Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 41 of 125
Found at i:12556976 original size:161 final size:160
Alignment explanation
Indices: 12556656--12557083 Score: 586
Period size: 161 Copynumber: 2.7 Consensus size: 160
12556646 GATCACAATG
* * * * *
12556656 ATGAAACGGTTATCTTCCTGATGAGATACAGAGAACTGGACCAAAA-CAATGAAGTAAAGCTCAA
1 ATGAAGCGGTAATCTTCCTGATGAGATACAAAGAAGTAGA-CAAAATCAATGAAG-AAAGCTCAA
* * * * *
12556720 TGTGAGTGAAACTTCAAA-CCCCATCTTCTTGATAAGATACAAAAAAGTGGACCAAATTCGCCTT
64 TGTGAGTGAAACTTCAAACCCCCATCTTCATGATAAGATATAGAGAAGTGGACCAAATCCGCCTT
* * *
12556784 CCTGATGAGATACAGAGAAGTGGATTAAATCA
129 CCTGATAAGATACAAAAAAGTGGATTAAATCA
* *
12556816 ATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACAAAATCAATGAAGCAAAGCTCAAT
1 ATGAAGCGGTAATCTTCCTGATGAGATACAAAGAAGTAGACAAAATCAATGAAG-AAAGCTCAAT
* *
12556881 GTGAGTAAAACTTCAAACCCCCATCTTCATGATGAGATATAGAGAAGTGGACCAAATCCGCCTTC
65 GTGAGTGAAACTTCAAACCCCCATCTTCATGATAAGATATAGAGAAGTGGACCAAATCCGCCTTC
12556946 CTGATAAGATACAAAAAAGTGGATTAAATCA
130 CTGATAAGATACAAAAAAGTGGATTAAATCA
*
12556977 ATGAAGCGGTAATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAAT---G-AAG--CAA-G
1 ATGAAGCGGTAATCTTCCTGATGAGATACAAAGAAGTAGACAAAATCAATGAAGAAAGCTCAATG
* *
12557035 TGAGTGAAACTTCAAACCCCCATCTTCCTGATTAGATATAGAGAAGTGG
66 TGAGTGAAACTTCAAACCCCCATCTTCATGATAAGATATAGAGAAGTGG
12557084 GTTAAAGCAA
Statistics
Matches: 243, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
153 47 0.19
154 3 0.01
156 3 0.01
158 1 0.00
159 5 0.02
160 68 0.28
161 116 0.48
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (160 bp):
ATGAAGCGGTAATCTTCCTGATGAGATACAAAGAAGTAGACAAAATCAATGAAGAAAGCTCAATG
TGAGTGAAACTTCAAACCCCCATCTTCATGATAAGATATAGAGAAGTGGACCAAATCCGCCTTCC
TGATAAGATACAAAAAAGTGGATTAAATCA
Found at i:12558919 original size:24 final size:24
Alignment explanation
Indices: 12558887--12558967 Score: 144
Period size: 24 Copynumber: 3.4 Consensus size: 24
12558877 AAACTCTGTT
12558887 TGGGCTCGTAAGAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
*
12558911 TGGGCTCGTAAAAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
*
12558935 TGGGCTCGTAAGAACTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
12558959 TGGGCTCGT
1 TGGGCTCGT
12558968 GTCGGTTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAATCATTC
Found at i:12564879 original size:15 final size:15
Alignment explanation
Indices: 12564859--12564887 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12564849 TCTAGTGAAT
12564859 TTGGGAAATCCTTAG
1 TTGGGAAATCCTTAG
12564874 TTGGGAAATCCTTA
1 TTGGGAAATCCTTA
12564888 AAGGTTCAAT
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:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
TTGGGAAATCCTTAG
Found at i:12573528 original size:43 final size:43
Alignment explanation
Indices: 12573479--12573562 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
12573469 TAAAGTGATT
12573479 TTAAACAAGTCAAAATAATTTGAACCAAGTCAAAATATTTTAA
1 TTAAACAAGTCAAAATAATTTGAACCAAGTCAAAATATTTTAA
* *
12573522 TTAAACAAGTCAAAATAATTTGAACCAAGTCAGAATCTTTT
1 TTAAACAAGTCAAAATAATTTGAACCAAGTCAAAATATTTT
12573563 TAACACTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (43 bp):
TTAAACAAGTCAAAATAATTTGAACCAAGTCAAAATATTTTAA
Found at i:12573534 original size:23 final size:20
Alignment explanation
Indices: 12573453--12573553 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
12573443 TCTTAGAAAC
* *
12573453 AATTTTAAAATCAAGTTAAAGT
1 AATTTT-AAA-CAAGTCAAAAT
*
12573475 GATTTTAAACAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* *
12573495 AATTTGAACCAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
*
12573515 ATTTTAATTAAACAAGTCAAAAT
1 A-ATT--TTAAACAAGTCAAAAT
* *
12573538 AATTTGAACCAAGTCA
1 AATTTTAAACAAGTCA
12573554 GAATCTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 37 0.58
21 5 0.08
22 7 0.11
23 15 0.23
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.31
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:12578311 original size:44 final size:44
Alignment explanation
Indices: 12578244--12578332 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
12578234 ATTGAGCATC
* *
12578244 CTATTTGTCAGTTTTACCAACCAGTGTTGGGCACATTTATCTGT
1 CTATTTGTCAGTTTTACCAACCAGTGCTAGGCACATTTATCTGT
*** * *
12578288 CTATTTGTCAGTTTTATTGACCAGTGCTAGGTACATTTATTTGT
1 CTATTTGTCAGTTTTACCAACCAGTGCTAGGCACATTTATCTGT
12578332 C
1 C
12578333 GGTTTTACCG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (44 bp):
CTATTTGTCAGTTTTACCAACCAGTGCTAGGCACATTTATCTGT
Found at i:12578338 original size:36 final size:36
Alignment explanation
Indices: 12578289--12578594 Score: 181
Period size: 36 Copynumber: 8.4 Consensus size: 36
12578279 TTTATCTGTC
* ** *
12578289 TATTTGTCAGTTTTATTGACCAGTGCTAGGTACATT
1 TATTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
**
12578325 TATTTGTCGGTTTTACCGACCAGTGCCGGGCACATT
1 TATTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
* * * * *
12578361 TATTTTTTTTGATTTT-CCTGACCAGTGTTGGGCACATT
1 TA--TTTGTCGGTTTTACC-GACCAGTGCTAGGCACATT
* *
12578399 TATTTATCGGTTTT-CTCGACCAGTG-TCAGGAACATT
1 TATTTGTCGGTTTTAC-CGACCAGTGCT-AGGCACATT
* * * * * *
12578435 TATTTTGCCGATTTTCCCGTCCAGTTCTAGACACATT
1 TA-TTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
* ** * * * *
12578472 TATTTTTCAATTTTACCAACAAGTACTAGACACATT
1 TATTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
* * *
12578508 TATTTTATCGG-TTTCCCAACCAGTGCTAGGCACATT
1 TA-TTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
* * ** * *
12578544 TATTTTTCGATTTTACCGATAAGTGTTGGGCACATT
1 TATTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
* *
12578580 T-GTTGTCGATTTTAC
1 TATTTGTCGGTTTTAC
12578595 AGCCAGCGTA
Statistics
Matches: 212, Mismatches: 48, Indels: 21
0.75 0.17 0.07
Matches are distributed among these distances:
35 19 0.09
36 130 0.61
37 33 0.16
38 30 0.14
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (36 bp):
TATTTGTCGGTTTTACCGACCAGTGCTAGGCACATT
Found at i:12578802 original size:2 final size:2
Alignment explanation
Indices: 12578797--12578822 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12578787 TATATATATA
12578797 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
12578823 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12584679 original size:37 final size:36
Alignment explanation
Indices: 12584616--12584691 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
12584606 ATTCCAAAAA
12584616 TAATATTATTTTAATAGGTTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGGTTAATATT-AATTTAATAT
**
12584652 TAATACTTATTTTAATA-GTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGGT-TAATATTAATTTAATAT
12584689 TAA
1 TAA
12584692 AGTGATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (36 bp):
TAATATTATTTTAATAGGTTAATATTAATTTAATAT
Found at i:12584689 original size:11 final size:11
Alignment explanation
Indices: 12584616--12584691 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
12584606 ATTCCAAAAA
*
12584616 TAATATTATTT
1 TAATATTAATT
12584627 TAATAGGTTAATAT
1 TAATA--TTAAT-T
12584641 TAA-ATTTAATT
1 TAATA-TTAATT
*
12584652 TAATACTTATTT
1 TAATA-TTAATT
*
12584664 TAATAGT-ATT
1 TAATATTAATT
12584674 T--TATTAATT
1 TAATATTAATT
12584683 TAATATTAA
1 TAATATTAA
12584692 AGTGATTATC
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.31
12 16 0.31
13 5 0.10
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:12584699 original size:20 final size:18
Alignment explanation
Indices: 12584617--12584723 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
12584607 TTCCAAAAAT
*
12584617 AATATTATTTTAATAGGTT-
1 AATATTAATTTAATA--TTA
12584636 AATATTAAATTTAAT-TT-
1 AATATT-AATTTAATATTA
* *
12584653 AATACTTATTTTAATAGTA
1 AATA-TTAATTTAATATTA
**
12584672 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
12584691 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
12584711 AAT-TTAATTTAAT
1 AATATTAATTTAAT
12584724 GTTTATCTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
17 20 0.29
18 5 0.07
19 22 0.31
20 23 0.33
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:12584749 original size:68 final size:66
Alignment explanation
Indices: 12584634--12584830 Score: 185
Period size: 68 Copynumber: 3.0 Consensus size: 66
12584624 TTTTAATAGG
* *
12584634 TTAATATTAAATTTAATTTAATACTTAT-TT-TAATAGTATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAATTTAATTTAATATTTATCTTGTAATA-TA-ATT-TTAATTTAATATTAAAGTGA
12584697 TTAT
63 TTAT
* *
12584701 CTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATA-AACTTTTAA-TT-AT-TTTAA-T-A
1 -TTAATATTAAATTTAATTTAATATTTATCTTGTA-ATATAA-TTTTAATTTAATATTAAAGTGA
**
12584760 AGAT
63 TTAT
* * *
12584764 TTAATATTAAATTTAATCTAATATTTATCTTGATATATATTATGTTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATTTAATATTTATCTTG-TA-ATATAATTTTAATTTAATATTAAAGTGAT
12584829 TA
64 TA
12584831 AGCATAATAA
Statistics
Matches: 104, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
62 30 0.29
63 13 0.12
64 4 0.04
65 6 0.06
66 6 0.06
67 3 0.03
68 32 0.31
69 5 0.05
70 2 0.02
71 3 0.03
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.52
Consensus pattern (66 bp):
TTAATATTAAATTTAATTTAATATTTATCTTGTAATATAATTTTAATTTAATATTAAAGTGATTA
T
Found at i:12585123 original size:29 final size:31
Alignment explanation
Indices: 12585078--12585150 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
12585068 CAAATTATTT
* *
12585078 TAAAATTATTAAGATTATTTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAAATAA
12585108 T-AAATTATTAAAATTATTTTTTAAAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAATAA
12585138 TAAAATTATTAAA
1 TAAAATTATTAAA
12585151 TAATTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 25 0.64
30 3 0.08
31 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTAAAAATAA
Found at i:12585791 original size:39 final size:39
Alignment explanation
Indices: 12585733--12585809 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
12585723 AGCAAATGAT
* * *
12585733 GGTTGTGAATATACAAAAACTCATATTTGGAATATTTAG
1 GGTTGTGAAGATACAAAAACCCAGATTTGGAATATTTAG
*
12585772 GGTTGTGAAGATACCAAAACCCAGATTTGGAATATTTA
1 GGTTGTGAAGATACAAAAACCCAGATTTGGAATATTTA
12585810 AGTTACTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (39 bp):
GGTTGTGAAGATACAAAAACCCAGATTTGGAATATTTAG
Found at i:12586224 original size:30 final size:30
Alignment explanation
Indices: 12586188--12586260 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
12586178 ATTAAAATTA
12586188 TTTAATAATTTTATTATTTT-AAAAGATAAT
1 TTTAATAATTTTA-TATTTTAAAAAGATAAT
*
12586218 TTTAATAATTTTATATTTTAAAAATATAAT
1 TTTAATAATTTTATATTTTAAAAAGATAAT
12586248 TTTAATAATTTTA
1 TTTAATAATTTTA
12586261 AAATAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 6 0.15
30 35 0.85
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTAATAATTTTATATTTTAAAAAGATAAT
Found at i:12586248 original size:21 final size:23
Alignment explanation
Indices: 12586222--12586263 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12586212 GATAATTTTA
12586222 ATAATTTT-AT-ATTTTAAAAAT
1 ATAATTTTAATAATTTTAAAAAT
12586243 ATAATTTTAATAATTTTAAAA
1 ATAATTTTAATAATTTTAAAA
12586264 TAATTTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATTTTAATAATTTTAAAAAT
Found at i:12587592 original size:89 final size:91
Alignment explanation
Indices: 12587400--12587597 Score: 242
Period size: 91 Copynumber: 2.2 Consensus size: 91
12587390 CAATCTCTCA
* * *
12587400 AAAAAAGCAATTAAGCCCCTCTTTTTTTTTTTACACTCAATTGAGCACTTGAACTTTTAAAATGC
1 AAAAAAGCAATTAAGCCCCTC-TTATTTTTTCACACTCAATTGAGCACTTGAACTTTCAAAATGC
*
12587465 ATAAAAAAAAAGCCCTCAAACTTCTTC
65 ATAAAAAAAAAGCCCTCAAAATTCTTC
* * *
12587492 AAAAAAGCAATTAAGCTCCTGC-TATTTTTTCCCACTCAATTG-GATACTTGAACTTTCAAAATG
1 AAAAAAGCAATTAAGCCCCT-CTTATTTTTTCACACTCAATTGAG-CACTTGAACTTTCAAAATG
* * * *
12587555 TAT-CAAAAAGA-CCCTCAAAATTTTTC
64 CATAAAAAAAAAGCCCTCAAAATTCTTC
12587581 AAAAAAGCAATTAAGCC
1 AAAAAAGCAATTAAGCC
12587598 ATTGCTCTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
89 29 0.32
90 7 0.08
91 36 0.39
92 19 0.21
93 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (91 bp):
AAAAAAGCAATTAAGCCCCTCTTATTTTTTCACACTCAATTGAGCACTTGAACTTTCAAAATGCA
TAAAAAAAAAGCCCTCAAAATTCTTC
Found at i:12587741 original size:20 final size:20
Alignment explanation
Indices: 12587718--12587758 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12587708 TTGTAAAATT
12587718 TTATAGAAAT-CATAAAAAAA
1 TTATA-AAATGCATAAAAAAA
*
12587738 TTATAAAATGCATCAAAAAA
1 TTATAAAATGCATAAAAAAA
12587758 T
1 T
12587759 CCCTTTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (20 bp):
TTATAAAATGCATAAAAAAA
Found at i:12587942 original size:9 final size:9
Alignment explanation
Indices: 12587928--12588118 Score: 77
Period size: 9 Copynumber: 20.2 Consensus size: 9
12587918 TTTTGGTACA
12587928 ATAATTTTT
1 ATAATTTTT
12587937 ATAATTTTTTT
1 ATAA--TTTTT
* *
12587948 ACAAATTTT
1 ATAATTTTT
*
12587957 ATATTTCTTT
1 ATAATT-TTT
*
12587967 AT-ATTTTGC
1 ATAATTTT-T
12587976 ATAATTTTCTT
1 ATAA-TTT-TT
* *
12587987 ATGA-CTTT
1 ATAATTTTT
*
12587995 ATAAAATTTT
1 AT-AATTTTT
12588005 ATAATTTTT
1 ATAATTTTT
*
12588014 -TATATTTCT
1 ATA-ATTTTT
12588023 AT-ATATTTT
1 ATAAT-TTTT
12588032 ATAAGGTTTTT
1 ATAA--TTTTT
**
12588043 ACGATTTTT
1 ATAATTTTT
*
12588052 ATAAAATTTT
1 AT-AATTTTT
*
12588062 ACAATTTTTT
1 ATAA-TTTTT
*
12588072 ATATTTTTT
1 ATAATTTTT
*
12588081 ACAATTTTT
1 ATAATTTTT
*
12588090 ATATTTTTT
1 ATAATTTTT
*
12588099 CTAATTTTT
1 ATAATTTTT
12588108 A-ATATTTTT
1 ATA-ATTTTT
12588117 AT
1 AT
12588119 TAAAATTTAA
Statistics
Matches: 132, Mismatches: 31, Indels: 37
0.66 0.16 0.19
Matches are distributed among these distances:
8 11 0.08
9 74 0.56
10 25 0.19
11 20 0.15
12 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:12588014 original size:10 final size:10
Alignment explanation
Indices: 12587928--12588116 Score: 73
Period size: 10 Copynumber: 19.9 Consensus size: 10
12587918 TTTTGGTACA
12587928 ATAA-TTTTT
1 ATAATTTTTT
12587937 ATAATTTTTT
1 ATAATTTTTT
**
12587947 -TACAAATTTT
1 ATA-ATTTTTT
12587957 AT-ATTTCTTT
1 ATAATTT-TTT
**
12587967 AT-ATTTTGC
1 ATAATTTTTT
12587976 ATAATTTTCTT
1 ATAATTTT-TT
* *
12587987 ATGA--CTTT
1 ATAATTTTTT
**
12587995 ATAAAATTTT
1 ATAATTTTTT
12588005 ATAATTTTTT
1 ATAATTTTTT
*
12588015 AT-A-TTTCT
1 ATAATTTTTT
*
12588023 AT-ATATTTT
1 ATAATTTTTT
*
12588032 ATAAGGTTTTT
1 ATAA-TTTTTT
**
12588043 ACGA-TTTTT
1 ATAATTTTTT
**
12588052 ATAAAATTTT
1 ATAATTTTTT
*
12588062 ACAATTTTTT
1 ATAATTTTTT
12588072 AT-ATTTTTT
1 ATAATTTTTT
*
12588081 ACAA-TTTTT
1 ATAATTTTTT
12588090 AT-ATTTTTT
1 ATAATTTTTT
* *
12588099 CTAATTTTTA
1 ATAATTTTTT
12588109 AT-ATTTTT
1 ATAATTTTT
12588117 ATTAAAATTT
Statistics
Matches: 132, Mismatches: 33, Indels: 30
0.68 0.17 0.15
Matches are distributed among these distances:
8 13 0.10
9 51 0.39
10 58 0.44
11 10 0.08
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:12588061 original size:57 final size:57
Alignment explanation
Indices: 12587944--12588077 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 57
12587934 TTTATAATTT
* * * *
12587944 TTTTACAA-ATTTTATATTTCTTTATATTTTGCATAATTTTCTTATGACTTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTT-CATAAGTTTCTTACGACTTTATAAAA
* *
12588001 TTTTATAATTTTTTATATTTCTATATATTTT-ATAAGGTTT-TTACGATTTTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTTCATAA-GTTTCTTACGA-CTTTATAAAA
12588058 TTTTACAATTTTTTATATTT
1 TTTTACAATTTTTTATATTT
12588078 TTTACAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 9 0.13
57 38 0.57
58 20 0.30
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (57 bp):
TTTTACAATTTTTTATATTTCTATATATTTTCATAAGTTTCTTACGACTTTATAAAA
Found at i:12588097 original size:19 final size:19
Alignment explanation
Indices: 12588038--12588126 Score: 76
Period size: 19 Copynumber: 4.6 Consensus size: 19
12588028 TTTTATAAGG
* **
12588038 TTTTTACGATTTTTATAAA
1 TTTTTACAATTTTTATATT
*
12588057 ATTTTACAATTTTT-TATAT
1 TTTTTACAATTTTTATAT-T
12588076 TTTTTACAATTTTTATA-T
1 TTTTTACAATTTTTATATT
12588094 TTTTT-CTAATTTTTAATATT
1 TTTTTAC-AATTTTT-ATATT
*
12588114 TTTATTAAAATTT
1 TTT-TTACAATTT
12588127 AATGATATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.02
18 15 0.26
19 28 0.49
20 6 0.11
21 7 0.12
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTTACAATTTTTATATT
Found at i:12590058 original size:18 final size:18
Alignment explanation
Indices: 12590035--12590069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12590025 CCCTCGTCTT
* *
12590035 CTAAGGGGAAGTAGAAAG
1 CTAAGGGAAAGAAGAAAG
12590053 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
12590070 CGACTAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.34, T:0.09
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:12594795 original size:37 final size:36
Alignment explanation
Indices: 12594746--12594821 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
12594736 ATTCCAAAAA
12594746 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
12594782 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
12594819 TAA
1 TAA
12594822 AGTGGTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:12594819 original size:11 final size:11
Alignment explanation
Indices: 12594746--12594821 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
12594736 ATTCCAAAAA
*
12594746 TAATATTATTT
1 TAATATTAATT
12594757 TAATAGTTTAATAT
1 TAATA--TTAAT-T
12594771 TAA-ATTTAATT
1 TAATA-TTAATT
*
12594782 TAATACTTATTT
1 TAATA-TTAATT
*
12594794 TAATAGT-ATT
1 TAATATTAATT
12594804 T--TATTAATT
1 TAATATTAATT
12594813 TAATATTAA
1 TAATATTAA
12594822 AGTGGTTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.31
12 17 0.33
13 5 0.10
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:12594909 original size:12 final size:12
Alignment explanation
Indices: 12594892--12594926 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
12594882 TTTTAATAAG
12594892 ATTTAATATTAA
1 ATTTAATATTAA
12594904 ATTT-A-ATTAA
1 ATTTAATATTAA
12594914 ATTTAATATTAA
1 ATTTAATATTAA
12594926 A
1 A
12594927 GTGATTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:12594909 original size:22 final size:22
Alignment explanation
Indices: 12594883--12594926 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12594873 ATTTTATTAT
12594883 TTTAA-TAAGATTTAATATTAAA
1 TTTAATTAA-ATTTAATATTAAA
12594905 TTTAATTAAATTTAATATTAAA
1 TTTAATTAAATTTAATATTAAA
12594927 GTGATTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAATTAAATTTAATATTAAA
Found at i:12594939 original size:21 final size:22
Alignment explanation
Indices: 12594888--12594942 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12594878 ATTATTTTAA
*
12594888 TAAGATTTAATATTAAATTTAAT
1 TAAG-TTTAATATTAAATGTAAT
* *
12594911 TAAATTTAATATTAAA-GTGAT
1 TAAGTTTAATATTAAATGTAAT
12594932 TAAGTTTAATA
1 TAAGTTTAATA
12594943 ATAGTTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 13 0.46
22 12 0.43
23 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TAAGTTTAATATTAAATGTAAT
Found at i:12596883 original size:42 final size:45
Alignment explanation
Indices: 12596836--12597022 Score: 156
Period size: 45 Copynumber: 4.2 Consensus size: 45
12596826 AATACCATGA
*
12596836 TTGAAAGATATC-ATGGCATTGTACCCGAAATGAGA-AAGA-C-T-G
1 TTGAAAGATATCTATGGCATT-TAACCGAAATGA-ATAAGACCATAG
* *
12596878 TTGAAAGACA-CTATGGCATTTAACCGGAATGAATAAGACCATAG
1 TTGAAAGATATCTATGGCATTTAACCGAAATGAATAAGACCATAG
** * * ** *
12596922 TTGAAAGATAT-TATTACATTAAATCGGAAATGTGTAAGACCATAA
1 TTGAAAGATATCTATGGCATTTAA-CCGAAATGAATAAGACCATAG
* * *
12596967 TTGAAAGATA-CTATGGCACTAAATCCGATATGAATAAGACCATAG
1 TTGAAAGATATCTATGGCATTTAA-CCGAAATGAATAAGACCATAG
*
12597012 TTGAAATATAT
1 TTGAAAGATAT
12597023 AATGGCACCA
Statistics
Matches: 115, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 15 0.13
42 18 0.16
43 1 0.01
44 19 0.17
45 61 0.53
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (45 bp):
TTGAAAGATATCTATGGCATTTAACCGAAATGAATAAGACCATAG
Found at i:12597050 original size:90 final size:89
Alignment explanation
Indices: 12596878--12597067 Score: 215
Period size: 90 Copynumber: 2.1 Consensus size: 89
12596868 AGAAAGACTG
* * * * * **
12596878 TTGAAAGACACTATGGCATTTAACCGGAATGAATAAGACCATAGTTGAAAGATATTATTACATTA
1 TTGAAAGATACTATGGCACTAAACCGGAATGAATAAGACCATAGTTGAAAGATATAATGACACCA
12596943 AATCGGAAATGTGTAAGACCA-TAA
66 AATCGGAAATGTGTAAGACCACT-A
* *
12596967 TTGAAAGATACTATGGCACTAAATCC-GATATGAATAAGACCATAGTTGAAATATATAATGGCAC
1 TTGAAAGATACTATGGCACTAAA-CCGGA-ATGAATAAGACCATAGTTGAAAGATATAATGACAC
** *
12597031 CACTTCGGGAAT-TGATAAGACCACTA
64 CAAATCGGAAATGTG-TAAGACCACTA
12597057 TTGAAAGATAC
1 TTGAAAGATAC
12597068 CATGACATCC
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
89 24 0.28
90 60 0.71
91 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (89 bp):
TTGAAAGATACTATGGCACTAAACCGGAATGAATAAGACCATAGTTGAAAGATATAATGACACCA
AATCGGAAATGTGTAAGACCACTA
Found at i:12603290 original size:13 final size:13
Alignment explanation
Indices: 12603269--12603300 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12603259 AATAAGTTAG
*
12603269 TTAATTTAATTAA
1 TTAAATTAATTAA
12603282 TTAAATTAATTAA
1 TTAAATTAATTAA
12603295 TTAAAT
1 TTAAAT
12603301 AAATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATTAATTAA
Found at i:12604271 original size:31 final size:30
Alignment explanation
Indices: 12604234--12604310 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
12604224 TTAAATTAGT
*
12604234 AATAATAAAATTATATTTTAATCATTTAAAA
1 AATAATAAAATTATAATTTAAT-ATTTAAAA
* *
12604265 AATAATAATAATT-TAATTTAATTTTTTAAA
1 AATAATAA-AATTATAATTTAATATTTAAAA
* *
12604295 AATTATAAAAATATAA
1 AATAATAAAATTATAA
12604311 ACTATTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.08
30 16 0.41
31 16 0.41
32 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAATATTTAAAA
Found at i:12606060 original size:18 final size:18
Alignment explanation
Indices: 12606039--12606077 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12606029 AGATAAATTT
* * *
12606039 TTAATTAAATAATTTTAA
1 TTAATAAAAAAATTTAAA
12606057 TTAATAAAAAAATTTAAA
1 TTAATAAAAAAATTTAAA
12606075 TTA
1 TTA
12606078 TTTACATATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATAAAAAAATTTAAA
Found at i:12606877 original size:44 final size:44
Alignment explanation
Indices: 12606814--12606909 Score: 183
Period size: 44 Copynumber: 2.2 Consensus size: 44
12606804 GATGGTATAG
*
12606814 TTTGGTCTGGTCATTGACGTGGGAAGCAGATTTATGTAGGTTAA
1 TTTGGTCTGGTCACTGACGTGGGAAGCAGATTTATGTAGGTTAA
12606858 TTTGGTCTGGTCACTGACGTGGGAAGCAGATTTATGTAGGTTAA
1 TTTGGTCTGGTCACTGACGTGGGAAGCAGATTTATGTAGGTTAA
12606902 TTTGGTCT
1 TTTGGTCT
12606910 TTAGATTTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (44 bp):
TTTGGTCTGGTCACTGACGTGGGAAGCAGATTTATGTAGGTTAA
Found at i:12621956 original size:24 final size:23
Alignment explanation
Indices: 12621929--12622051 Score: 138
Period size: 24 Copynumber: 5.1 Consensus size: 23
12621919 GTATACTGGT
12621929 TAACCATTTTGGACTCGTGAGAGC
1 TAACCATTTTGG-CTCGTGAGAGC
* *
12621953 TAACCATTCTAGGCTCGTAAGAGC
1 TAACCATT-TTGGCTCGTGAGAGC
*
12621977 TAACCATTTTGGGCTTGTGAGAGC
1 TAACCATTTT-GGCTCGTGAGAGC
* *
12622001 TAACCATTCTAGGCTCGTAAGAGC
1 TAACCATT-TTGGCTCGTGAGAGC
* *
12622025 TAACCATTCTGGGCTTGTGAGAGC
1 TAACCATT-TTGGCTCGTGAGAGC
12622049 TAA
1 TAA
12622052 TGTTATCTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.01
24 80 0.94
25 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (23 bp):
TAACCATTTTGGCTCGTGAGAGC
Found at i:12621997 original size:48 final size:48
Alignment explanation
Indices: 12621929--12622051 Score: 219
Period size: 48 Copynumber: 2.6 Consensus size: 48
12621919 GTATACTGGT
* *
12621929 TAACCATTTTGGACTCGTGAGAGCTAACCATTCTAGGCTCGTAAGAGC
1 TAACCATTTTGGGCTTGTGAGAGCTAACCATTCTAGGCTCGTAAGAGC
12621977 TAACCATTTTGGGCTTGTGAGAGCTAACCATTCTAGGCTCGTAAGAGC
1 TAACCATTTTGGGCTTGTGAGAGCTAACCATTCTAGGCTCGTAAGAGC
*
12622025 TAACCATTCTGGGCTTGTGAGAGCTAA
1 TAACCATTTTGGGCTTGTGAGAGCTAA
12622052 TGTTATCTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (48 bp):
TAACCATTTTGGGCTTGTGAGAGCTAACCATTCTAGGCTCGTAAGAGC
Found at i:12623876 original size:22 final size:23
Alignment explanation
Indices: 12623846--12623888 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12623836 TAAAGTGGGT
12623846 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
12623869 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
12623889 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:12638714 original size:25 final size:25
Alignment explanation
Indices: 12638686--12638741 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
12638676 TTATTCCTGC
12638686 AGAAAACT-AAAGA-AAACAAGTTAAA-
1 AGAAAA-TAAAAGACAAA-AAG-TAAAT
12638711 AGAAAATAAAAGACAAAAAGTAAAT
1 AGAAAATAAAAGACAAAAAGTAAAT
12638736 AGAAAA
1 AGAAAA
12638742 ATGTGAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.18
25 20 0.71
26 3 0.11
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.11
Consensus pattern (25 bp):
AGAAAATAAAAGACAAAAAGTAAAT
Found at i:12652521 original size:16 final size:16
Alignment explanation
Indices: 12652500--12652530 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12652490 TTGTGGATCC
12652500 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
12652516 CATTTTATCTTTATT
1 CATTTTACCTTTATT
12652531 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:12658719 original size:46 final size:46
Alignment explanation
Indices: 12658657--12658755 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
12658647 ATTTTGCGTC
*
12658657 AAGAGATGCGTTGACAATAAAAGGTAATGTCTCGTTGTCACCAAGA
1 AAGACATGCGTTGACAATAAAAGGTAATGTCTCGTTGTCACCAAGA
*
12658703 AAGACATGCGTTGACAATAACAGGTAATGTCTCGTTGTCACCAAGA
1 AAGACATGCGTTGACAATAAAAGGTAATGTCTCGTTGTCACCAAGA
12658749 AAGACAT
1 AAGACAT
12658756 ACTTCAGATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (46 bp):
AAGACATGCGTTGACAATAAAAGGTAATGTCTCGTTGTCACCAAGA
Found at i:12663261 original size:7 final size:7
Alignment explanation
Indices: 12663251--12663277 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12663241 TCTTAATGCT
12663251 TTCTTCA
1 TTCTTCA
12663258 TTCTTCA
1 TTCTTCA
12663265 TTCTTCA
1 TTCTTCA
12663272 TTCTTC
1 TTCTTC
12663278 TATTTATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:12664093 original size:124 final size:124
Alignment explanation
Indices: 12663873--12664120 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 124
12663863 GAGAATAAAA
*
12663873 AATATTTGCAGGCCAGAATCTCAGCCGTCAACTAGCGTAATAATTACATCTGTGGAACAAGAAAG
1 AATATTTGCAGGCCAGAATCTCAGCCGTCAACTAGCGTAATAATTACATCCGTGGAACAAGAAAG
12663938 TGTGCATTCGTGGGATAGGCAATTATTGCAATGGTACCACGAGCCACAGGAAACATAGT
66 TGTGCATTCGTGGGATAGGCAATTATTGCAATGGTACCACGAGCCACAGGAAACATAGT
*
12663997 AATATTTGCAGGCTAGAATCTCAGCCGTCAACTAGCGTAATAATTACATCCGTGGAACAAGAAAG
1 AATATTTGCAGGCCAGAATCTCAGCCGTCAACTAGCGTAATAATTACATCCGTGGAACAAGAAAG
12664062 TGTGCATTCGTGGGATAGGCAATTATTGCAATGGTACCACGAGCCACAGGAAACATAGT
66 TGTGCATTCGTGGGATAGGCAATTATTGCAATGGTACCACGAGCCACAGGAAACATAGT
12664121 TCGGTGATGG
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (124 bp):
AATATTTGCAGGCCAGAATCTCAGCCGTCAACTAGCGTAATAATTACATCCGTGGAACAAGAAAG
TGTGCATTCGTGGGATAGGCAATTATTGCAATGGTACCACGAGCCACAGGAAACATAGT
Found at i:12664761 original size:21 final size:22
Alignment explanation
Indices: 12664716--12664763 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12664706 AATAGAAACT
*
12664716 GAGGGCTATGTCGCAACATTAG
1 GAGGCCTATGTCGCAACATTAG
* *
12664738 GAGGCCTATGTTGCAATA-TAG
1 GAGGCCTATGTCGCAACATTAG
12664759 GAGGC
1 GAGGC
12664764 AGTCTGCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (22 bp):
GAGGCCTATGTCGCAACATTAG
Found at i:12679220 original size:38 final size:37
Alignment explanation
Indices: 12679177--12679266 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
12679167 CCCAAGACTG
* *
12679177 TCGCAGCATAAATATTCTTCAATTTGCATCCAGAACTA
1 TCGCAGCATAAATATTCTTCAA-TTGCACCCAGAAATA
* *
12679215 TCGCAGCATAAGTATTCTTCAATTGCACCCAGAAATG
1 TCGCAGCATAAATATTCTTCAATTGCACCCAGAAATA
* *
12679252 TCGCTGCATGAATAT
1 TCGCAGCATAAATAT
12679267 GTCCAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 24 0.53
38 21 0.47
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (37 bp):
TCGCAGCATAAATATTCTTCAATTGCACCCAGAAATA
Found at i:12679282 original size:26 final size:26
Alignment explanation
Indices: 12679252--12679302 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
12679242 CCCAGAAATG
*
12679252 TCGCTGCATGAATATGTCCAAAATTA
1 TCGCTGCATGAACATGTCCAAAATTA
12679278 TCGCTGCATGAACATGTCCAAAATT
1 TCGCTGCATGAACATGTCCAAAATT
12679303 GAGCCCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (26 bp):
TCGCTGCATGAACATGTCCAAAATTA
Found at i:12692524 original size:12 final size:12
Alignment explanation
Indices: 12692503--12692572 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 12
12692493 CGCTACAATG
*
12692503 TCTTTTTCTTTT
1 TCTTTCTCTTTT
12692515 TCTTTCTCTTCTCT
1 TCTTTCTCTT-T-T
12692529 TCTTTCTTCTCTTT
1 TCTTTC-TCT-TTT
12692543 TCTCTTCTCTTCTT
1 TCT-TTCTCTT-TT
12692557 TC-TTCTCTTTT
1 TCTTTCTCTTTT
12692568 CTCTT
1 -TCTT
12692573 CTTCTTCAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
11 2 0.04
12 18 0.37
13 3 0.06
14 18 0.37
15 7 0.14
16 1 0.02
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTTCTCTTTT
Found at i:12692526 original size:5 final size:5
Alignment explanation
Indices: 12692514--12692579 Score: 52
Period size: 5 Copynumber: 13.6 Consensus size: 5
12692504 CTTTTTCTTT
*
12692514 TTCT- TTCTC TTCTC TTCT- TTCT- TCTCTT TTCTC TTCTC TTCT- TTCT-
1 TTCTC TTCTC TTCTC TTCTC TTCTC T-TCTC TTCTC TTCTC TTCTC TTCTC
*
12692560 TCTCTT TTCTC TTCTTC TTC
1 T-TCTC TTCTC TTC-TC TTC
12692580 AATACCCACA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 14 0.26
5 33 0.61
6 7 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TTCTC
Found at i:12692535 original size:24 final size:24
Alignment explanation
Indices: 12692517--12692579 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
12692507 TTTCTTTTTC
12692517 TTTCTCTTCTCTTCTTTCTTCTCT
1 TTTCTCTTCTCTTCTTTCTTCTCT
12692541 TTTCTCTTCTCTTCTTTCTTCTCT
1 TTTCTCTTCTCTTCTTTCTTCTCT
12692565 TTTCTCTTCTTCTTC
1 TTTCTCTTC-TCTTC
12692580 AATACCCACA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 33 0.87
25 5 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTCTCTTCTCTTCTTTCTTCTCT
Found at i:12692573 original size:12 final size:12
Alignment explanation
Indices: 12692517--12692574 Score: 84
Period size: 12 Copynumber: 4.8 Consensus size: 12
12692507 TTTCTTTTTC
12692517 TTTCTCTTCTCT
1 TTTCTCTTCTCT
12692529 TCTT-TCTTCTCT
1 T-TTCTCTTCTCT
12692541 TTTCTCTTCTCT
1 TTTCTCTTCTCT
12692553 TCTT-TCTTCTCT
1 T-TTCTCTTCTCT
12692565 TTTCTCTTCT
1 TTTCTCTTCT
12692575 TCTTCAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.10
12 34 0.81
13 4 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTCTTCTCT
Found at i:12703274 original size:2 final size:2
Alignment explanation
Indices: 12703267--12703297 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12703257 AATGAAATAA
12703267 AT AT AT 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 AT AT AT A
12703298 ATTATGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12709095 original size:14 final size:14
Alignment explanation
Indices: 12709076--12709103 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12709066 CTTTCAGTTG
12709076 CTTTGACATTTAAC
1 CTTTGACATTTAAC
12709090 CTTTGACATTTAAC
1 CTTTGACATTTAAC
12709104 TCTGATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTTGACATTTAAC
Found at i:12716949 original size:15 final size:15
Alignment explanation
Indices: 12716929--12716958 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12716919 GATAAAGGAG
*
12716929 AAGGAAGAAGAAGAA
1 AAGGAAGAACAAGAA
12716944 AAGGAAGAACAAGAA
1 AAGGAAGAACAAGAA
12716959 GAAGAGAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGGAAGAACAAGAA
Found at i:12717307 original size:24 final size:24
Alignment explanation
Indices: 12717262--12717308 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12717252 TGGTTCGACG
* * **
12717262 GATAAAAAGAGGAGGAGGCACAAA
1 GATAAAAAGAAGAAGAAACACAAA
12717286 GATAAAAAGAAGAAGAAACACAA
1 GATAAAAAGAAGAAGAAACACAA
12717309 GGAAGAGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.26, T:0.04
Consensus pattern (24 bp):
GATAAAAAGAAGAAGAAACACAAA
Found at i:12718057 original size:12 final size:11
Alignment explanation
Indices: 12718036--12718086 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
12718026 TAGTCACTTG
12718036 AAAAAGA-AAA
1 AAAAAGAGAAA
*
12718046 AAAATGAGAAA
1 AAAAAGAGAAA
12718057 AACAAAGAGAAA
1 AA-AAAGAGAAA
12718069 AGAAAAGAAGAAA
1 A-AAAAG-AGAAA
12718082 AAAAA
1 AAAAA
12718087 ATTATTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.17
11 5 0.14
12 17 0.49
13 7 0.20
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:12723592 original size:21 final size:21
Alignment explanation
Indices: 12723547--12723599 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
12723537 TTGTGCTAGT
**
12723547 TCTACCAATACAAGTATAGTT
1 TCTACCAATACAAGTATAGCA
12723568 TCTACCAATACAAGTCAT-GCA
1 TCTACCAATACAAGT-ATAGCA
*
12723589 TCTACCGATAC
1 TCTACCAATAC
12723600 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (21 bp):
TCTACCAATACAAGTATAGCA
Found at i:12729419 original size:14 final size:14
Alignment explanation
Indices: 12729400--12729435 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12729390 TTGTTTGACT
*
12729400 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
12729414 GAAAATGATTTCTG
1 GAAAATGATTTCTG
12729428 GAAAATGA
1 GAAAATGA
12729436 ATTACTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:12734986 original size:25 final size:25
Alignment explanation
Indices: 12734924--12734986 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
12734914 ATATTTAATG
* *
12734924 TAATGTGATGATAAAAAATTATATA
1 TAATGTAATGTTAAAAAATTATATA
* * *
12734949 CAAAGTCATATGTTAAAAAATTATATT
1 TAATGT-A-ATGTTAAAAAATTATATA
12734976 TAATGTAATGT
1 TAATGTAATGT
12734987 AATGGGATGC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 8 0.28
26 1 0.03
27 20 0.69
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (25 bp):
TAATGTAATGTTAAAAAATTATATA
Found at i:12755292 original size:12 final size:12
Alignment explanation
Indices: 12755275--12755314 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
12755265 TCTTGATCTC
*
12755275 TTAAAAATTCTT
1 TTAAAAATTATT
12755287 TTAAAAA-TATT
1 TTAAAAATTATT
*
12755298 TTGAAAATTATT
1 TTAAAAATTATT
12755310 TTAAA
1 TTAAA
12755315 GAACATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (12 bp):
TTAAAAATTATT
Found at i:12778946 original size:18 final size:20
Alignment explanation
Indices: 12778923--12778971 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
12778913 GCAGATTAGT
12778923 AATAAATAAAATT-CAAG-A
1 AATAAATAAAATTGCAAGTA
*
12778941 AATAAAGAATAATTGCAAGTA
1 AATAAATAA-AATTGCAAGTA
*
12778962 AAAAAATAAA
1 AATAAATAAA
12778972 CATCAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 5 0.20
21 8 0.32
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.20
Consensus pattern (20 bp):
AATAAATAAAATTGCAAGTA
Found at i:12784766 original size:50 final size:49
Alignment explanation
Indices: 12784711--12784840 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 49
12784701 AATCTTATAC
** * *
12784711 CCCTAAAGCTATAGAGGAACAGATTGAAGCCGCAATGGTGAATCACATA
1 CCCTAAAGCTATAGAGGGGCAGATTGAAGCCGCAATAGCGAATCACATA
* * * **
12784760 CACCTAAAGATGTAGAGGGGCAAATTGAAGCCGCAATAGCGAATCTTATA
1 C-CCTAAAGCTATAGAGGGGCAGATTGAAGCCGCAATAGCGAATCACATA
12784810 CCCTTAAAGCTATAGAGGGGCAGATTGAAGC
1 CCC-TAAAGCTATAGAGGGGCAGATTGAAGC
12784841 TATAGAAGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
49 3 0.04
50 64 0.96
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (49 bp):
CCCTAAAGCTATAGAGGGGCAGATTGAAGCCGCAATAGCGAATCACATA
Found at i:12794845 original size:17 final size:17
Alignment explanation
Indices: 12794823--12794861 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12794813 AGGTGGAGAA
*
12794823 CTTGTTCGTTA-AGAGTT
1 CTTGTTCG-TAGAGAATT
12794840 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
12794857 CTTGT
1 CTTGT
12794862 GAAGGTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:12797468 original size:31 final size:31
Alignment explanation
Indices: 12797405--12797468 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
12797395 AAAATTAGTT
** *
12797405 ATTTTAGTCACTCCCATTAGGTATGTTATCA
1 ATTTTAGTCACTCCCATTACATAAGTTATCA
* * *
12797436 ATTTTAGTCACTCTCGTTACATAAGTTGTCA
1 ATTTTAGTCACTCCCATTACATAAGTTATCA
12797467 AT
1 AT
12797469 ATTCGTCTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (31 bp):
ATTTTAGTCACTCCCATTACATAAGTTATCA
Found at i:12806164 original size:22 final size:22
Alignment explanation
Indices: 12806137--12806190 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
12806127 TTCGACTTCA
12806137 CTATTTTCTATTT-CTTTCAATT
1 CTATTTTCT-TTTACTTTCAATT
* *
12806159 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTCAATT
12806181 CTA-TTTCTTT
1 CTATTTTCTTT
12806191 CATTTTCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.69
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTCAATT
Found at i:12814876 original size:12 final size:12
Alignment explanation
Indices: 12814859--12814888 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12814849 AGCCATTTTT
12814859 ATTTTTAAGTTA
1 ATTTTTAAGTTA
*
12814871 ATTTTTAATTTA
1 ATTTTTAAGTTA
12814883 ATTTTT
1 ATTTTT
12814889 TTGTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTTTAAGTTA
Found at i:12817449 original size:80 final size:80
Alignment explanation
Indices: 12817316--12817475 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
12817306 TTGGTTGTGG
*
12817316 ATGTCAACTTGACTTGTTATTCTAGAACTTGCTTTGATTATGCATGTTGAGACCACATTATTAAT
1 ATGTCAACTTGACTTGTTATTCTAGAACTTGCTTTGACTATGCATGTTGAGACCACATTATTAAT
12817381 TTCATATGCTGAGAT
66 TTCATATGCTGAGAT
* *
12817396 ATGTCAACTTGATTTGTTATTCTAGAACTTGCTTTGACTATGCATGTTGAGACCACATTATTGAT
1 ATGTCAACTTGACTTGTTATTCTAGAACTTGCTTTGACTATGCATGTTGAGACCACATTATTAAT
*
12817461 TTGATATGCTGAGAT
66 TTCATATGCTGAGAT
12817476 GATAGAGGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (80 bp):
ATGTCAACTTGACTTGTTATTCTAGAACTTGCTTTGACTATGCATGTTGAGACCACATTATTAAT
TTCATATGCTGAGAT
Found at i:12828343 original size:18 final size:17
Alignment explanation
Indices: 12828310--12828343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12828300 CTTAACTATT
*
12828310 GAACTTACTAAGTTATA
1 GAACTTACCAAGTTATA
12828327 GAACTTACCACAGTTAT
1 GAACTTACCA-AGTTAT
12828344 TGTTGTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (17 bp):
GAACTTACCAAGTTATA
Found at i:12837264 original size:27 final size:26
Alignment explanation
Indices: 12837234--12837301 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
12837224 AATTTGGCCA
* *
12837234 TTTTATTTTTATTTTCATATTT-TTTGT
1 TTTTA-TTTTATTTTCACATTTAATT-T
* *
12837261 TTTTAATTTAATTTTTACATTTAATTT
1 TTTT-ATTTTATTTTCACATTTAATTT
12837288 TTTTATTTTATTTT
1 TTTTATTTTATTTT
12837302 ATAGGTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 9 0.26
27 22 0.65
28 3 0.09
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTATTTTATTTTCACATTTAATTT
Found at i:12837277 original size:12 final size:13
Alignment explanation
Indices: 12837260--12837289 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12837250 ATATTTTTTG
12837260 TTTTTA-ATTTAA
1 TTTTTACATTTAA
12837272 TTTTTACATTTAA
1 TTTTTACATTTAA
12837285 TTTTT
1 TTTTT
12837290 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:12837295 original size:13 final size:13
Alignment explanation
Indices: 12837260--12837301 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12837250 ATATTTTTTG
12837260 TTTTTAATTTAA-
1 TTTTTAATTTAAT
12837272 TTTTTACATTTAAT
1 TTTTTA-ATTTAAT
* *
12837286 TTTTTTATTTTAT
1 TTTTTAATTTAAT
12837299 TTT
1 TTT
12837302 ATAGGTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:12840239 original size:20 final size:19
Alignment explanation
Indices: 12840216--12840260 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
12840206 AGAAAAAGAA
12840216 AAAAAAGTCAAAAAAAATGG
1 AAAAAA-TCAAAAAAAATGG
* *
12840236 AAAAGAATCGAAAAAAATTG
1 AAAA-AATCAAAAAAAATGG
12840256 AAAAA
1 AAAAA
12840261 GAAAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.86
21 2 0.09
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.11
Consensus pattern (19 bp):
AAAAAATCAAAAAAAATGG
Found at i:12840261 original size:21 final size:20
Alignment explanation
Indices: 12840208--12840271 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
12840198 TATTATTTAG
12840208 AAAAA-GAAAAA-AAAGTCAAA
1 AAAAATGAAAAAGAAAG--AAA
* *
12840228 AAAAATGGAAAAGAATCGAAA
1 AAAAATGAAAAAGAA-AGAAA
*
12840249 AAAATTGAAAAAGAAAGAAA
1 AAAAATGAAAAAGAAAGAAA
12840269 AAA
1 AAA
12840272 TTGGGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 12 0.33
21 21 0.58
22 2 0.06
23 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (20 bp):
AAAAATGAAAAAGAAAGAAA
Found at i:12841370 original size:24 final size:24
Alignment explanation
Indices: 12841334--12841379 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
12841324 CCAATTAGGA
12841334 AATTACTGTTTAG-ATTTAATTCT
1 AATTACTGTTTAGAATTTAATTCT
*
12841357 AATTATCTTTTTAGAATTTAATT
1 AATTA-CTGTTTAGAATTTAATT
12841380 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTACTGTTTAGAATTTAATTCT
Found at i:12853084 original size:27 final size:27
Alignment explanation
Indices: 12853052--12853109 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
12853042 TGTAACTTGA
12853052 GTGGTCGTTAGCCGGAGAGTCACTTAG
1 GTGGTCGTTAGCCGGAGAGTCACTTAG
12853079 GTGGTCGTTAGCCGGAGAGTCACTTAG
1 GTGGTCGTTAGCCGGAGAGTCACTTAG
12853106 GTGG
1 GTGG
12853110 CTAATGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.26
Consensus pattern (27 bp):
GTGGTCGTTAGCCGGAGAGTCACTTAG
Found at i:12858930 original size:20 final size:20
Alignment explanation
Indices: 12858905--12858945 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12858895 TTCATCATCT
12858905 TCATGAACTGATTTTTCGAA
1 TCATGAACTGATTTTTCGAA
12858925 TCATGAACTGATTTTTCGAA
1 TCATGAACTGATTTTTCGAA
12858945 T
1 T
12858946 TTTCGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TCATGAACTGATTTTTCGAA
Found at i:12861706 original size:23 final size:24
Alignment explanation
Indices: 12861663--12861708 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
12861653 TAGGATAGAT
12861663 TGAAGATTTGAAGCTAAAATTTGC
1 TGAAGATTTGAAGCTAAAATTTGC
12861687 TGAAGAGTTTGAA-C-AAAATTTG
1 TGAAGA-TTTGAAGCTAAAATTTG
12861709 GATAACACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 7 0.33
25 6 0.29
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (24 bp):
TGAAGATTTGAAGCTAAAATTTGC
Found at i:12862569 original size:57 final size:57
Alignment explanation
Indices: 12862508--12862674 Score: 212
Period size: 57 Copynumber: 2.9 Consensus size: 57
12862498 TTGACCGGTG
** * * *
12862508 AAAAACGTCACGAAAAGTTATTTTTGGTGACGTCTAAAAACGTCACAAAA-AATACAA
1 AAAAACGTCACGAAAAAATAGTTTTGGTGATGTTTAAAAACGTCACAAAATAATAC-A
* * * *
12862565 AAAAAGGTAACGAAAAAATAGTTATGGTGATGTTTAAAAACATCACAAAATAATACA
1 AAAAACGTCACGAAAAAATAGTTTTGGTGATGTTTAAAAACGTCACAAAATAATACA
* *
12862622 ACAAACGTCAGGAAAAAATAGTTTTGGTGATGTTTAAAAACGTCAC-AAATAAT
1 AAAAACGTCACGAAAAAATAGTTTTGGTGATGTTTAAAAACGTCACAAAATAAT
12862675 TTTAGTAAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
56 7 0.07
57 82 0.87
58 5 0.05
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (57 bp):
AAAAACGTCACGAAAAAATAGTTTTGGTGATGTTTAAAAACGTCACAAAATAATACA
Found at i:12867731 original size:32 final size:32
Alignment explanation
Indices: 12867672--12867737 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
12867662 GACACATGAA
*
12867672 AATGCAATGACAATGCACATGTAGTGACAATT
1 AATGCAATGACAAGGCACATGTAGTGACAATT
* *
12867704 AATGCAATGACAAAGGGA-ATGTGGTGACAATT
1 AATGCAATGAC-AAGGCACATGTAGTGACAATT
12867736 AA
1 AA
12867738 ATTACAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (32 bp):
AATGCAATGACAAGGCACATGTAGTGACAATT
Found at i:12877917 original size:9 final size:9
Alignment explanation
Indices: 12877903--12877929 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12877893 AGTGCAAGAT
12877903 CTTATAGTA
1 CTTATAGTA
12877912 CTTATAGTA
1 CTTATAGTA
12877921 CTTATAGTA
1 CTTATAGTA
12877930 TTGCAAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (9 bp):
CTTATAGTA
Found at i:12877942 original size:18 final size:19
Alignment explanation
Indices: 12877895--12877943 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
12877885 GAAGGTTAAG
12877895 TGCAAGATCTTATAGTACT
1 TGCAAGATCTTATAGTACT
12877914 T--ATAG-TACTTATAGTA-T
1 TGCA-AGAT-CTTATAGTACT
12877931 TGCAAGATCTTAT
1 TGCAAGATCTTAT
12877944 CTATGTGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
17 4 0.16
18 18 0.72
19 3 0.12
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (19 bp):
TGCAAGATCTTATAGTACT
Found at i:12878155 original size:21 final size:22
Alignment explanation
Indices: 12878131--12878185 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12878121 TAAAGCTATG
*
12878131 AAAAGCGTCACAAAAAG-ATCT
1 AAAAACGTCACAAAAAGTATCT
* *
12878152 AAAAATGTCACAAAAAGTATTT
1 AAAAACGTCACAAAAAGTATCT
*
12878174 AAAAACGGCACA
1 AAAAACGTCACA
12878186 GAAATTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (22 bp):
AAAAACGTCACAAAAAGTATCT
Found at i:12878185 original size:22 final size:21
Alignment explanation
Indices: 12878139--12878185 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
12878129 TGAAAAGCGT
* *
12878139 CACAAAAAGATCTAAAAATGT
1 CACAAAAAGATCTAAAAACGG
*
12878160 CACAAAAAGTATTTAAAAACGG
1 CACAAAAAG-ATCTAAAAACGG
12878182 CACA
1 CACA
12878186 GAAATTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (21 bp):
CACAAAAAGATCTAAAAACGG
Found at i:12878455 original size:14 final size:14
Alignment explanation
Indices: 12878436--12878464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12878426 CGTTTAAGTA
12878436 AACGTCACAAAAAG
1 AACGTCACAAAAAG
12878450 AACGTCACAAAAAG
1 AACGTCACAAAAAG
12878464 A
1 A
12878465 CTACTTTTCC
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:0.59, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGTCACAAAAAG
Found at i:12879057 original size:44 final size:44
Alignment explanation
Indices: 12878997--12879086 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
12878987 AGTATTTAAG
12878997 AAAAGTTTTCCAGAACATTCCATTCAAAATACTATATTCTTTTT
1 AAAAGTTTTCCAGAACATTCCATTCAAAATACTATATTCTTTTT
12879041 AAAAGTTTTCCAGAACATTCCATTCAAAATACTATATTCTTTTT
1 AAAAGTTTTCCAGAACATTCCATTCAAAATACTATATTCTTTTT
12879085 AA
1 AA
12879087 CTTCTTGTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (44 bp):
AAAAGTTTTCCAGAACATTCCATTCAAAATACTATATTCTTTTT
Found at i:12887968 original size:15 final size:15
Alignment explanation
Indices: 12887944--12888079 Score: 91
Period size: 15 Copynumber: 9.1 Consensus size: 15
12887934 GCTTGGAAGA
*
12887944 TGCGAGCACTAGTGT
1 TGCGAACACTAGTGT
12887959 TGCGAACACTCA-TGT
1 TGCGAACACT-AGTGT
* * * *
12887974 TGAGAACACTGGAGC
1 TGCGAACACTAGTGT
12887989 TGCGAACACT-GATGT
1 TGCGAACACTAG-TGT
*
12888004 TGTGAACACTAGTGT
1 TGCGAACACTAGTGT
*
12888019 TGCGAGCACTCA-TGT
1 TGCGAACACT-AGTGT
* * *
12888034 TGCGAACACTGGAGC
1 TGCGAACACTAGTGT
*
12888049 TGCGATCACT-GATGT
1 TGCGAACACTAG-TGT
* *
12888064 TGTGAACACTCGTGT
1 TGCGAACACTAGTGT
12888079 T
1 T
12888080 ACGAGCATGG
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
14 2 0.02
15 87 0.94
16 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (15 bp):
TGCGAACACTAGTGT
Found at i:12887995 original size:30 final size:30
Alignment explanation
Indices: 12887959--12888073 Score: 149
Period size: 30 Copynumber: 3.8 Consensus size: 30
12887949 GCACTAGTGT
*
12887959 TGCGAACACTCATGTTGAGAACACTGGAGC
1 TGCGAACACTCATGTTGTGAACACTGGAGC
* * * *
12887989 TGCGAACACTGATGTTGTGAACACTAGTGT
1 TGCGAACACTCATGTTGTGAACACTGGAGC
* *
12888019 TGCGAGCACTCATGTTGCGAACACTGGAGC
1 TGCGAACACTCATGTTGTGAACACTGGAGC
* *
12888049 TGCGATCACTGATGTTGTGAACACT
1 TGCGAACACTCATGTTGTGAACACT
12888074 CGTGTTACGA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (30 bp):
TGCGAACACTCATGTTGTGAACACTGGAGC
Found at i:12888043 original size:60 final size:60
Alignment explanation
Indices: 12887950--12888086 Score: 229
Period size: 60 Copynumber: 2.3 Consensus size: 60
12887940 AAGATGCGAG
*
12887950 CACTAGTGTTGCGAACACTCATGTTGAGAACACTGGAGCTGCGAACACTGATGTTGTGAA
1 CACTAGTGTTGCGAGCACTCATGTTGAGAACACTGGAGCTGCGAACACTGATGTTGTGAA
* *
12888010 CACTAGTGTTGCGAGCACTCATGTTGCGAACACTGGAGCTGCGATCACTGATGTTGTGAA
1 CACTAGTGTTGCGAGCACTCATGTTGAGAACACTGGAGCTGCGAACACTGATGTTGTGAA
* *
12888070 CACTCGTGTTACGAGCA
1 CACTAGTGTTGCGAGCA
12888087 TGGATGAAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (60 bp):
CACTAGTGTTGCGAGCACTCATGTTGAGAACACTGGAGCTGCGAACACTGATGTTGTGAA
Found at i:12890272 original size:28 final size:28
Alignment explanation
Indices: 12890236--12890291 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
12890226 AAACTAGACT
*
12890236 TCATTTATTTTATTTTAATTAGAATAAG
1 TCATCTATTTTATTTTAATTAGAATAAG
12890264 TCATCTATTTTATTTTAATTAGAATAAG
1 TCATCTATTTTATTTTAATTAGAATAAG
12890292 GTGTTTCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (28 bp):
TCATCTATTTTATTTTAATTAGAATAAG
Found at i:12893254 original size:17 final size:17
Alignment explanation
Indices: 12893232--12893270 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12893222 AGGTGAAGAA
*
12893232 CTTGTTCGTTA-AGAGTT
1 CTTGTTCG-TAGAGAATT
12893249 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
12893266 CTTGT
1 CTTGT
12893271 CAAGGTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:12893317 original size:41 final size:41
Alignment explanation
Indices: 12893260--12893355 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
12893250 TTGTTCGTAG
*
12893260 AGAATTCTTGTCAAGGTGAAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
* *
12893301 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGATT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
12893342 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
12893356 AATAAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
Found at i:12893427 original size:28 final size:28
Alignment explanation
Indices: 12893391--12893446 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12893381 AAACTAGACT
* *
12893391 TCATTTATTTTATTTTAATTAGAATAAG
1 TCATCTATTTCATTTTAATTAGAATAAG
12893419 TCATCTATTTCATTTTAATTAGAATAAG
1 TCATCTATTTCATTTTAATTAGAATAAG
12893447 GTGTTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (28 bp):
TCATCTATTTCATTTTAATTAGAATAAG
Found at i:12898990 original size:30 final size:28
Alignment explanation
Indices: 12898938--12899100 Score: 125
Period size: 29 Copynumber: 5.5 Consensus size: 28
12898928 ACTTAGGACA
12898938 TTCGGGG-AAAAATGGTAATTTTTGGAAGG
1 TTCGGGGTAAAAATGG-AATTTTT-GAAGG
* *
12898967 TTCGGGGTTAAAAATGGAATTTTTAAACG
1 TTCGGGG-TAAAAATGGAATTTTTGAAGG
* **
12898996 TCCGAGGGT-AAAATGGTGTTTTTTGGAAGG
1 TTCG-GGGTAAAAATGG-AATTTTT-GAAGG
*
12899026 TTCGGGGTTAAAAATGGAATTTTT-AAGCA
1 TTCGGGG-TAAAAATGGAATTTTTGAAG-G
* *
12899055 TTCGAGGGTAAAAATGTAATTTTTTGAAAG
1 TTCG-GGGTAAAAATGGAA-TTTTTGAAGG
12899085 TTCGGGGGGTAAAAAT
1 TTC--GGGGTAAAAAT
12899101 ATGATTTTTG
Statistics
Matches: 107, Mismatches: 14, Indels: 24
0.74 0.10 0.17
Matches are distributed among these distances:
28 10 0.09
29 36 0.34
30 33 0.31
31 27 0.25
32 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (28 bp):
TTCGGGGTAAAAATGGAATTTTTGAAGG
Found at i:12899010 original size:59 final size:60
Alignment explanation
Indices: 12898945--12899100 Score: 217
Period size: 59 Copynumber: 2.6 Consensus size: 60
12898935 ACATTCGGGG
*
12898945 AAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAAACGTCCGAGGGT
1 AAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAAACATCCGAGGGT
** * *
12899005 -AAAATGGTGTTTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAAGCATTCGAGGGT
1 AAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAAACATCCGAGGGT
* * *
12899064 AAAAAT-GTAATTTTTTGAAAGTTCGGGGGGTAAAAAT
1 AAAAATGGTAATTTTTGGAAGGTTC-GGGGTTAAAAAT
12899101 ATGATTTTTG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 68 0.81
60 16 0.19
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (60 bp):
AAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAAACATCCGAGGGT
Found at i:12899953 original size:17 final size:17
Alignment explanation
Indices: 12899931--12899964 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12899921 TTTTAAACAG
*
12899931 TGTTTTTTATTATTATT
1 TGTTTTCTATTATTATT
*
12899948 TGTTTTCTGTTATTATT
1 TGTTTTCTATTATTATT
12899965 AAAAAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (17 bp):
TGTTTTCTATTATTATT
Found at i:12900177 original size:15 final size:15
Alignment explanation
Indices: 12900140--12900181 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
12900130 CTTTTTTTCA
* *
12900140 ATTATTAATAATAAT
1 ATTATTATTATTAAT
12900155 ATTATTATTATTAAT
1 ATTATTATTATTAAT
12900170 ATTATTATTATT
1 ATTATTATTATT
12900182 TATTAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATTAAT
Found at i:12900894 original size:6 final size:6
Alignment explanation
Indices: 12900880--12900966 Score: 51
Period size: 6 Copynumber: 15.2 Consensus size: 6
12900870 TAATTGGACA
* *
12900880 TTAAAT TTAATT TTAAAT TTATAA- -TAAAT TTAAAT TTCCAA- -TAAAT
1 TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT TT-AAAT TTAAAT
* * * * *
12900926 TTAAAT TTAAA- ATAAAC ATAATT TTAAA- ATAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
12900967 CTGTTGGGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
4 4 0.06
5 11 0.18
6 43 0.69
7 4 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:12900913 original size:17 final size:17
Alignment explanation
Indices: 12900891--12900966 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
12900881 TAAATTTAAT
*
12900891 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
**
12900908 TTTAAATTTCCAATAAA
1 TTTAAATTTAAAATAAA
12900925 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
** *
12900942 CATAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
12900959 TTTAAATT
1 TTTAAATT
12900967 CTGTTGGGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12901655 original size:201 final size:201
Alignment explanation
Indices: 12901301--12901813 Score: 796
Period size: 201 Copynumber: 2.6 Consensus size: 201
12901291 ATTCAGTCTT
* * * * * * *
12901301 CTTCTCAGCATCTCATCAAGAAGATGACCGCATCGCTTGTTTCAATCTGCTTCTTTGTATCTCAT
1 CTTCTCTGTATCTCATCAAGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
12901366 CAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
*
12901431 CCTACTTCTCAGTATCTCATCAGGAAGCGGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
131 CCTACTTCTCAGTATCTCATCAGGAAGCGGGGGTTCGAAGATTTGCTCGCATTGAGCCTTAAGTT
12901496 GGTATA
196 GGTATA
*
12901502 CTTCTCTGTATCTCATCAAGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGAATCTCAT
1 CTTCTCTGTATCTCATCAAGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
12901567 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
12901632 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCTTTAAGTT
131 CCTACTTCTCAGTATCTCATCAGGAAGCGGGGGTTCGAAGATTTGCTCGCATTGAGCCTTAAGTT
12901697 GGTATA
196 GGTATA
* * * * *
12901703 CTTCTCTGTACCTCATTAGGAAGAT-AATCGCCTCATTTGTTTCAATTCC-CTTCTCTGTATCTC
1 CTTCTCTGTATCTCATCAAGAAGATGACT-GCCTCACTTGTTTCAA-TCCGCTTCTCTGTATCTC
*
12901766 ATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
64 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
12901814 GGGGTTCAAA
Statistics
Matches: 285, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
200 2 0.01
201 280 0.98
202 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAAGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTACTTCTCAGTATCTCATCAGGAAGCGGGGGTTCGAAGATTTGCTCGCATTGAGCCTTAAGTT
GGTATA
Found at i:12914114 original size:59 final size:59
Alignment explanation
Indices: 12914041--12914849 Score: 1069
Period size: 59 Copynumber: 13.7 Consensus size: 59
12914031 ATTCGGGGGC
* * * * * *
12914041 AAAATTGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATCCGATGGC
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* * *
12914100 AAAATGGTATTTTTTTGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* *
12914159 AAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* * * *
12914218 AAAATGGTAA-TTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATCCG-GTGGC
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAG-GGT
* * *
12914276 AAAATGGTATTTTTTTGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
*
12914335 AAAATGGTAATTTTTGGAAGGCTT-GAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGG-TTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* * * *
12914394 AAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATCCG-GTGGC
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAG-GGT
* * *
12914453 AAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGAT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* *
12914512 AAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* * ** * *
12914571 AAAATGGTAATTTTTGGAAGGTTTGAGGTTAAAAATGGAATTTTTAAATGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* * * **
12914630 AAAATGGTGATTTTTGGAAGGTT-TAGAGTTAAAAATGGAATTTTTAAACAT-TTAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAG-GTTAAAAATGGAATTTTTAGACATCCGA-GGGT
* * * *
12914689 AAATTGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAAGTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
* *
12914748 AAAATGATAATTTTTGGAAGGTTC-AGGGTTAAAAATGGAATTTTTAGATAAT-CGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGA-GGTTAAAAATGGAATTTTTAGA-CATCCGAGGGT
* *
12914807 AAAATGGTAATTTTTGGAAGGTTCGGGGTT-AAAATGAAATTTT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTT
12914850 GGAAAGTTTA
Statistics
Matches: 660, Mismatches: 76, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.00
58 67 0.10
59 584 0.88
60 8 0.01
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGGT
Found at i:12914524 original size:177 final size:177
Alignment explanation
Indices: 12914028--12914849 Score: 1237
Period size: 177 Copynumber: 4.7 Consensus size: 177
12914018 GGTAACTTTG
* * *
12914028 GACATTCGGGGGCAAAATTGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
* *
12914093 CGATGGCAAAATGGTATTTTTTTGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
66 CGGTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
12914158 TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
131 TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
12914205 GACATTCGAGGGTAAAATGGTAA-TTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
*
12914269 CGGTGGCAAAATGGTATTTTTTTGAAGGTTTGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
66 CGGTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
*
12914334 TAAAATGGTAATTTTTGGAAGGCTTGAGGTTAAAAATGGAATTTTTA
131 TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
12914381 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
*
12914446 CGGTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGA
66 CGGTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
12914511 TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
131 TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
** * ** *
12914558 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTGAGGTTAAAAATGGAATTTTTAAATGTT
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
* * * * * **
12914623 CGGGGGTAAAATGGTGA-TTTTTGGAAGGTT-TAGAGTTAAAAATGGAATTTTTAAACAT-TTAG
66 CGGTGGCAAAATGGT-ATTTTTTTGAAGGTTCGAG-GTTAAAAATGGAATTTTTAGACATCCGA-
* * *
12914685 GGGTAAATTGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAAGTTTTA
128 GGGTAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
* * * *
12914735 GACATTCGGGGGTAAAATGATAATTTTTGGAAGGTTCAGGGTTAAAAATGGAATTTTTAGATA-A
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTA-A-ACA
* * * * *
12914799 T-CGAG-GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT-AAAATGAAATTTT
64 TCCG-GTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTT
12914850 GGAAAGTTTA
Statistics
Matches: 602, Mismatches: 34, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
176 190 0.32
177 406 0.67
178 5 0.01
179 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (177 bp):
GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAAACATC
CGGTGGCAAAATGGTATTTTTTTGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGAGGG
TAAAATGGTAATTTTTGGAAGGCTCGAGGTTAAAAATGGAATTTTTA
Found at i:12916744 original size:17 final size:17
Alignment explanation
Indices: 12916721--12916796 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
12916711 TAAATTTAAT
*
12916721 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
* **
12916738 ATTAAATTTCCAATAAA
1 TTTAAATTTAAAATAAA
12916755 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
12916772 CTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
12916789 TTTAAATT
1 TTTAAATT
12916797 CTGTTGGGCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12918000 original size:24 final size:23
Alignment explanation
Indices: 12917973--12918017 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
12917963 TGGGGTAGAT
12917973 TGAAGA-TTTGAAGCTAAAATTTAC
1 TGAAGAGTTTGAA-C-AAAATTTAC
12917997 TGAAGAGTTTGAACAAAATTT
1 TGAAGAGTTTGAACAAAATTT
12918018 GGATAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (23 bp):
TGAAGAGTTTGAACAAAATTTAC
Found at i:12926520 original size:31 final size:31
Alignment explanation
Indices: 12926457--12926520 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
12926447 ACAATTAGTT
** *
12926457 ATTTTAGTCACTCCCATTAGGTATGTTATCA
1 ATTTTAGTCACTCCCATTACATAAGTTATCA
* * *
12926488 ATTTTAGTCACTCTCGTTACATAAGTTGTCA
1 ATTTTAGTCACTCCCATTACATAAGTTATCA
12926519 AT
1 AT
12926521 ATTCATCTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (31 bp):
ATTTTAGTCACTCCCATTACATAAGTTATCA
Found at i:12933435 original size:29 final size:30
Alignment explanation
Indices: 12933401--12933468 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
12933391 CGCTTACGTA
*
12933401 CAGTTCGCAGATAAAC-ATCTTGCATACAAT
1 CAGTTCGCAGATAAACAAT-TCGCATACAAT
* *
12933431 -AGTTCACATATAAACAATTCGCATACAAT
1 CAGTTCGCAGATAAACAATTCGCATACAAT
*
12933460 CAGCTCGCA
1 CAGTTCGCA
12933469 TGTGAGCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (30 bp):
CAGTTCGCAGATAAACAATTCGCATACAAT
Found at i:12936091 original size:17 final size:19
Alignment explanation
Indices: 12936058--12936093 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
12936048 CTTAGGATTC
12936058 AATTTAGTCCTTTTTATTT
1 AATTTAGTCCTTTTTATTT
12936077 AATTTAG-CC-TTTTATTT
1 AATTTAGTCCTTTTTATTT
12936094 TCTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTAGTCCTTTTTATTT
Found at i:12936141 original size:30 final size:31
Alignment explanation
Indices: 12936077--12936141 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
12936067 CTTTTTATTT
*
12936077 AATTTAGCCTTTTATTTTCTATTTTTTTTGC
1 AATTTAGCCTTTTATTTTCTATTTTTCTTGC
*
12936108 AATTTAG-GTTTTAATTTTCT-TTATTTCTT-C
1 AATTTAGCCTTTT-ATTTTCTATT-TTTCTTGC
12936138 AATT
1 AATT
12936142 CGTTCCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (31 bp):
AATTTAGCCTTTTATTTTCTATTTTTCTTGC
Found at i:12936213 original size:15 final size:15
Alignment explanation
Indices: 12936181--12936249 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
12936171 ATTCGATCCC
* * *
12936181 TTATTTTATGTTTCT
1 TTATTTTTTATTTAT
*
12936196 TTATTTTTTATGTAT
1 TTATTTTTTATTTAT
*
12936211 TTATTATTTATTTAT
1 TTATTTTTTATTTAT
*
12936226 TTGTCTTTTTATTTTAT
1 TTAT-TTTTTA-TTTAT
12936243 TTATTTT
1 TTATTTT
12936250 CTAGTATATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
15 27 0.63
16 8 0.19
17 8 0.19
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.75
Consensus pattern (15 bp):
TTATTTTTTATTTAT
Found at i:12936221 original size:4 final size:4
Alignment explanation
Indices: 12936195--12936248 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
12936185 TTTATGTTTC
* *
12936195 TTTA TTT- TTTA TGTA TTTA -TTA TTTA TTTA TTTG TCTT- TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA -TTTA
12936242 TTTA TTT
1 TTTA TTT
12936249 TCTAGTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
3 8 0.19
4 28 0.67
5 6 0.14
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:12936243 original size:21 final size:21
Alignment explanation
Indices: 12936195--12936248 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
12936185 TTTATGTTTC
*
12936195 TTTATTTTTTATGTATTTATTA
1 TTTATTTATT-TGTATTTATTA
*
12936217 TTTATTTATTTGTCTTT-TTA
1 TTTATTTATTTGTATTTATTA
12936237 TTTTATTTATTT
1 -TTTATTTATTT
12936249 TCTAGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.10
21 17 0.59
22 9 0.31
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTATTTATTTGTATTTATTA
Found at i:12936259 original size:21 final size:21
Alignment explanation
Indices: 12936217--12936260 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12936207 GTATTTATTA
* *
12936217 TTTATTTATTTGTCTTTTTAT
1 TTTATTTATTTGTCTGTATAT
12936238 TTTATTTATTT-TCTAGTATAT
1 TTTATTTATTTGTCT-GTATAT
12936259 TT
1 TT
12936261 AATCTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTATTTATTTGTCTGTATAT
Found at i:12940081 original size:14 final size:15
Alignment explanation
Indices: 12940062--12940094 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12940052 ACGGGCTTTA
*
12940062 AAAAAAAGGAAA-AG
1 AAAAAAAGAAAACAG
12940076 AAAAAAAGAAAACAG
1 AAAAAAAGAAAACAG
12940091 AAAA
1 AAAA
12940095 GGAGAGATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAACAG
Found at i:12941593 original size:100 final size:99
Alignment explanation
Indices: 12941386--12941724 Score: 344
Period size: 100 Copynumber: 3.4 Consensus size: 99
12941376 CCCAAAAGAT
* * * * *
12941386 AGTGGAGAAAGATGAAGCTACAACATCATATCCTATATCC-TAAAGTTGTAG-GGATCATATTAA
1 AGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTAAA-TTGTAGTGGGTCAGATTGA
* * *
12941449 AACTACAGTAGCAAATCATTATCT-CTCTGAAGTTGC
65 AGCTACAGAAGCAAAT-ATTATCTCCT-TGAAGATGC
*
12941485 AGTAGAGCAAGATGAAGCTACAACATCAAATCCTATA-CCTGTGAAATTGTAGTGGGTCAGATTG
1 AGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCT-T-AAATTGTAGTGGGTCAGATTG
*
12941549 AAGCTATAGAAGCAAATATTATCTCCTTGAAGATGC
64 AAGCTACAGAAGCAAATATTATCTCCTTGAAGATGC
** ** * * * *
12941585 AGTGGAGCAAGATGAATTTATGACATCAAATCCTATATCCCTTAAGTTATAGTTGGTTAGATTGA
1 AGTGGAGCAAGATGAAGCTACAACATCAAATCCTATAT-CCTTAAATTGTAGTGGGTCAGATTGA
* * * * *
12941650 AGCTACAAAAGCAAATCTTATCTCCCTGAATATGA
65 AGCTACAGAAGCAAATATTATCTCCTTGAAGATGC
* * * * *
12941685 AATGGAGCAAAATGAAGTTACGACATCAAATCCTACATCC
1 AGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCC
12941725 CTGAAGTTGC
Statistics
Matches: 203, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
98 2 0.01
99 36 0.18
100 134 0.66
101 28 0.14
102 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (99 bp):
AGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTAAATTGTAGTGGGTCAGATTGAA
GCTACAGAAGCAAATATTATCTCCTTGAAGATGC
Found at i:12941751 original size:100 final size:99
Alignment explanation
Indices: 12941355--12941755 Score: 339
Period size: 100 Copynumber: 4.0 Consensus size: 99
12941345 GGAATGAAAT
* ** * * * * *
12941355 TACAAACAACAAATCTTATCTCCCAAAAGAT--AGTGGAGAAAGATGAAGCTACAACATCATATC
1 TACAAA-AGCAAATCTTATCTCCCTGAATATGCAGTGGAGCAAGATGAAGTTACGACATCAAATC
* * * * *
12941418 CTATAT-CCTAAAGTTGTAG-GGATCATATTAAAAC
65 CTATATCCCTGAAGTTGTAGTGG-GCAGATTGAAGC
** * * * *
12941452 TACAGTAGCAAATCATTATCTCTCTGAAGT-TGCAGTAGAGCAAGATGAAGCTACAACATCAAAT
1 TACAAAAGCAAATC-TTATCTCCCTGAA-TATGCAGTGGAGCAAGATGAAGTTACGACATCAAAT
* *
12941516 CCTATA-CCTGTGAAATTGTAGTGGGTCAGATTGAAGC
64 CCTATATCC-CTGAAGTTGTAGTGGG-CAGATTGAAGC
* * * * * * *
12941553 TATAGAAGCAAATATTATCTCCTTGAAGATGCAGTGGAGCAAGATGAATTTATGACATCAAATCC
1 TACAAAAGCAAATCTTATCTCCCTGAATATGCAGTGGAGCAAGATGAAGTTACGACATCAAATCC
* * **
12941618 TATATCCCTTAAGTTATAGTTGGTTAGATTGAAGC
66 TATATCCCTGAAGTTGTAG-TGGGCAGATTGAAGC
* * *
12941653 TACAAAAGCAAATCTTATCTCCCTGAATATGAAATGGAGCAAAATGAAGTTACGACATCAAATCC
1 TACAAAAGCAAATCTTATCTCCCTGAATATGCAGTGGAGCAAGATGAAGTTACGACATCAAATCC
* *
12941718 TACATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGC
66 TATATCCCTGAAGTTGTAGTGG-GC-AGATTGAAGC
12941753 TAC
1 TAC
12941756 CACACCAAAT
Statistics
Matches: 241, Mismatches: 50, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
96 7 0.03
97 15 0.06
99 38 0.16
100 152 0.63
101 29 0.12
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (99 bp):
TACAAAAGCAAATCTTATCTCCCTGAATATGCAGTGGAGCAAGATGAAGTTACGACATCAAATCC
TATATCCCTGAAGTTGTAGTGGGCAGATTGAAGC
Found at i:12941765 original size:50 final size:50
Alignment explanation
Indices: 12941475--12941790 Score: 171
Period size: 50 Copynumber: 6.3 Consensus size: 50
12941465 CATTATCTCT
* *
12941475 CTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATA-CC
1 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTACATCC
* * * * * **
12941524 TGTGAAATTGTAGTGG-GTC-AGATTGAAGCTATAGA-AGCAAATATTATC-TCC
1 -CTGAAGTTGCAGTGGAG-CAAGA-TGAAGCTACA-ACATCAAATCCTA-CATCC
* * ** ** *
12941575 TTGAAGATGCAGTGGAGCAAGATGAATTTATGACATCAAATCCTATATCC
1 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTACATCC
* ** * ** * * *
12941625 CTTAAGTTATAGTTG-GTTAGATTGAAGCTACAAAAGCAAATCTTATC-TCC
1 CTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAACATCAAATCCTA-CATCC
* * * * *
12941675 CTGAA-TATGAAATGGAGCAAAATGAAGTTACGACATCAAATCCTACATCC
1 CTGAAGT-TGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTACATCC
* * * *
12941725 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCATATATCC
1 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTACATCC
* * *
12941775 TTAAAGTTGTAGTGGA
1 CTGAAGTTGCAGTGGA
12941791 TTGGATTGAA
Statistics
Matches: 191, Mismatches: 60, Indels: 30
0.68 0.21 0.11
Matches are distributed among these distances:
49 11 0.06
50 169 0.88
51 11 0.06
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (50 bp):
CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTACATCC
Found at i:12941815 original size:100 final size:100
Alignment explanation
Indices: 12941711--12942047 Score: 317
Period size: 100 Copynumber: 3.4 Consensus size: 100
12941701 GTTACGACAT
* * *
12941711 CAAATCCTA-CATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCATATATCC
1 CAAATCCTATC-TCTCTGAAGATGCAGTAGAGCAAGATGAAGCTACCACACCAAATCATATATCC
*
12941775 TTAAAGTTGTAGTGGATTGGATTGAAACTGCAATGA
65 TTAAAGTTGTAGTGGATTGGATTGAAACTACAATGA
* * * * * *
12941811 CAAATCTTTATCTCTCTAAAGTTGCAGTAGAG-TA-ATGAAACTACCACACCAAATCTTATAT-C
1 CAAATC-CTATCTCTCTGAAGATGCAGTAGAGCAAGATGAAGCTACCACACCAAATCATATATCC
* * * * *
12941873 TCTGAAGTTGTAGTGGATCGAATTGAAGCTACGAAAG-
65 T-TAAAGTTGTAGTGGATTGGATTGAAACTAC-AATGA
* * * * * * *** * *
12941910 CAAATCTTATCTCTCTGAAGATGCAATAGGGCAAAATGAAGTTACAATGTCAAATCCTATATCCC
1 CAAATCCTATCTCTCTGAAGATGCAGTAGAGCAAGATGAAGCTACCACACCAAATCATATATCCT
* * *
12941975 TAAAGTTGCAATGGATTGGATTGAAACTAC-ATTA
66 TAAAGTTGTAGTGGATTGGATTGAAACTACAATGA
*
12942009 GCAAATCCTATCTCTCTGAAGATGGAGTAGAGCAAGATG
1 -CAAATCCTATCTCTCTGAAGATGCAGTAGAGCAAGATG
12942048 CAGTAACAAT
Statistics
Matches: 189, Mismatches: 39, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
98 24 0.13
99 57 0.30
100 87 0.46
101 20 0.11
102 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (100 bp):
CAAATCCTATCTCTCTGAAGATGCAGTAGAGCAAGATGAAGCTACCACACCAAATCATATATCCT
TAAAGTTGTAGTGGATTGGATTGAAACTACAATGA
Found at i:12941914 original size:50 final size:50
Alignment explanation
Indices: 12941645--12941934 Score: 151
Period size: 50 Copynumber: 5.8 Consensus size: 50
12941635 AGTTGGTTAG
* * * * * *
12941645 ATTGAAGCTACAAAAGCAAATCTTATCTCCCTGAA-TATGAAATGGAGCAA
1 ATTGAAGCTACCAAAGCAAATCTTATATCTCTGAAGT-TGCAGTGGAGCGA
* * * * * * * *
12941695 AATGAAGTTACGACATCAAATCCTACATCCCTGAAGTTGCAGTGGAGC-A
1 ATTGAAGCTACCAAAGCAAATCTTATATCTCTGAAGTTGCAGTGGAGCGA
* * * * * * ** *
12941744 AGATGAAGCTACCACACCAAATCATATATC-CTTAAAGTTGTAGTGGATTGG
1 A-TTGAAGCTACCAAAGCAAATCTTATATCTC-TGAAGTTGCAGTGGAGCGA
* * * * * * *
12941795 ATTGAAACT-GCAATGACAAATCTTTATCTCTCTAAAGTTGCAGTAGAG-TA
1 ATTGAAGCTACCAAAG-CAAATC-TTATATCTCTGAAGTTGCAGTGGAGCGA
* * * * *
12941845 A-TGAAACTACCACACCAAATCTTATATCTCTGAAGTTGTAGTGGATCGA
1 ATTGAAGCTACCAAAGCAAATCTTATATCTCTGAAGTTGCAGTGGAGCGA
* * *
12941894 ATTGAAGCTACGAAAGCAAATCTTATCTCTCTGAAGATGCA
1 ATTGAAGCTACCAAAGCAAATCTTATATCTCTGAAGTTGCA
12941935 ATAGGGCAAA
Statistics
Matches: 180, Mismatches: 50, Indels: 20
0.72 0.20 0.08
Matches are distributed among these distances:
48 20 0.11
49 20 0.11
50 119 0.66
51 20 0.11
52 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (50 bp):
ATTGAAGCTACCAAAGCAAATCTTATATCTCTGAAGTTGCAGTGGAGCGA
Found at i:12942082 original size:349 final size:349
Alignment explanation
Indices: 12941386--12942067 Score: 777
Period size: 349 Copynumber: 2.0 Consensus size: 349
12941376 CCCAAAAGAT
* * * *
12941386 AGTGGAGAAAGATGAAGCTACAACATCATATCCTATATCCTAAAGTTGTAGGGATCATATTAAAA
1 AGTGGAGAAAGATGAAGCTACAACACCAAATCATATATCCTAAAGTTGTAGGGATCAGATTAAAA
* * * *
12941451 CTACAGTAGCAAATCATTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAAT
66 CTACAATAGCAAATCATTATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAACTACAACACCAAAT
* * *
12941516 CCTATACCTGTGAAATTGTAGTGGGTCAGATTGAAGCTATAGAAGCAAATATTATCTCCTTGAAG
131 CCTATACCTCTGAAATTGTAGTGGATCAGATTGAAGCTAGAGAAGCAAATATTATCTCCTTGAAG
* * * ** * * *
12941581 ATGCAGTGGAGCAAGATGAATTTATGACATCAAATCCTATATCCCTTAAGTTATAGTTGGTTAGA
196 ATGCAATGGAGCAAAATGAAGTTACAACATCAAATCCTATATCCCTAAAGTTACAGATGGTTAGA
* * * * * *
12941646 TTGAAGCTACAAAAGCAAATCTTATCTCCCTGAATATGAAATGGAGCAAAATGAAGTTACGACAT
261 TTGAAACTACAAAAGCAAATCCTATCTCCCTGAAGATGAAATAGAGCAAAATGAAGTAACAACAT
12941711 CAAATCCTACATCCCTGAAGTTGC
326 CAAATCCTACATCCCTGAAGTTGC
* * ** *
12941735 AGTGGAGCAAGATGAAGCTACCACACCAAATCATATATCCTTAAAGTTGTAGTGGATTGGATTGA
1 AGTGGAGAAAGATGAAGCTACAACACCAAATCATATATCC-TAAAGTTGTAG-GGATCAGATTAA
* * * *
12941800 AACTGCAAT-GACAAATCTTTATCTCTCTAAAGTTGCAGTAGAG-TA-ATGAAACTACCACACCA
64 AACTACAATAG-CAAATCATTATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAACTACAACACCA
* * * *
12941862 AATCTTATATCTCTGAAGTTGTAGTGGATC-GAATTGAAGCTACGA-AAGCAAATCTTATCT-CT
128 AATCCTATACCTCTGAAATTGTAGTGGATCAG-ATTGAAGCTA-GAGAAGCAAATATTATCTCCT
** *
12941924 CTGAAGATGCAATAGG-GCAAAATGAAGTTACAATGTCAAATCCTATATCCCTAAAGTTGCA-AT
191 -TGAAGATGCAAT-GGAGCAAAATGAAGTTACAACATCAAATCCTATATCCCTAAAGTTACAGAT
* ** * * * * *
12941987 GGATTGGATTGAAACTACATTAGCAAATCCTATCTCTCTGAAGATGGAGTAGAGCAAGATGCAGT
254 GG-TTAGATTGAAACTACAAAAGCAAATCCTATCTCCCTGAAGATGAAATAGAGCAAAATGAAGT
**
12942052 AACAATGTCAAATCCT
318 AACAACATCAAATCCT
12942068 GTCTTCCTGA
Statistics
Matches: 274, Mismatches: 51, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
348 6 0.02
349 207 0.76
350 16 0.06
351 45 0.16
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (349 bp):
AGTGGAGAAAGATGAAGCTACAACACCAAATCATATATCCTAAAGTTGTAGGGATCAGATTAAAA
CTACAATAGCAAATCATTATCTCTCTAAAGTTGCAGTAGAGCAAGATGAAACTACAACACCAAAT
CCTATACCTCTGAAATTGTAGTGGATCAGATTGAAGCTAGAGAAGCAAATATTATCTCCTTGAAG
ATGCAATGGAGCAAAATGAAGTTACAACATCAAATCCTATATCCCTAAAGTTACAGATGGTTAGA
TTGAAACTACAAAAGCAAATCCTATCTCCCTGAAGATGAAATAGAGCAAAATGAAGTAACAACAT
CAAATCCTACATCCCTGAAGTTGC
Found at i:12943846 original size:31 final size:31
Alignment explanation
Indices: 12943786--12943855 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
12943776 CAATTTAGGT
* *
12943786 TTTAATTTTCTTTATTTCTTCAATTCGATCC
1 TTTAATTTTCATTATTTCTTCAATCCGATCC
12943817 TTTAATATTTCATTATTT-TT-ACATCCGATCC
1 TTTAAT-TTTCATTATTTCTTCA-ATCCGATCC
*
12943848 CTT-ATTTT
1 TTTAATTTT
12943856 ATGTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 3 0.09
30 3 0.09
31 18 0.53
32 10 0.29
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.57
Consensus pattern (31 bp):
TTTAATTTTCATTATTTCTTCAATCCGATCC
Found at i:12948738 original size:29 final size:29
Alignment explanation
Indices: 12948661--12948748 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
12948651 TCGTGGAAGA
* * *
12948661 GGTGGAGAACTTGTTCGTTAAGAGTTTAT
1 GGTGAAGAACTTGTTCGTTGAGAGTTTGT
*
12948690 GGTGAAGAACTTGTTTGTTGAGAGTTTGT
1 GGTGAAGAACTTGTTCGTTGAGAGTTTGT
* *
12948719 GGTGAAGAACTTGTTCGTTGTGAATTTGT
1 GGTGAAGAACTTGTTCGTTGAGAGTTTGT
12948748 G
1 G
12948749 TCAAGGTGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.40
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTGAGAGTTTGT
Found at i:12957081 original size:23 final size:25
Alignment explanation
Indices: 12957055--12957111 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
12957045 TTTCTTACTC
12957055 TTTTCTTTTTGTAT-TTCT-ACTTAT
1 TTTTCTTTTTGT-TCTTCTCACTTAT
* *
12957079 TTTT-ATTTTGTTCTTTTCACTTAT
1 TTTTCTTTTTGTTCTTCTCACTTAT
12957103 TTTTCTTTT
1 TTTTCTTTT
12957112 CTTTGGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 9 0.33
24 14 0.52
25 3 0.11
ACGTcount: A:0.11, C:0.12, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTCTTTTTGTTCTTCTCACTTAT
Found at i:12961477 original size:20 final size:20
Alignment explanation
Indices: 12961452--12961500 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12961442 ATATGAAAGC
*
12961452 ATAAAATAATA-AAAATAAAA
1 ATAAAATAAGACAAAAT-AAA
12961472 ATAAAA-AAGACGAAAATAAA
1 ATAAAATAAGAC-AAAATAAA
12961492 ATAAAATAA
1 ATAAAATAA
12961501 AAATGAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (20 bp):
ATAAAATAAGACAAAATAAA
Done.