 AAGA AAGA AAGA AAGA AAG- AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
613695 GGGAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:613682 original size:19 final size:19
Alignment explanation
Indices: 613658--613724 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
613648 GCTGAACGGG
613658 GAAGAAAGAAAGAAAGAAA
1 GAAGAAAGAAAGAAAGAAA
*
613677 GAAGAAAGAAAGAAAGAAGG
1 GAAGAAAGAAAGAAAGAA-A
* * *
613697 GAAAAAATAAA-AAGGAAA
1 GAAGAAAGAAAGAAAGAAA
613715 GAA-AAAGAAA
1 GAAGAAAGAAA
613725 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.15
18 3 0.07
19 23 0.56
20 9 0.22
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (19 bp):
GAAGAAAGAAAGAAAGAAA
Found at i:613683 original size:15 final size:15
Alignment explanation
Indices: 613663--613695 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
613653 ACGGGGAAGA
613663 AAGAAAGAAAGAAAG
1 AAGAAAGAAAGAAAG
613678 AAGAAAGAAAGAAAG
1 AAGAAAGAAAGAAAG
613693 AAG
1 AAG
613696 GGAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:614237 original size:18 final size:20
Alignment explanation
Indices: 614216--614254 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
614206 TATTATTGCA
614216 TATTTT-TAATTAT-TTTTT
1 TATTTTGTAATTATGTTTTT
*
614234 TATTTTGTATTTATGTTTTT
1 TATTTTGTAATTATGTTTTT
614254 T
1 T
614255 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TATTTTGTAATTATGTTTTT
Found at i:614617 original size:17 final size:19
Alignment explanation
Indices: 614591--614629 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
614581 ACTAATCGTG
614591 TTTCAAAAATTT-TCCTGT
1 TTTCAAAAATTTCTCCTGT
*
614609 TTTC-AAAATTTCTCGTGT
1 TTTCAAAAATTTCTCCTGT
614627 TTT
1 TTT
614630 ATATTCGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTCAAAAATTTCTCCTGT
Found at i:614697 original size:21 final size:20
Alignment explanation
Indices: 614671--614751 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 20
614661 TAATTTATCG
614671 AAATTTTTGTGTTTTCAAAA
1 AAATTTTTGTGTTTTCAAAA
*
614691 TAAATTTTTGTATTTT---AA
1 -AAATTTTTGTGTTTTCAAAA
*
614709 AAATTTTCGTGTTTTCAAAA
1 AAATTTTTGTGTTTTCAAAA
614729 AAATTTTCCTGTGTTTTCAAAA
1 AAATTTT--TGTGTTTTCAAAA
614751 A
1 A
614752 TTTTCTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
17 13 0.25
18 2 0.04
20 9 0.18
21 14 0.27
22 13 0.25
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
AAATTTTTGTGTTTTCAAAA
Found at i:614714 original size:17 final size:18
Alignment explanation
Indices: 614692--615057 Score: 148
Period size: 17 Copynumber: 20.2 Consensus size: 18
614682 TTTTCAAAAT
*
614692 AAATTTTTGTATTTT-AA
1 AAATTTTCGTATTTTCAA
*
614709 AAATTTTCGTGTTTTCAAAA
1 AAATTTTCGTATTTTC--AA
*
614729 AAATTTTCCTGTGTTTTCAA
1 AAATTTT-C-GTATTTTCAA
*
614749 AAATTTTCTTATTTTCAGA
1 AAATTTTCGTATTTTCA-A
* *
614768 AAATAAAATTTCCGTGTTTT-AT
1 AAAT----TTT-CGTATTTTCAA
* * *
614790 AAATTTCCGTGTTTTTAA
1 AAATTTTCGTATTTTCAA
*
614808 AAATTTTGGTA-TTTCAA
1 AAATTTTCGTATTTTCAA
*
614825 AAATTTTCGTGTTTTC-A
1 AAATTTTCGTATTTTCAA
* *
614842 AAATTTCTGGTGA---TAAA
1 AAATTT-TCGT-ATTTTCAA
** *
614859 AAAAATTCGTGTTTTCAAA
1 AAATTTTCGTATTTTC-AA
* *
614878 GAAAATTTCGT-GTTTC-A
1 -AAATTTTCGTATTTTCAA
** *
614895 AAATCCTCGTGTTTTCAA
1 AAATTTTCGTATTTTCAA
*
614913 AAA-TTTCGGTGTTTT-AA
1 AAATTTTC-GTATTTTCAA
*
614930 AAATTTTCGTGTTTTCAAA
1 AAATTTTCGTATTTTC-AA
** *
614949 AAATTCCCGTGTTTT-AA
1 AAATTTTCGTATTTTCAA
* *
614966 AAATTTCCGTGTTTTCAA
1 AAATTTTCGTATTTTCAA
* *
614984 AAATTTTCGTGTTTTTAA
1 AAATTTTCGTATTTTCAA
* * * *
615002 GAATTTTCGT-GTCTCTA
1 AAATTTTCGTATTTTCAA
* *
615019 AAATTCTCGTGTTTT-AA
1 AAATTTTCGTATTTTCAA
*
615036 AAATTTTTCGTGTTTTCAA
1 AAA-TTTTCGTATTTTCAA
615055 AAA
1 AAA
615058 AATAATTGTT
Statistics
Matches: 271, Mismatches: 47, Indels: 60
0.72 0.12 0.16
Matches are distributed among these distances:
16 11 0.04
17 97 0.36
18 81 0.30
19 32 0.12
20 27 0.10
21 1 0.00
22 12 0.04
23 4 0.01
24 6 0.02
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
AAATTTTCGTATTTTCAA
Found at i:614805 original size:18 final size:17
Alignment explanation
Indices: 614772--615057 Score: 188
Period size: 17 Copynumber: 16.2 Consensus size: 17
614762 TTCAGAAAAT
614772 AAAATTTCCGTGTTTTA
1 AAAATTTCCGTGTTTTA
*
614789 TAAATTTCCGTGTTTTTA
1 AAAATTTCCGTG-TTTTA
** * *
614807 AAAATTTTGGTATTTCA
1 AAAATTTCCGTGTTTTA
* *
614824 AAAATTTTCGTGTTTTC
1 AAAATTTCCGTGTTTTA
* * **
614841 AAAATTTCTGGTGATAAA
1 AAAATTTC-CGTGTTTTA
*
614859 AAAAATT-CGTGTTTTCAAA
1 AAAATTTCCGTGTTTT---A
*
614878 GAAAATTT-CGTG-TTTC
1 -AAAATTTCCGTGTTTTA
*
614894 AAAA-TCCTCGTGTTTTCA
1 AAAATTTC-CGTGTTTT-A
*
614912 AAAATTTCGGTGTTTTA
1 AAAATTTCCGTGTTTTA
*
614929 AAAATTTTCGTGTTTTCAA
1 AAAATTTCCGTGTTTT--A
*
614948 AAAATTCCCGTGTTTTA
1 AAAATTTCCGTGTTTTA
614965 AAAATTTCCGTGTTTTCA
1 AAAATTTCCGTGTTTT-A
*
614983 AAAATTTTCGTGTTTTTA
1 AAAATTTCCGTG-TTTTA
* * *
615001 AGAATTTTCGTGTCTCT-
1 AAAATTTCCGTGT-TTTA
615018 AAAA-TTCTCGTGTTTTA
1 AAAATTTC-CGTGTTTTA
*
615035 AAAATTTTTCGTGTTTTCA
1 AAAA-TTTCCGTGTTTT-A
615054 AAAA
1 AAAA
615058 AATAATTGTT
Statistics
Matches: 209, Mismatches: 39, Indels: 40
0.73 0.14 0.14
Matches are distributed among these distances:
14 1 0.00
15 4 0.02
16 12 0.06
17 82 0.39
18 68 0.33
19 32 0.15
20 10 0.05
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (17 bp):
AAAATTTCCGTGTTTTA
Found at i:614911 original size:36 final size:34
Alignment explanation
Indices: 614679--615096 Score: 256
Period size: 36 Copynumber: 11.5 Consensus size: 34
614669 CGAAATTTTT
* *
614679 GTGTTTTCAAAATAAATTTTTGTATTTTAAAAATTTTC
1 GTGTTTTC-AAA-AAA-TTTCGTGTTTTAAAAA-TTTC
614717 GTGTTTTCAAAAAAATTTTCCTGTGTTTTCAAAAATTTTC
1 GTGTTTTC-AAAAAA-TTT-C-GTGTTTT-AAAAA-TTTC
* * *
614757 TTATTTTCAGAAAATAAAATTTCCGTGTTTTATAAATTTCC
1 GTGTTTTC----AA-AAAATTT-CGTGTTTTAAAAATTT-C
* * * * *
614798 GTGTTTTTAAAAATTTTGGTATTTCAAAAATTTTC
1 GTGTTTTCAAAAAATTTCGTGTTTTAAAAA-TTTC
* ** *
614833 GTGTTTTC--AAAATTTCTGGTGATAAAAAAAATTC
1 GTGTTTTCAAAAAATTTC--GTGTTTTAAAAATTTC
* *
614867 GTGTTTTCAAAGAAAATTTCGTG-TTTCAAAATCCTC
1 GTGTTTTC-AA-AAAATTTCGTGTTTTAAAAAT-TTC
614903 GTGTTTTC-AAAAATTTCGGTGTTTTAAAAATTTTC
1 GTGTTTTCAAAAAATTTC-GTGTTTTAAAAA-TTTC
*
614938 GTGTTTTCAAAAAATTCCCGTGTTTTAAAAATTTCC
1 GTGTTTTCAAAAAATT-TCGTGTTTTAAAAATTT-C
* *
614974 GTGTTTTCAAAAATTTTCGTGTTTTTAAGAATTTTC
1 GTGTTTTCAAAAAATTTCGTG-TTTTAA-AAATTTC
* *
615010 GTG-TCTC-TAAAATTCTCGTGTTTTAAAAATTTTTC
1 GTGTTTTCAAAAAATT-TCGTGTTTTAAAAA--TTTC
* *** *
615045 GTGTTTTCAAAAAAATAATTGTTTCAAAAATCTTC
1 GTGTTTTCAAAAAATTTCGTGTTTTAAAAAT-TTC
615080 GTGTTTT-AAAAAATTTC
1 GTGTTTTCAAAAAATTTC
615097 TTGTATTTTA
Statistics
Matches: 304, Mismatches: 46, Indels: 64
0.73 0.11 0.15
Matches are distributed among these distances:
33 16 0.05
34 34 0.11
35 79 0.26
36 81 0.27
37 20 0.07
38 20 0.07
39 6 0.02
40 19 0.06
41 10 0.03
42 7 0.02
43 8 0.03
44 4 0.01
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (34 bp):
GTGTTTTCAAAAAATTTCGTGTTTTAAAAATTTC
Found at i:614917 original size:71 final size:70
Alignment explanation
Indices: 614831--614989 Score: 182
Period size: 71 Copynumber: 2.3 Consensus size: 70
614821 TCAAAAATTT
*
614831 TCGTGTTTTC-AAAATTTCTGGTG-ATAAAAAAAATTCGTGTTTTCAAAGAAAATT-TCGTG-TT
1 TCGTGTTTTCAAAAATTTC-GGTGTATAAAAAAAATTCGTGTTTTC-AA-AAAATTCCCGTGTTT
*
614892 TCAAAATCC
63 TAAAAAT-C
* * **
614901 TCGTGTTTTCAAAAATTTCGGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTCCCGTGTTTTAA
1 TCGTGTTTTCAAAAATTTCGGTGTATAAAAAAAATTCGTGTTTTCAAAAAATTCCCGTGTTTTAA
*
614966 AAATT
66 AAATC
614971 TCCGTGTTTTCAAAAATTT
1 T-CGTGTTTTCAAAAATTT
614990 TCGTGTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
69 6 0.08
70 21 0.27
71 50 0.65
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (70 bp):
TCGTGTTTTCAAAAATTTCGGTGTATAAAAAAAATTCGTGTTTTCAAAAAATTCCCGTGTTTTAA
AAATC
Found at i:614995 original size:35 final size:35
Alignment explanation
Indices: 614671--615095 Score: 311
Period size: 35 Copynumber: 11.7 Consensus size: 35
614661 TAATTTATCG
* * *
614671 AAATTTTTGTGTTTTCAAAATAAATTTTTGTATTTTAA
1 AAATTTTCGTGTTTTC--AA-AAATTTTCGTGTTTTAA
614709 AAATTTTCGTGTTTTCAAAAAAATTTTCCTGTGTTTTCAA
1 AAATTTTCGTGTTTTC--AAAAATTTT-C-GTGTTTT-AA
* * *
614749 AAATTTTCTTATTTTCAGAAAATAAAATTTCCGTGTTTTAT
1 AAATTTTCGTGTTTTCA-AAAAT----TTT-CGTGTTTTAA
* * * * *
614790 AAATTTCCGTGTTTTTAAAAATTTTGGTATTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTAA
* * *
614825 AAATTTTCGTGTTTTC-AAAATTTCTGGTG-ATAAA
1 AAATTTTCGTGTTTTCAAAAATTT-TCGTGTTTTAA
** * *
614859 AAAAATTCGTGTTTTCAAAGAAAATTTCGTG-TTTCA
1 AAATTTTCGTGTTTTC-AA-AAATTTTCGTGTTTTAA
**
614895 AAATCCTCGTGTTTTCAAAAA-TTTCGGTGTTTTAA
1 AAATTTTCGTGTTTTCAAAAATTTTC-GTGTTTTAA
**
614930 AAATTTTCGTGTTTTCAAAAAATTCCCGTGTTTTAA
1 AAATTTTCGTGTTTTC-AAAAATTTTCGTGTTTTAA
*
614966 AAATTTCCGTGTTTTCAAAAATTTTCGTGTTTTTAA
1 AAATTTTCGTGTTTTCAAAAATTTTCGTG-TTTTAA
* * * *
615002 GAATTTTCGTG-TCTCTAAAATTCTCGTGTTTTAA
1 AAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTAA
** *** *
615036 AAATTTTTCGTGTTTTCAAAAAAATAATTGTTTCAA
1 AAA-TTTTCGTGTTTTCAAAAATTTTCGTGTTTTAA
* *
615072 AAATCTTCGTGTTTTAAAAAATTT
1 AAATTTTCGTGTTTTCAAAAATTT
615096 CTTGTATTTT
Statistics
Matches: 312, Mismatches: 56, Indels: 41
0.76 0.14 0.10
Matches are distributed among these distances:
33 4 0.01
34 38 0.12
35 94 0.30
36 84 0.27
37 14 0.04
38 20 0.06
39 11 0.04
40 21 0.07
41 14 0.04
42 7 0.02
43 5 0.02
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (35 bp):
AAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTAA
Found at i:615075 original size:53 final size:51
Alignment explanation
Indices: 614772--615096 Score: 221
Period size: 53 Copynumber: 6.2 Consensus size: 51
614762 TTCAGAAAAT
* * * * * *
614772 AAAATTTCCGTGTTTT-ATAAATTTCCGTGTTTTTAAAAATTTTG-GTATTTCA
1 AAAATTTTCGTGTTTTCAAAAAATTACGTG-TTTCAAAAATTTCGTGT-TTT-A
* * ** *
614824 AAAATTTTCGTGTTTTC--AAAATTTCTGGTGATAAAAAAAATTCGTGTTTTCAA
1 AAAATTTTCGTGTTTTCAAAAAATTAC--GTGTTTCAAAAATTTCGTGTTTT--A
* ***
614877 AGAAAATTTCGTG-TTTCAAAATCCT-CGTGTTTTCAAAAATTTCGGTGTTTTA
1 A-AAATTTTCGTGTTTTCAAAAAATTACGTG-TTTCAAAAATTTC-GTGTTTTA
* *
614929 AAAATTTTCGTGTTTTCAAAAAATTCCCGTGTTTTAAAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCAAAAAATT-ACGTGTTTCAAAAATTT-CGTGTTTT-A
* * * * * *
614983 AAAATTTTCGTGTTTTTAAGAATTTTCGTGTCTCTAAAATTCTCGTGTTTTA
1 AAAATTTTCGTGTTTTCAAAAAATTACGTGTTTCAAAAATT-TCGTGTTTTA
* **
615035 AAAATTTTTCGTGTTTTCAAAAAAATAATTGTTTCAAAAATCTTCGTGTTTTA
1 AAAA-TTTTCGTGTTTTCAAAAAATTACGTGTTTCAAAAAT-TTCGTGTTTTA
*
615088 AAAAATTTC
1 AAAATTTTC
615097 TTGTATTTTA
Statistics
Matches: 216, Mismatches: 39, Indels: 36
0.74 0.13 0.12
Matches are distributed among these distances:
51 16 0.07
52 50 0.23
53 99 0.46
54 48 0.22
55 3 0.01
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (51 bp):
AAAATTTTCGTGTTTTCAAAAAATTACGTGTTTCAAAAATTTCGTGTTTTA
Found at i:615091 original size:18 final size:16
Alignment explanation
Indices: 614772--615096 Score: 188
Period size: 18 Copynumber: 18.5 Consensus size: 16
614762 TTCAGAAAAT
614772 AAAATTTCCGTGTTTTA
1 AAAATTT-CGTGTTTTA
*
614789 TAAATTTCCGTGTTTTTA
1 AAAATTT-CGTG-TTTTA
*
614807 AAAATTTTG-GTATTTCA
1 AAAATTTCGTGT-TTT-A
*
614824 AAAATTTTCGTGTTTTC
1 AAAA-TTTCGTGTTTTA
* **
614841 AAAATTTCTGGTGATAAA
1 AAAATTTC--GTGTTTTA
*
614859 AAAAATTCGTGTTTTCAAA
1 AAAATTTCGTGTTTT---A
*
614878 GAAAATTTCGTG-TTTC
1 -AAAATTTCGTGTTTTA
*
614894 AAAATCCTCGTGTTTTCA
1 AAAAT-TTCGTGTTTT-A
614912 AAAATTTCGGTGTTTTA
1 AAAATTTC-GTGTTTTA
614929 AAAATTTTCGTGTTTTCAA
1 AAAA-TTTCGTGTTTT--A
*
614948 AAAATTCCCGTGTTTTA
1 AAAATT-TCGTGTTTTA
614965 AAAATTTCCGTGTTTTCA
1 AAAATTT-CGTGTTTT-A
614983 AAAATTTTCGTGTTTTTA
1 AAAA-TTTCGTG-TTTTA
* *
615001 AGAATTTTCGTGTCTCT-
1 A-AAATTTCGTGT-TTTA
615018 AAAATTCTCGTGTTTTA
1 AAAATT-TCGTGTTTTA
615035 AAAATTTTTCGTGTTTTCAA
1 AAAA--TTTCGTGTTTT--A
* *** *
615055 AAAAATAATTGTTTCA
1 AAAATTTCGTGTTTTA
615071 AAAATCTTCGTGTTTTAA
1 AAAAT-TTCGTGTTTT-A
615089 AAAATTTC
1 AAAATTTC
615097 TTGTATTTTA
Statistics
Matches: 241, Mismatches: 34, Indels: 66
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.02
16 28 0.12
17 74 0.31
18 88 0.37
19 30 0.12
20 15 0.06
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (16 bp):
AAAATTTCGTGTTTTA
Found at i:623512 original size:11 final size:11
Alignment explanation
Indices: 623496--623537 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
623486 AAGCTTTTTT
623496 TATTAAAAAAA
1 TATTAAAAAAA
*
623507 TATT-AAAAAG
1 TATTAAAAAAA
*
623517 CATTAAAAATAA
1 TATTAAAAA-AA
623529 TATTAAAAA
1 TATTAAAAA
623538 CATTATAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 8 0.32
12 9 0.36
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (11 bp):
TATTAAAAAAA
Found at i:623523 original size:21 final size:21
Alignment explanation
Indices: 623497--623556 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
623487 AGCTTTTTTT
623497 ATTAAAAA-AATATTAAAAAGC
1 ATTAAAAATAATATTAAAAA-C
623518 ATTAAAAATAATATTAAAAAC
1 ATTAAAAATAATATTAAAAAC
* *
623539 ATTATAGATAAT-TTAAAA
1 ATTAAAAATAATATTAAAA
623557 GTCATTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 6 0.17
21 19 0.53
22 11 0.31
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
ATTAAAAATAATATTAAAAAC
Found at i:623562 original size:21 final size:21
Alignment explanation
Indices: 623497--623568 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
623487 AGCTTTTTTT
623497 ATTAAAAA-AATATTAAAAAGC
1 ATTAAAAATAATATT-AAAAGC
*
623518 ATTAAAAATAATATTAAAAAC
1 ATTAAAAATAATATTAAAAGC
* *
623539 ATTATAGATAAT-TTAAAAGTC
1 ATTAAAAATAATATTAAAAG-C
*
623560 ATTTAAAAT
1 ATTAAAAAT
623569 GGAATTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
ATTAAAAATAATATTAAAAGC
Found at i:624502 original size:2 final size:2
Alignment explanation
Indices: 624495--624519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
624485 TAAAATTTTA
624495 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
624520 AATTCTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624725 original size:26 final size:27
Alignment explanation
Indices: 624679--624743 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
624669 AATTAACAGA
* * *
624679 AATAGTTAATGCTATATTTTAATTTCG
1 AATAGTTAATGCCATATTTTAATTGCC
*
624706 AATAGTTAATGCCATA-TTTACTTGCC
1 AATAGTTAATGCCATATTTTAATTGCC
*
624732 TATAGTTAATGC
1 AATAGTTAATGC
624744 TGATTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (27 bp):
AATAGTTAATGCCATATTTTAATTGCC
Found at i:626966 original size:12 final size:12
Alignment explanation
Indices: 626949--626976 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
626939 CTAAATCCTT
626949 TCTCTAATATTC
1 TCTCTAATATTC
626961 TCTCTAATATTC
1 TCTCTAATATTC
626973 TCTC
1 TCTC
626977 AAATTCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTAATATTC
Found at i:626982 original size:10 final size:10
Alignment explanation
Indices: 626948--627014 Score: 66
Period size: 11 Copynumber: 6.3 Consensus size: 10
626938 ACTAAATCCT
626948 TTCTCT-AATA
1 TTCTCTCAA-A
626958 TTCTCTCTAATA
1 TTCTCTC-AA-A
626970 TTCTCTCAAA
1 TTCTCTCAAA
626980 TTCCTCTC-AA
1 TT-CTCTCAAA
626990 TTCCTCTCAAA
1 TT-CTCTCAAA
627001 TTCCTCTCAAA
1 TT-CTCTCAAA
627012 TTC
1 TTC
627015 CTATTTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
10 20 0.38
11 22 0.42
12 11 0.21
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.43
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:626988 original size:11 final size:11
Alignment explanation
Indices: 626972--627016 Score: 83
Period size: 11 Copynumber: 4.2 Consensus size: 11
626962 CTCTAATATT
626972 CTCTCAAATTC
1 CTCTCAAATTC
626983 CTCTC-AATTC
1 CTCTCAAATTC
626993 CTCTCAAATTC
1 CTCTCAAATTC
627004 CTCTCAAATTC
1 CTCTCAAATTC
627015 CT
1 CT
627017 ATTTAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.30
11 23 0.70
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:626996 original size:21 final size:22
Alignment explanation
Indices: 626972--627016 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
626962 CTCTAATATT
626972 CTCTCAAATTCCTCTC-AATTC
1 CTCTCAAATTCCTCTCAAATTC
626993 CTCTCAAATTCCTCTCAAATTC
1 CTCTCAAATTCCTCTCAAATTC
627015 CT
1 CT
627017 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (22 bp):
CTCTCAAATTCCTCTCAAATTC
Found at i:627209 original size:18 final size:18
Alignment explanation
Indices: 627186--627250 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
627176 TAAGTGTTAA
627186 ATTTAATTTTTAAATATT
1 ATTTAATTTTTAAATATT
**
627204 ATTTAAGATTTTTTTAT-TT
1 ATTT-A-ATTTTTAAATATT
*
627223 ATGTAA-TTTTAAATAATT
1 ATTTAATTTTTAAAT-ATT
627241 A-TTAATTTTT
1 ATTTAATTTTT
627251 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
16 6 0.17
17 4 0.11
18 12 0.33
19 6 0.17
20 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:628205 original size:7 final size:7
Alignment explanation
Indices: 628195--628219 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
628185 TTGGTATTTA
628195 GTATTAT
1 GTATTAT
628202 GTATTAT
1 GTATTAT
628209 GTATTAT
1 GTATTAT
628216 GTAT
1 GTAT
628220 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:628816 original size:44 final size:44
Alignment explanation
Indices: 628750--628833 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
628740 GGCCATGCGC
* *
628750 TACTGTAGCAAAAGTGCATCCACGTGGGAGCTTTTTTCAGGGGT
1 TACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGGGGT
*
628794 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAG
1 TACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAG
628834 TACTTCTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (44 bp):
TACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGGGGT
Found at i:628977 original size:44 final size:44
Alignment explanation
Indices: 628907--629003 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 44
628897 CTCGAAATTA
* *
628907 TTTTTTCAAGGGTTACAGTAGTAAAAGCACATCCACGTGGGAGC
1 TTTTTTCAGGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGC
* * *
628951 TTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGC
1 TTTTTTCAGGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGC
*
628995 TTCTTTCAG
1 TTTTTTCAG
629004 TACTTCTACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (44 bp):
TTTTTTCAGGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGC
Found at i:629053 original size:170 final size:170
Alignment explanation
Indices: 628766--629129 Score: 692
Period size: 170 Copynumber: 2.1 Consensus size: 170
628756 AGCAAAAGTG
628766 CATCCACGTGGGAGCTTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
1 CATCCACGTGGGAGCTTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
* * * *
628831 CAGTACTTCTGCTGACAAAGCATCTTGCTTAAAGCGTTTTTGACATTGTTTGCTCAGAAACGTCT
66 CAGTACTTCTACTGACAAAGCATCCTGATTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCT
628896 ACTCGAAATTATTTTTTCAAGGGTTACAGTAGTAAAAGCA
131 ACTCGAAATTATTTTTTCAAGGGTTACAGTAGTAAAAGCA
628936 CATCCACGTGGGAGCTTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
1 CATCCACGTGGGAGCTTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
629001 CAGTACTTCTACTGACAAAGCATCCTGATTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCT
66 CAGTACTTCTACTGACAAAGCATCCTGATTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCT
629066 ACTCGAAATTATTTTTTCAAGGGTTACAGTAGTAAAAGCA
131 ACTCGAAATTATTTTTTCAAGGGTTACAGTAGTAAAAGCA
629106 CATCCACGTGGGAGCTTTTTTCAG
1 CATCCACGTGGGAGCTTTTTTCAG
629130 TACTTCTGCT
Statistics
Matches: 190, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 190 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (170 bp):
CATCCACGTGGGAGCTTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
CAGTACTTCTACTGACAAAGCATCCTGATTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCT
ACTCGAAATTATTTTTTCAAGGGTTACAGTAGTAAAAGCA
Found at i:629176 original size:126 final size:126
Alignment explanation
Indices: 628951--629252 Score: 417
Period size: 126 Copynumber: 2.4 Consensus size: 126
628941 ACGTGGGAGC
* * * *
628951 TTTTTTCAGGGGTTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
1 TTTTTTCAAGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
* * *
629016 CAAAGCATCCTGATTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
66 CAAAGCATCATGATTAAAGCATTTTTAACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
* * *
629077 TTTTTTCAAGGGTTACAGTAGTAAAAGCACATCCACGTGGGAGCTTTTTTCAGTACTTCTGCTGA
1 TTTTTTCAAGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
**
629142 CAAAGCATCATTCTTAAAGCATTTTTAACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
66 CAAAGCATCATGATTAAAGCATTTTTAACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
* ** * * * *
629203 TTTTCTC-AGGACCTACTGTAGCAAAAGCGCGTCCACGTGGGAGGTTCTTT
1 TTTTTTCAAGG-GTTACAGTAGCAAAAGCACATCCACGTGGGAGCTTCTTT
629253 AAATTAACAA
Statistics
Matches: 154, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
125 3 0.02
126 151 0.98
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
TTTTTTCAAGGGTTACAGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
CAAAGCATCATGATTAAAGCATTTTTAACACTGTTTGCTCAGAAACGTCTACTCGAAATTA
Found at i:629481 original size:95 final size:96
Alignment explanation
Indices: 629296--629515 Score: 289
Period size: 95 Copynumber: 2.3 Consensus size: 96
629286 AACGCCAAAG
*
629296 CCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATTTTTTAAAAA
1 CCTAATTTAATTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATTTTTTAAAAA
* *
629361 ATTATAATTAATTTACTCAAGTAACCCTGAAC
65 ATTATAATTAAATTACTCAAGTAACCCTAAAC
* * * * * * * ***
629393 CCTAATTTACTTGATTTTTCCTTTAAAACCCTTAACTCTAAACCTTAATCTAA-TTTTTAAATTT
1 CCTAATTTAATTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATTTTTTAAAAAA
*
629457 TTTTAATTAAATTACTCAAGTAACCCTAAAC
66 TTATAATTAAATTACTCAAGTAACCCTAAAC
*
629488 CCTAATTTAATTGATTTTTTCTTAAAAA
1 CCTAATTTAATTGATTTTTACTTAAAAA
629516 ACAATAAACA
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
95 61 0.57
96 33 0.31
97 13 0.12
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (96 bp):
CCTAATTTAATTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATTTTTTAAAAAA
TTATAATTAAATTACTCAAGTAACCCTAAAC
Found at i:629559 original size:95 final size:95
Alignment explanation
Indices: 629296--629561 Score: 248
Period size: 95 Copynumber: 2.8 Consensus size: 95
629286 AACGCCAAAG
* * ** * * * * * *
629296 CCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATTTTTTAAAAA
1 CCTAATTTAATTGA-TTTTTCCTTAAAAACAATAAACTCGAAAACTTAATCCAA-TTTTTAAAAA
* * *
629361 ATTATAATTAATTTACTCAAGTAACCCTGAAC
64 TTTATAATTAAATTACTCAAGTAACCCTAAAC
* * ** * * * * **
629393 CCTAATTTACTTGATTTTTCCTTTAAAACCCTTAACTCTAAACCTTAATCTAATTTTTAAATTTT
1 CCTAATTTAATTGATTTTTCCTTAAAAACAATAAACTCGAAAACTTAATCCAATTTTTAAAAATT
*
629458 TTTAATTAAATTACTCAAGTAACCCTAAAC
66 TATAATTAAATTACTCAAGTAACCCTAAAC
* *
629488 CCTAATTTAATTGATTTTTTCTTAAAAAACAATAAACAT-GAAAAC-TAATCCAATTTTGAAAAA
1 CCTAATTTAATTGATTTTTCCTT-AAAAACAATAAAC-TCGAAAACTTAATCCAATTTTTAAAAA
629551 TTTATAATTAA
64 TTTATAATTAA
629562 TTTAATTGAC
Statistics
Matches: 141, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
95 81 0.57
96 46 0.33
97 14 0.10
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (95 bp):
CCTAATTTAATTGATTTTTCCTTAAAAACAATAAACTCGAAAACTTAATCCAATTTTTAAAAATT
TATAATTAAATTACTCAAGTAACCCTAAAC
Found at i:642652 original size:22 final size:23
Alignment explanation
Indices: 642612--642671 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
642602 TTCAACTTTG
* *
642612 TTAATTAAGCTTTAA-TAAATCA-
1 TTAATTAAGC-ATAATTAAACCAC
*
642634 TTAATTAAGCCTAATTAAACCAC
1 TTAATTAAGCATAATTAAACCAC
*
642657 TTTATTAAGCATAAT
1 TTAATTAAGCATAAT
642672 CTCAAATCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 13 0.41
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.38
Consensus pattern (23 bp):
TTAATTAAGCATAATTAAACCAC
Found at i:645693 original size:31 final size:31
Alignment explanation
Indices: 645658--645721 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
645648 AATTCACAAC
* * *
645658 TTAATAATTTAAGTAAAAACTTTCGAATAAT
1 TTAATAACTTAAATAAAAACTTTCAAATAAT
*
645689 TTAATAACTTAAATGAAAACTTTCAAATAAT
1 TTAATAACTTAAATAAAAACTTTCAAATAAT
645720 TT
1 TT
645722 TAAAACTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (31 bp):
TTAATAACTTAAATAAAAACTTTCAAATAAT
Found at i:646079 original size:3 final size:3
Alignment explanation
Indices: 646027--646064 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
646017 TAAAATTATT
646027 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
646065 TCTCTTCAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:650048 original size:80 final size:80
Alignment explanation
Indices: 649915--650077 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
649905 ACTCCAAATT
649915 AAAGAAATATATACCCATAATTAGTTATTCTCTCCTATTCTAATTAAAGGCTTTTTATCTTTTAA
1 AAAGAAATATATACCCATAATTAGTTATTCTCTCCTATTCTAATTAAAGGCTTTTTATCTTTTAA
*
649980 AAAGAGAAAAAAAAA
66 AAAGAAAAAAAAAAA
649995 AAAGAAATATATACCCATAATTAGTTATTCTCTCCTATTCTAATTAAAGGCTTTTTATCTTTTAA
1 AAAGAAATATATACCCATAATTAGTTATTCTCTCCTATTCTAATTAAAGGCTTTTTATCTTTTAA
650060 AAAGAAAAAAAAAAA
66 AAAGAAAAAAAAAAA
650075 AAA
1 AAA
650078 AAAAAAGGAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (80 bp):
AAAGAAATATATACCCATAATTAGTTATTCTCTCCTATTCTAATTAAAGGCTTTTTATCTTTTAA
AAAGAAAAAAAAAAA
Found at i:652785 original size:25 final size:25
Alignment explanation
Indices: 652751--652800 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
652741 ACTATAAAAG
652751 ATTGATTGGATCCTCAAGATGCCTC
1 ATTGATTGGATCCTCAAGATGCCTC
652776 ATTGATTGGATCCTCAAGATGCCTC
1 ATTGATTGGATCCTCAAGATGCCTC
652801 GGATGCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (25 bp):
ATTGATTGGATCCTCAAGATGCCTC
Found at i:655038 original size:22 final size:22
Alignment explanation
Indices: 655008--655060 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
654998 ACACAATATG
* *
655008 ATTCTGAGGAATTAATAAACCT
1 ATTCCGAGGAATCAATAAACCT
*
655030 ATTTCGAGGAATCAATAAACCT
1 ATTCCGAGGAATCAATAAACCT
*
655052 CTTCCGAGG
1 ATTCCGAGG
655061 TCACCTTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (22 bp):
ATTCCGAGGAATCAATAAACCT
Found at i:655223 original size:34 final size:35
Alignment explanation
Indices: 655184--655249 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
655174 CTAGCAAGCC
*
655184 AGTCGATA-ATTGCCATCGCAGTGTCGCTCTATAA
1 AGTCGATAGATTGCCATCACAGTGTCGCTCTATAA
* *
655218 AGTCGATAGATTGTCATCACAGTGTTGCTCTA
1 AGTCGATAGATTGCCATCACAGTGTCGCTCTA
655250 GCATGCCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (35 bp):
AGTCGATAGATTGCCATCACAGTGTCGCTCTATAA
Found at i:658684 original size:25 final size:24
Alignment explanation
Indices: 658655--658707 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
658645 CACAAATGCA
658655 GCTCTTTGTGAGCGTCCTGATATAG
1 GCTCTTTGTGAGCGTCCTGATAT-G
*
658680 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTGTGAGCGTCCTGATATG
658704 GCTC
1 GCTC
658708 GCTTGAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (24 bp):
GCTCTTTGTGAGCGTCCTGATATG
Found at i:665056 original size:40 final size:42
Alignment explanation
Indices: 664950--665057 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 42
664940 CAGTATTTTT
*
664950 AGTGGGCATGCTTAACATGCGAATCAGATTTATAATCAATAC
1 AGTGAGCATGCTTAACATGCGAATCAGATTTATAATCAATAC
** * ** * * *
664992 AGCCAGTATGCTTAACATTTGAATCGGA-TT-TAATTAGTAC
1 AGTGAGCATGCTTAACATGCGAATCAGATTTATAATCAATAC
665032 AGTGAGCATGCTTAACATGCGAATCA
1 AGTGAGCATGCTTAACATGCGAATCA
665058 TATATCAATT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
40 28 0.55
41 2 0.04
42 21 0.41
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (42 bp):
AGTGAGCATGCTTAACATGCGAATCAGATTTATAATCAATAC
Found at i:665106 original size:3 final size:3
Alignment explanation
Indices: 665100--665157 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
665090 TTTATATTTC
* * *
665100 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TAT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
665148 TCT TCT TCT T
1 TCT TCT TCT T
665158 TGCTTCTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:665120 original size:15 final size:15
Alignment explanation
Indices: 665100--665158 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
665090 TTTATATTTC
665100 TCTTCTTCTTCTTTT
1 TCTTCTTCTTCTTTT
*
665115 TCTTCTTCTTCTTCT
1 TCTTCTTCTTCTTTT
*
665130 TCTTCTTCTTATTTT
1 TCTTCTTCTTCTTTT
665145 TCTTCTTCTTCTTT
1 TCTTCTTCTTCTTT
665159 GCTTCTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTCTTCTTCTTTT
Found at i:666401 original size:29 final size:29
Alignment explanation
Indices: 666350--666405 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
666340 CATAATATTT
* *
666350 CCAATGTGGTACTTATAATTTGAAAATGC
1 CCAATGTGATACTTATAACTTGAAAATGC
* *
666379 CCAATGTGATACTTGTACCTTGAAAAT
1 CCAATGTGATACTTATAACTTGAAAAT
666406 TTTCAATGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (29 bp):
CCAATGTGATACTTATAACTTGAAAATGC
Found at i:680085 original size:22 final size:23
Alignment explanation
Indices: 680052--680097 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
680042 AATTCACAAA
680052 AAAAAAACAAAATTCACATGGCC
1 AAAAAAACAAAATTCACATGGCC
680075 AAAAAAA-AAAATTCACATGGCC
1 AAAAAAACAAAATTCACATGGCC
680097 A
1 A
680098 CCATACACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAAAAACAAAATTCACATGGCC
Found at i:680802 original size:25 final size:25
Alignment explanation
Indices: 680743--680835 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
680733 GTACATGTAT
680743 GCTCATACGAG-TG-ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
* *
680767 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * * * *
680792 TCTCATACGAGATGAGTATCAGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
680817 GCTCATAAGAGCTAGAATA
1 GCTCATACGAGCT-GAATA
680836 GGTAACCCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 9 0.17
25 38 0.72
26 6 0.11
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:685502 original size:21 final size:21
Alignment explanation
Indices: 685478--685528 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
685468 TTCTTTTGAA
685478 CCTCTGCTT-CTCTCGCTGCAG
1 CCTCTGCTTCCT-TCGCTGCAG
* * *
685499 CCTCTACTTCCTTCGCTTCCG
1 CCTCTGCTTCCTTCGCTGCAG
685520 CCTCTGCTT
1 CCTCTGCTT
685529 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.04, C:0.45, G:0.14, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCCTTCGCTGCAG
Done.