Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008983.1 Hibiscus syriacus cultivar Beakdansim tig00112347_pilon, whole genome shotgun sequence
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: 1350231
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1082682 original size:50 final size:49
Alignment explanation
Indices: 1082562--1082682 Score: 124
Period size: 50 Copynumber: 2.4 Consensus size: 49
1082552 TATTAATATT
*
1082562 TATAATAAT-ATAATATTATATTTTAGTTTAATAATATAATCAATTATA
1 TATAATAATAATAATATTATTTTTTAGTTTAATAATATAATCAATTATA
* * * *
1082610 TAATAAT-ATAA-GATATTATATTTTTTATTTTAATAATATAAT-ATTTTTTA
1 T-ATAATAATAATAATA-T-TATTTTTTAGTTTAATAATATAATCA-ATTATA
1082660 TATAATAATGAATAATATTATTT
1 TATAATAAT-AATAATATTATTT
1082683 ATATATTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
48 6 0.10
49 13 0.22
50 34 0.58
51 3 0.05
52 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (49 bp):
TATAATAATAATAATATTATTTTTTAGTTTAATAATATAATCAATTATA
Found at i:1082685 original size:22 final size:21
Alignment explanation
Indices: 1082633--1082685 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1082623 TATTATATTT
1082633 TTTATTT-TAATAATATAATA
1 TTTATTTATAATAATATAATA
*
1082653 TTTTTTATATAATAATGAATAATA
1 TTTATT-TATAATAAT--ATAATA
1082677 -TTATTTATA
1 TTTATTTATA
1082686 TATTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 11 0.41
23 4 0.15
24 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTATTTATAATAATATAATA
Found at i:1083074 original size:20 final size:20
Alignment explanation
Indices: 1083014--1083065 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1083004 CATCATAAAA
* *
1083014 CATTTTCCAGAAATGTAATT
1 CATTTTACAGAAATATAATT
1083034 CATTTTACAGAAATATAATT
1 CATTTTACAGAAATATAATT
*
1083054 CATTTTTCAGAA
1 CATTTTACAGAA
1083066 TTCAAATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (20 bp):
CATTTTACAGAAATATAATT
Found at i:1083082 original size:29 final size:30
Alignment explanation
Indices: 1083049--1083120 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1083039 TACAGAAATA
*
1083049 TAATTCATTTTTCAG-AATTCAAATTCTAG
1 TAATTCATTTTTCAGTAATTCAAATTCCAG
1083078 TAATTCATTTTTCAGTAATTCAAATTCCAG
1 TAATTCATTTTTCAGTAATTCAAATTCCAG
1083108 TAATTCATTTTTC
1 TAATTCATTTTTC
1083121 GAAAAACCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (30 bp):
TAATTCATTTTTCAGTAATTCAAATTCCAG
Found at i:1083084 original size:15 final size:15
Alignment explanation
Indices: 1083064--1083114 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1083054 CATTTTTCAG
1083064 AATTCAAATTCTAGT
1 AATTCAAATTCTAGT
* *
1083079 AATTC-ATTTTTCAGT
1 AATTCAAATTCT-AGT
*
1083094 AATTCAAATTCCAGT
1 AATTCAAATTCTAGT
1083109 AATTCA
1 AATTCA
1083115 TTTTTCGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 4 0.14
15 22 0.76
16 3 0.10
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTCTAGT
Found at i:1090989 original size:18 final size:18
Alignment explanation
Indices: 1090966--1091008 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1090956 AAATATGGTT
* *
1090966 ATCATAAGTGTTATTGTC
1 ATCATAAGTGCTACTGTC
*
1090984 ATCATAGGTGCTACTGTC
1 ATCATAAGTGCTACTGTC
1091002 ATCATAA
1 ATCATAA
1091009 ATTTGACATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (18 bp):
ATCATAAGTGCTACTGTC
Found at i:1095903 original size:15 final size:15
Alignment explanation
Indices: 1095883--1095919 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1095873 TACGTAATGC
1095883 ACTCCTCCGTCATAA
1 ACTCCTCCGTCATAA
1095898 ACTCCTCCGTCATAA
1 ACTCCTCCGTCATAA
1095913 ACTCCTC
1 ACTCCTC
1095920 TGTACGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.43, G:0.05, T:0.27
Consensus pattern (15 bp):
ACTCCTCCGTCATAA
Found at i:1102284 original size:11 final size:12
Alignment explanation
Indices: 1102258--1102299 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1102248 GCTACGATTC
1102258 TTTTAAAATGAT
1 TTTTAAAATGAT
1102270 TTTTAAAATGAT
1 TTTTAAAATGAT
*
1102282 TTTAAAAGAT-AT
1 TTTTAAA-ATGAT
1102294 TTTTAA
1 TTTTAA
1102300 GTATTCGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 25 0.93
13 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TTTTAAAATGAT
Found at i:1106362 original size:20 final size:21
Alignment explanation
Indices: 1106332--1106375 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1106322 TAATCTCTAT
1106332 TTTTATTAAATAAAAATAATA
1 TTTTATTAAATAAAAATAATA
* *
1106353 TTTT-TTAAATAAATATATTA
1 TTTTATTAAATAAAAATAATA
1106373 TTT
1 TTT
1106376 CAGACCGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTATTAAATAAAAATAATA
Found at i:1106698 original size:23 final size:23
Alignment explanation
Indices: 1106672--1106731 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1106662 ATCAAATACA
*
1106672 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** *
1106695 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
* *
1106718 ATAATAAAATAGGT
1 ATAACATAATAGGT
1106732 TAATTACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:1106804 original size:87 final size:87
Alignment explanation
Indices: 1106653--1106818 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
1106643 TCATTTAACC
* * * *
1106653 GGAAACATTATCAAATACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTAT
1 GGAAACATTATCAAACACAATAACATATTAGGTAACACTTATATAATGTAATAGGTAGCACTTAT
1106718 ATAATAAAATAGGTTAATTACT
66 ATAATAAAATAGGTTAATTACT
* *
1106740 GGAAACATTATCAAGCACAATAACATATTAGGTAATACTTATATAATGTAATAGGTAGCACTTAT
1 GGAAACATTATCAAACACAATAACATATTAGGTAACACTTATATAATGTAATAGGTAGCACTTAT
**
1106805 ATAATGTAATAGGT
66 ATAATAAAATAGGT
1106819 AACGCTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (87 bp):
GGAAACATTATCAAACACAATAACATATTAGGTAACACTTATATAATGTAATAGGTAGCACTTAT
ATAATAAAATAGGTTAATTACT
Found at i:1106830 original size:25 final size:23
Alignment explanation
Indices: 1106768--1106841 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
1106758 AATAACATAT
*
1106768 TAGGTAATACTTATATAATGTAA
1 TAGGTAACACTTATATAATGTAA
*
1106791 TAGGTAGCACTTATATAATGTAA
1 TAGGTAACACTTATATAATGTAA
* **
1106814 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACACTTATATAATGTAA
1106837 TAGGT
1 TAGGT
1106842 TAATTACTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (23 bp):
TAGGTAACACTTATATAATGTAA
Found at i:1106915 original size:110 final size:110
Alignment explanation
Indices: 1106672--1106917 Score: 375
Period size: 110 Copynumber: 2.2 Consensus size: 110
1106662 ATCAAATACA
* * * *
1106672 ATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAACGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
* *
1106737 ACTGGAAACATTATCAAGCACAATAACATATTAGGTAATACTTAT
66 ACTGGAAACATTATCAAGCACAATAACATATTAGCTAACACTTAT
* * *
1106782 ATAATGTAATAGGTAGCACTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAACGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
* * *
1106847 ACTTGAAACATTATCAAGCACAATAACATATTAGCTAGCGCTTAT
66 ACTGGAAACATTATCAAGCACAATAACATATTAGCTAACACTTAT
*
1106892 ATAACGTAATAGGTAACGTTTATATA
1 ATAACGTAATAGGTAACGCTTATATA
1106918 TTAAAATAGG
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 121 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (110 bp):
ATAACGTAATAGGTAACGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGGTTAATT
ACTGGAAACATTATCAAGCACAATAACATATTAGCTAACACTTAT
Found at i:1107499 original size:19 final size:20
Alignment explanation
Indices: 1107475--1107523 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1107465 CATGTAAAAA
1107475 TATGACAAAACCA-TTTCAT
1 TATGACAAAACCAGTTTCAT
*
1107494 TATGACAAAATCAGTTTCAT
1 TATGACAAAACCAGTTTCAT
1107514 TATGACAAAA
1 TATGACAAAA
1107524 ATGGTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (20 bp):
TATGACAAAACCAGTTTCAT
Found at i:1107602 original size:130 final size:131
Alignment explanation
Indices: 1107364--1107636 Score: 469
Period size: 130 Copynumber: 2.1 Consensus size: 131
1107354 CATGTAAAAA
1107364 TATGACAAAACCAATTTCATTATGAAAAAACCGGTAAAATTTACTTGATATGTTGAAAGTATCGA
1 TATGACAAAACCAATTTCATTATGAAAAAACCGGTAAAATTTACTTGATATGTTGAAAGTATCGA
* *
1107429 TCTTTTTATAAAAAGGATAGATACTTTACAATATAACATGTAAAAATATGACAAAACCA-TTTCA
66 TCCTTTTATAAAAAGGATAGATACTTTACAATATAACACGTAAAAATATGACAAAACCAGTTTCA
1107493 T
131 T
* * *
1107494 TATGACAAAATCAGTTTCATTATGACAAAAA-TGGTAAAATTTACTTGATATGTTGAAAGTATCG
1 TATGACAAAACCAATTTCATTATGA-AAAAACCGGTAAAATTTACTTGATATGTTGAAAGTATCG
*
1107558 ATCCTTTTATAAAAAGGATAGATACTTTACAATATAACACGTAAAAATATGACAAAATCAGTTTC
65 ATCCTTTTATAAAAAGGATAGATACTTTACAATATAACACGTAAAAATATGACAAAACCAGTTTC
1107623 AT
130 AT
1107625 TATGACAAAACC
1 TATGACAAAACC
1107637 GGTAAAATTT
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
130 112 0.84
131 22 0.16
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (131 bp):
TATGACAAAACCAATTTCATTATGAAAAAACCGGTAAAATTTACTTGATATGTTGAAAGTATCGA
TCCTTTTATAAAAAGGATAGATACTTTACAATATAACACGTAAAAATATGACAAAACCAGTTTCA
T
Found at i:1108361 original size:112 final size:111
Alignment explanation
Indices: 1108130--1108530 Score: 565
Period size: 110 Copynumber: 3.6 Consensus size: 111
1108120 TAACGCCTAT
* * * * *
1108130 AAAGTATCGAT-ATTTTATAAATATGTATCA-ATATTTTACAATAGAACAAGTAAAAATATGACA
1 AAAGTATCGATCCTTTTATAAAAAAG-AT-AGATACTTTACAATATAACAAGTAAAAATATGACA
*
1108193 AAACCAATTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTG
64 AAACCAATTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* * *
1108241 AAAGTATCGATCCTTTTTATAAAAAAGATCGATACTTTACAATATAACAAATAAAAATATGAAAA
1 AAAGTATCGATCC-TTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAA
* * * *
1108306 AATCAATTTTATTATGATAAAAAGGGTAAAATTTACCTAATATGTTG
65 AACCAATTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* *
1108353 AAAGTATCGATACTTTTAT-AAAAAGATAGATATTTTACAATATAACAAGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
* * *
1108417 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGCTG
66 ACCAATTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* * *
1108463 AAAGTATCAATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
1108528 ACC
66 ACC
1108531 GGTAAAATTT
Statistics
Matches: 256, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
110 97 0.38
111 62 0.24
112 86 0.34
113 11 0.04
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.31
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
ACCAATTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
Found at i:1108761 original size:894 final size:897
Alignment explanation
Indices: 1107308--1109393 Score: 3109
Period size: 894 Copynumber: 2.3 Consensus size: 897
1107298 TAGAGCCTCT
* *
1107308 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACATGTAAAAATATGACAA
1 AAAGTATCGAT-CTTTTATAAAAATG-ATCGATACTTTACAATATAACAAGTAAAAATATGACAA
*
1107372 AACCAATTTCATTATGAAAAAACCGGTAAAATTTACTTGATATGTTGAAAGTATCGATCTTTTTA
64 AACCAATTTCATTATGAAAAAA-CGGTAAAATTTACCTGATATGTTGAAAGTATCGATC-TTTTA
*
1107437 TAAAAAGGATAGATACTTTACAATATAACATGTAAAAATATGACAAAACCATTTCATTATGACAA
127 TAAAAAGGATAGATACTTTACAATATAACAAGTAAAAATATG-----A-CA----A--A--AC--
* * *
1107502 AATCAGTTTCATTATGACAAAAATGGTAAAATTTACTTGATATGTTGAAAGTATCGATCCTTTTA
176 ---CAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTA
1107567 TAAAAAGGATAGATACTTTACAATATAACACGTAAAAATATGACAAAATCAGTTTCATTATGACA
238 TAAAAAGGATAGATACTTTACAATATAACACG-------A-GA-AAAA-CA---T-ATTATGACA
1107632 AAACCGGTAAAATTTACCTGATATGTTGAAAGTATAGATACTTTTTATAAAAATGATCAATACTT
289 AAACCGGTAAAATTTACCTGATATGTTGAAAGTATAGATACTTTTTATAAAAATGATCAATACTT
1107697 TTTTGAAAGTTATGTAATTTATGTTTCAAGAATTTTTAATAGTATTTCATGTTTTCCACCTACAA
354 TTTTGAAAGTTATGTAATTTATGTTTCAAGAATTTTTAATAGTATTTCATGTTTTCCACCTACAA
*
1107762 TATTAATTTAATAATTTCATTTATACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
419 TATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
* *
1107827 ATTTAGAATTTAAATTTAACAATTTTAACCAAATATAATAATAAATATGTAATATCTATGTTTAT
484 ATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAATATCTATATTTAT
**
1107892 TGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACGTGTATAATTA
549 TGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACGCATATAATTA
1107957 CTAAATTAATATCTTAAAACTCACTCAAAACATAACTTTAAATTAATGATTTTT-ACAGTGAAAT
614 CTAAATTAATATCTTAAAACTCACTCAAAACATAACTTTAAATTAATG-TTTTTCACAGTGAAAT
* *
1108021 ATC-TACCTATTACATTAAACTACCTACTAGATACGTTGAACGTATCGATTCCAGTTAAATAAGT
678 A-CATACCTATTACATTAAACTACCTACCAGATACGTTGAAAGTATCGATTCCAGTTAAATAAGT
* * *
1108085 ATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAACGCCTATAAAGTATCGATATTTTATAA
742 ATCGAAACTTTTGGAATTTAAAACAAAAGCAGTAATAACGCCTATAAAGTATCGATACTTTATAA
*
1108150 ATATGTATCAATATTTTACAATAGAACAAGTAAAAATATGACAAAACCAATTTCATTATGACA-A
807 AAATGTATCAATATTTTACAATAGAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAGA
*
1108214 AACCGGTAAAATTTACCTAATATGTTG
872 AA-AGGTAAAATTTACCTAATATGTTG
* * *
1108241 AAAGTATCGATCCTTTTTATAAAAAAGATCGATACTTTACAATATAACAAATAAAAATATGAAAA
1 AAAGTATCGAT-C-TTTTATAAAAATGATCGATACTTTACAATATAACAAGTAAAAATATGACAA
* * * *
1108306 AATCAATTTTATTATGATAAAAAGGGTAAAATTTACCTAATATGTTGAAAGTATCGATACTTTTA
64 AACCAATTTCATTATGA-AAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGAT-CTTTTA
*
1108371 TAAAAA-GATAGATATTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACA
127 TAAAAAGGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACA
*
1108435 AAAACGGTAAAATTTACCTGATATGCTGAAAGTATCAATCCTTTTATAAAAAGGATAGATACTTT
192 AAAACGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTATAAAAAGGATAGATACTTT
*
1108500 ACAATATAACA-G-G-TAAA-A-A-TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGT
257 ACAATATAACACGAGAAAAACATATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGT
* * *
1108559 ATATATACTTTTTATAAAAATGATCGATACTTTTTTGAAAGTTATGTAATTTATGTTTTAA-AAT
322 ATAGATACTTTTTATAAAAATGATCAATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAGAA-
* *
1108623 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATA
386 TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1108688 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
451 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
*
1108753 AGATAATAATAAATATGTAATATGTATATTTATTGTTTTTAATTTAATAATAATATATACCGTAA
516 AGATAATAATAAATATGTAATATCTATATTTATTGTTTTTAATTTAATAATAATATATACCGTAA
* *
1108818 CATAAAAAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAATCTCACTCAAAAGA
581 CATAAAAAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAACA
*
1108883 TAACTTTAAATTAATGTTTTTCACAGTGAAATACATACCTATTACATTAAACTACCTACCGGATA
646 TAACTTTAAATTAATGTTTTTCACAGTGAAATACATACCTATTACATTAAACTACCTACCAGATA
* * * * *
1108948 TGTTGAAAGTATCGATTCTATTTAAATAAGTATTGAAACTTTTGGAATTTAAAACAAAAGTAGTA
711 CGTTGAAAGTATCGATTCCAGTTAAATAAGTATCGAAACTTTTGGAATTTAAAACAAAAGCAGTA
* * * *
1109013 ATAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAA
776 ATAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCAATATTTTACAATAGAACAAGTAAA
* *
1109078 AATATGACAAAACCAGTTTCATTATGACAGAAAAGGTAAAATTTACCTGATATGTTG
841 AATATGACAAAACCAATTTCATTATGACAGAAAAGGTAAAATTTACCTAATATGTTG
* * *
1109135 AAAGTATCGATCATTTTATAAAAATGATAGATACTATACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATC-TTTTATAAAAATGATCGATACTTTACAATATAACAAGTAAAAATATGACAAA
*
1109200 ACCAGTTTCATTATGAAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATA
65 ACCAATTTCATTATGAAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGAT-CTTTTATA
* *
1109265 AAAAGGATCGATACTTTACAATATAAC-AGATATAAATATGACAAAACCAGTTTCATTATGACAA
129 AAAAGGATAGATACTTTACAATATAACAAG-TAAAAATATGACAAAACCAGTTTCATTATGACAA
* * * *
1109329 AACCGGTAAAATTTACCTGATATGTTGAAAGTATAAATACATTTTATAAAAAGGATCGATACTTT
193 AAACGGTAAAATTTACCTGATATGTTGAAAGTATCAAT-CCTTTTATAAAAAGGATAGATACTTT
1109394 TTTGAAAGTT
Statistics
Matches: 1071, Mismatches: 71, Indels: 61
0.89 0.06 0.05
Matches are distributed among these distances:
892 52 0.05
893 156 0.15
894 604 0.56
895 4 0.00
900 1 0.00
902 3 0.00
904 1 0.00
913 1 0.00
914 88 0.08
919 2 0.00
921 1 0.00
923 1 0.00
927 2 0.00
928 1 0.00
933 45 0.04
934 92 0.09
935 17 0.02
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (897 bp):
AAAGTATCGATCTTTTATAAAAATGATCGATACTTTACAATATAACAAGTAAAAATATGACAAAA
CCAATTTCATTATGAAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCTTTTATAAA
AAGGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAA
CGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTATAAAAAGGATAGATACTTTACAA
TATAACACGAGAAAAACATATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATAG
ATACTTTTTATAAAAATGATCAATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAGAATTTTT
AATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATT
TGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATA
ATAATAAATATGTAATATCTATATTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAA
AAAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAACATAACT
TTAAATTAATGTTTTTCACAGTGAAATACATACCTATTACATTAAACTACCTACCAGATACGTTG
AAAGTATCGATTCCAGTTAAATAAGTATCGAAACTTTTGGAATTTAAAACAAAAGCAGTAATAAC
GCCTATAAAGTATCGATACTTTATAAAAATGTATCAATATTTTACAATAGAACAAGTAAAAATAT
GACAAAACCAATTTCATTATGACAGAAAAGGTAAAATTTACCTAATATGTTG
Found at i:1109267 original size:110 final size:111
Alignment explanation
Indices: 1109024--1109393 Score: 584
Period size: 111 Copynumber: 3.3 Consensus size: 111
1109014 TAGCGCCTAT
* * *
1109024 AAAGTATCGAT-ACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATCATTTTATAAAAA-GGATCGATACTTTACAATATAACAGGTAAAAATATGACAA
1109088 AACCAGTTTCATTATGACAGAAAA-GGTAAAATTTACCTGATATGTTG
65 AACCAGTTTCATTATGACA-AAAACGGTAAAATTTACCTGATATGTTG
* * *
1109135 AAAGTATCGATCATTTTATAAAAATGATAGATACTATACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCATTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1109200 ACCAGTTTCATTATGA-AAAAACGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* * *
1109245 AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAGATATAAATATGACAAA
1 AAAGTATCGATCATTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
1109310 ACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
**
1109356 AAAGTATAAATACATTTTATAAAAAGGATCGATACTTT
1 AAAGTATCGAT-CATTTTATAAAAAGGATCGATACTTT
1109394 TTTGAAAGTT
Statistics
Matches: 239, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
109 4 0.02
110 99 0.41
111 100 0.42
112 36 0.15
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (111 bp):
AAAGTATCGATCATTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:1113069 original size:20 final size:18
Alignment explanation
Indices: 1113034--1113074 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1113024 CTAATAATTG
*
1113034 AATCGAATATAATATTTA
1 AATCGAATATAATATTAA
1113052 AATCGAATATAAAATATTAA
1 AATCGAATAT--AATATTAA
1113072 AAT
1 AAT
1113075 AATTTTACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATCGAATATAATATTAA
Found at i:1113495 original size:27 final size:27
Alignment explanation
Indices: 1113443--1113495 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1113433 AAATACTAAA
*
1113443 TATCCATAATCATTCAAAACACACAAG
1 TATCCATAATCATTCAAAACAAACAAG
*
1113470 TATCCA-AATCATTCAAACATAAACAA
1 TATCCATAATCATTCAAA-ACAAACAA
1113496 CCAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (27 bp):
TATCCATAATCATTCAAAACAAACAAG
Found at i:1115526 original size:23 final size:22
Alignment explanation
Indices: 1115473--1115530 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
1115463 ACCCATTCAT
*
1115473 ATAGTATCGATACTATAAGAAC
1 ATAGTATCGATACTATAAGAAA
1115495 A-A-TATCGATACTCGATAA-AAA
1 ATAGTATCGATACT--ATAAGAAA
1115516 ATAGTATCGATACTA
1 ATAGTATCGATACTA
1115531 GGCTAGTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 10 0.32
21 5 0.16
22 6 0.19
23 10 0.32
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (22 bp):
ATAGTATCGATACTATAAGAAA
Found at i:1115542 original size:20 final size:19
Alignment explanation
Indices: 1115517--1115590 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
1115507 CGATAAAAAA
1115517 TAGTATCGATACTAGGCTAG
1 TAGTATCGATACTA-GCTAG
* *
1115537 TAGTATGGATACCTAGCAAG
1 TAGTATCGATA-CTAGCTAG
*
1115557 AATAGCATCGATACTATG-TAAG
1 --TAGTATCGATACTA-GCT-AG
1115579 TAGTATCGATAC
1 TAGTATCGATAC
1115591 CAAGTGCACA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 25 0.58
21 6 0.14
22 12 0.28
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (19 bp):
TAGTATCGATACTAGCTAG
Found at i:1120824 original size:55 final size:54
Alignment explanation
Indices: 1120755--1121255 Score: 506
Period size: 55 Copynumber: 9.1 Consensus size: 54
1120745 TAGATAAACG
* * * * * * *
1120755 AGACTTGAAAAATCTTCAAATGACGGGTTCACTCCCTATTCTTTTAGGGAGTATA
1 AGACTCGAACAATCTTCAAA-AACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* ** * * **
1120810 AGACTCGGACAATCTTCGGCAAACGTGTCTGCTCCCTATTTATTCAGGGAGTATA
1 AGACTCGAACAATCTTC-AAAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* * * * *
1120865 AGACTCAAACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTTAGGGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* *
1120920 AGACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* * *
1120975 GGACTCGAACAATCTTCAATAAATGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* * *
1121029 AGAACTCAAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* *
1121084 AGAACTCGAACAATCTTCAATAAATGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-
1 AG-ACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* * *
1121139 AGAACTCGAACAATCTTCATAAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAACAATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
* * ** * *
1121194 AGAACTCGAGCAATCTTCAACGAACTTGTTCGCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAACAATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
*
1121250 GGACTC
1 AGACTC
1121256 AATCTTTAAC
Statistics
Matches: 380, Mismatches: 56, Indels: 20
0.83 0.12 0.04
Matches are distributed among these distances:
54 4 0.01
55 371 0.98
56 5 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (54 bp):
AGACTCGAACAATCTTCAAAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATA
Found at i:1120959 original size:110 final size:110
Alignment explanation
Indices: 1120777--1121255 Score: 595
Period size: 110 Copynumber: 4.4 Consensus size: 110
1120767 TCTTCAAATG
* * * * * *** * *
1120777 ACGGGTTCACTCCCTATTCTTTTAGGGAGTATAAGACTCGGACAATCTTCGGCAAACGTGTCTGC
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCATAAAACGGGTCCGC
* ** * *
1120842 TCCCTATTTATTCAGGGAGTATA-AGACTCAAACAATCTTCAACAA
66 TCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * *
1120887 ACGTGTCTGTTCCCTATTCCTTTAGGGAGTATAAGACTCGAACAATCTTCATAAAACGGGTCCGC
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCATAAAACGGGTCCGC
* *
1120952 TCTCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAATAA
66 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
1120997 ATGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCAAACAATCTTCATAAAACGGGTCCG
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCATAAAACGGGTCCG
*
1121061 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAA
65 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
1121107 ATGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAAACAGGTCCG
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCATAAAACGGGTCCG
* *
1121171 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCAACGA
65 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
** * * *
1121217 ACTTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTC
1121256 AATCTTTAAC
Statistics
Matches: 327, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
109 2 0.01
110 324 0.99
111 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (110 bp):
ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCATAAAACGGGTCCGC
TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:1122630 original size:7 final size:7
Alignment explanation
Indices: 1122618--1122667 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
1122608 TTTTTTTTTC
1122618 TTTCATT
1 TTTCATT
1122625 TTTCATT
1 TTTCATT
1122632 TTTCATT
1 TTTCATT
1122639 TTTCA-T
1 TTTCATT
1122645 TTT--TT
1 TTTCATT
1122650 TTTCATTT
1 TTTCA-TT
1122658 TTTCATT
1 TTTCATT
1122665 TTT
1 TTT
1122668 TTTATTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.10
6 4 0.10
7 24 0.62
8 7 0.18
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCATT
Found at i:1122635 original size:18 final size:17
Alignment explanation
Indices: 1122612--1122718 Score: 86
Period size: 14 Copynumber: 6.6 Consensus size: 17
1122602 CCCTGCTTTT
1122612 TTTTTCTTTCATTTTTCA
1 TTTTT-TTTCATTTTTCA
1122630 ---TTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA
1122644 TTTTTTTTTCATTTTTTCA
1 -TTTTTTTTCA-TTTTTCA
1122663 TTTTTTTT-ATTTTTC-
1 TTTTTTTTCATTTTTCA
* *
1122678 -CTTTTTT-ATTTCTC-
1 TTTTTTTTCATTTTTCA
* *
1122692 CTTTTTTTCTTTTTTCA
1 TTTTTTTTCATTTTTCA
*
1122709 TTTCTTTTCA
1 TTTTTTTTCA
1122719 GGCGAAATAT
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 24 0.33
15 8 0.11
16 11 0.15
17 8 0.11
18 15 0.21
19 7 0.10
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCATTTTTCA
Found at i:1122641 original size:8 final size:8
Alignment explanation
Indices: 1122618--1122711 Score: 65
Period size: 8 Copynumber: 12.0 Consensus size: 8
1122608 TTTTTTTTTC
1122618 TTTCA-TT
1 TTTCATTT
1122625 TTTCA-TT
1 TTTCATTT
1122632 TTTCA-TT
1 TTTCATTT
1122639 TTTCATTTTTT
1 TTTCA---TTT
1122650 TTTCATTT
1 TTTCATTT
1122658 TTTCATTT
1 TTTCATTT
*
1122666 TTT-TTATT
1 TTTCAT-TT
*
1122674 TTTCCTTT
1 TTTCATTT
1122682 TTT-ATTT
1 TTTCATTT
* * *
1122689 CTCCTTTT
1 TTTCATTT
1122697 TTTC-TTT
1 TTTCATTT
1122704 TTTCATTT
1 TTTCATTT
1122712 CTTTTCAGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
7 31 0.44
8 32 0.45
9 1 0.01
11 7 0.10
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCATTT
Found at i:1122652 original size:19 final size:20
Alignment explanation
Indices: 1122618--1122670 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1122608 TTTTTTTTTC
1122618 TTTCATTTTTCATTTTTCA-TT
1 TTTCATTTTT--TTTTTCATTT
1122639 TTTCA-TTTTTTTTTCATTT
1 TTTCATTTTTTTTTTCATTT
1122658 TTTCATTTTTTTT
1 TTTCATTTTTTTT
1122671 ATTTTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 7 0.23
20 11 0.37
21 5 0.17
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCATTTTTTTTTTCATTT
Found at i:1122698 original size:23 final size:24
Alignment explanation
Indices: 1122646--1122713 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
1122636 ATTTTTCATT
* **
1122646 TTTTTTTCATTTTTTCATTT-TTT
1 TTTTTTTCCTTTTTTCATTTCTCC
1122669 TTATTTTTCCTTTTTT-ATTTCTCC
1 TT-TTTTTCCTTTTTTCATTTCTCC
1122693 TTTTTTT-CTTTTTTCATTTCT
1 TTTTTTTCCTTTTTTCATTTCT
1122714 TTTCAGGCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.18
23 17 0.44
24 15 0.38
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTCCTTTTTTCATTTCTCC
Found at i:1132416 original size:45 final size:47
Alignment explanation
Indices: 1132345--1132450 Score: 153
Period size: 45 Copynumber: 2.3 Consensus size: 47
1132335 CCATGCTTTG
*
1132345 TTATTCACAAAAATAAATCCTTACCGCATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
1132392 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
1132438 TTTATTCGAAAAA
1 -TTATTCAAAAAA
1132451 CGAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
45 27 0.50
46 9 0.17
47 18 0.33
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:1150864 original size:15 final size:15
Alignment explanation
Indices: 1150844--1150892 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1150834 AACTAGACCA
*
1150844 AACCAGACCAAGTTG
1 AACCAGACCAAGTCG
1150859 AACCAGACCAAGTCG
1 AACCAGACCAAGTCG
* *
1150874 AACAAGACCAAGCCG
1 AACCAGACCAAGTCG
1150889 AACC
1 AACC
1150893 GAGCCGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.43, C:0.33, G:0.18, T:0.06
Consensus pattern (15 bp):
AACCAGACCAAGTCG
Found at i:1150956 original size:17 final size:17
Alignment explanation
Indices: 1150912--1150957 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1150902 ATCGTTGATC
*
1150912 GACCATTGACCGGTGTT
1 GACCATTGACCGCTGTT
* *
1150929 AACCGTTGACCGCTGTT
1 GACCATTGACCGCTGTT
*
1150946 GACCATGGACCG
1 GACCATTGACCG
1150958 GCTGCTGACT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (17 bp):
GACCATTGACCGCTGTT
Found at i:1152090 original size:16 final size:17
Alignment explanation
Indices: 1152063--1152096 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1152053 TCTTCATTCT
1152063 TTTTGTAAAAGTAAATA
1 TTTTGTAAAAGTAAATA
*
1152080 TTTTG-AAAAGTCAATA
1 TTTTGTAAAAGTAAATA
1152096 T
1 T
1152097 GACACCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATA
Found at i:1169559 original size:30 final size:30
Alignment explanation
Indices: 1169523--1169636 Score: 210
Period size: 30 Copynumber: 3.8 Consensus size: 30
1169513 ACTATCCAGA
*
1169523 ATCCTCGGTAACTTTCCAGAGGTCATAAAG
1 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1169553 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1169583 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
*
1169613 ATCCTCGGTAACTGTCCATAGGTC
1 ATCCTCGGTAACTGTCCAGAGGTC
1169637 CCGAAGAACC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (30 bp):
ATCCTCGGTAACTGTCCAGAGGTCATAAAG
Found at i:1169653 original size:60 final size:60
Alignment explanation
Indices: 1169520--1169653 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 60
1169510 GTAACTATCC
* *
1169520 AGAATCCTCGGTAACTTTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAA
1 AGAA-CCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAA
* * * *
1169581 AGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGA
1 AGAACCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAA
*
1169641 AGAACCTAGGTAA
1 AGAACCTCGGTAA
1169654 ACTTTCCATA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 62 0.95
61 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (60 bp):
AGAACCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAA
Found at i:1170840 original size:21 final size:21
Alignment explanation
Indices: 1170816--1170860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170806 TGTTGTTCGT
* *
1170816 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1170837 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1170858 TTG
1 TTG
1170861 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1173626 original size:30 final size:30
Alignment explanation
Indices: 1173590--1173673 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
1173580 ACTATCCAGA
*
1173590 ATCCTCGGTAACTATCCAGAGGTCATAAAG
1 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1173620 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
1 ATCCTCGGTAACTGTCCAGAGGTCATAAAG
*
1173650 ATCCTCGGTAACTGTCCATAGGTC
1 ATCCTCGGTAACTGTCCAGAGGTC
1173674 CCGAAGAACC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
ATCCTCGGTAACTGTCCAGAGGTCATAAAG
Found at i:1174411 original size:22 final size:22
Alignment explanation
Indices: 1174367--1174408 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1174357 TAAATCAATT
*
1174367 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1174389 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1174409 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1174880 original size:21 final size:21
Alignment explanation
Indices: 1174856--1174900 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1174846 TGTTGTTCGT
*
1174856 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1174877 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1174898 TTG
1 TTG
1174901 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1185775 original size:30 final size:32
Alignment explanation
Indices: 1185706--1185786 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 32
1185696 AATTTTACAC
* * *
1185706 AAAATATTAATTTAATCATAAATTTTAGAGAGA
1 AAAATATTAATTTAACCTTAAACTTTA-AGAGA
*
1185739 AAAATATTAATTTAACCTTAAACTTT-AGA-T
1 AAAATATTAATTTAACCTTAAACTTTAAGAGA
* *
1185769 AAAATATCAATTTGACCT
1 AAAATATTAATTTAACCT
1185787 CTGAATTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 16 0.38
31 3 0.07
33 23 0.55
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (32 bp):
AAAATATTAATTTAACCTTAAACTTTAAGAGA
Found at i:1186153 original size:14 final size:14
Alignment explanation
Indices: 1186134--1186161 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1186124 ATTATAATTA
1186134 TATATTTTAATTTT
1 TATATTTTAATTTT
1186148 TATATTTTAATTTT
1 TATATTTTAATTTT
1186162 GATAAAATTA
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:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATATTTTAATTTT
Found at i:1186161 original size:13 final size:13
Alignment explanation
Indices: 1186123--1186161 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1186113 TTAAATTGTG
* *
1186123 TATTATAATTATA
1 TATTTTAATTTTA
1186136 TATTTTAATTTTTA
1 TATTTTAA-TTTTA
1186150 TATTTTAATTTT
1 TATTTTAATTTT
1186162 GATAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:1187164 original size:14 final size:13
Alignment explanation
Indices: 1187139--1187191 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1187129 ATCTATGAAA
1187139 AATATGTTAAAATT
1 AATAT-TTAAAATT
1187153 GAATATTTAAAATT
1 -AATATTTAAAATT
*
1187167 AATAATTTTAAATT
1 AAT-ATTTAAAATT
*
1187181 ATAAATTTAAA
1 A-ATATTTAAA
1187192 TATTTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 3 0.09
14 24 0.73
15 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
AATATTTAAAATT
Found at i:1189322 original size:46 final size:45
Alignment explanation
Indices: 1189224--1189329 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
1189214 GTGCACTAAG
* * *
1189224 AGTGCATCGATGAATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
1189269 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
1189315 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
1189330 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:1189404 original size:65 final size:63
Alignment explanation
Indices: 1189270--1189413 Score: 150
Period size: 65 Copynumber: 2.2 Consensus size: 63
1189260 AATAGCCAGA
* *
1189270 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGATAT
* **
1189335 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGA-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGATA
1189397 TT
63 -T
*
1189399 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
1189414 TACTCTGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.04
63 4 0.06
64 20 0.29
65 41 0.60
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGATAT
Found at i:1190465 original size:21 final size:21
Alignment explanation
Indices: 1190441--1190484 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1190431 GTGCCAGAGG
*
1190441 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
1190462 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
1190483 AG
1 AG
1190485 CTCACGGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:1192057 original size:23 final size:22
Alignment explanation
Indices: 1192023--1192100 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1192013 CATGACCCTG
1192023 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* *
1192046 TGCATCGGTGCATCA-GCAA-GA
1 TGCATCGATGCA-CATTCAAGGA
*
1192067 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
1192091 TGCATCGATG
1 TGCATCGATG
1192101 TATAAAGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.05
21 12 0.27
22 3 0.07
23 14 0.32
24 13 0.30
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1196235 original size:22 final size:23
Alignment explanation
Indices: 1196196--1196240 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1196186 TTTTATTTCA
* *
1196196 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATATAATATTATTAT
1196219 TTTGTTTTA-ATAATATTATTAT
1 TTTGTTTTATATAATATTATTAT
1196241 ATTATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTGTTTTATATAATATTATTAT
Found at i:1197704 original size:15 final size:15
Alignment explanation
Indices: 1197686--1197715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1197676 TTATTTAATA
1197686 ATTTATGTATTTATT
1 ATTTATGTATTTATT
*
1197701 ATTTATGTTTTTATT
1 ATTTATGTATTTATT
1197716 CACTAATATT
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:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (15 bp):
ATTTATGTATTTATT
Found at i:1199087 original size:46 final size:49
Alignment explanation
Indices: 1198999--1199089 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 49
1198989 TTTATTTCAT
* * *
1198999 TTTTTCCTAAATAAATGCATGCGAACTAGTAATCATGCGGTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGCGAACTAGTAAGCATGAGGTTAGGTTAA
1199048 TTTTTCC-AAACAAA-GCATG-GAACTAG-AAGGCATGAGGTTAGG
1 TTTTTCCTAAACAAATGCATGCGAACTAGTAA-GCATGAGGTTAGG
1199090 ATATATTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
45 2 0.05
46 18 0.47
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGCGAACTAGTAAGCATGAGGTTAGGTTAA
Found at i:1199832 original size:30 final size:30
Alignment explanation
Indices: 1199798--1199861 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1199788 AGAGAATGTC
* *
1199798 ATGGAAGAAGCTGCAGTCTAGATAAGCAAT
1 ATGGAAGAAGCTGCAGTCCAGACAAGCAAT
1199828 ATGGAAGAAGCTGCAGTCCAGACAAGCAAT
1 ATGGAAGAAGCTGCAGTCCAGACAAGCAAT
1199858 ATGG
1 ATGG
1199862 CCCATAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.17
Consensus pattern (30 bp):
ATGGAAGAAGCTGCAGTCCAGACAAGCAAT
Found at i:1205861 original size:75 final size:75
Alignment explanation
Indices: 1205712--1205871 Score: 214
Period size: 75 Copynumber: 2.1 Consensus size: 75
1205702 AATCATAGAA
* * *
1205712 CATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACACATTTTGAACGTTTATATTAGCC
1 CATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACGTTTATATCAGCA
**
1205777 AATGTTGGGG
66 AATAATGGGG
* *** *
1205787 CATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATGTATTTTGAACGTTTGTATCAGCA
1 CATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACGTTTATATCAGCA
1205852 AATAATGGGG
66 AATAATGGGG
*
1205862 AATGCT-AAAG
1 CATGCTGAAAG
1205872 GCGTATGTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 4 0.05
75 70 0.95
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (75 bp):
CATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATTGACACATTTTGAACGTTTATATCAGCA
AATAATGGGG
Found at i:1208195 original size:113 final size:110
Alignment explanation
Indices: 1207990--1208298 Score: 424
Period size: 113 Copynumber: 2.8 Consensus size: 110
1207980 GTTCATAATG
* * *
1207990 AGCAGTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCATGAT
1 AGCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAG-AAGAAG--GTTCATAAT
*
1208055 AAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATT
63 AAGAAGAACTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATT
*
1208103 ATCATTGCCA-ATTAGAGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGGGGTTCATAA
1 AGCATTGCCAGA-TAGAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAA--GGTTCATAA
*
1208167 TAAGAAGAATTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATT
62 TAAGAAGAACTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATT
* * * * * *
1208216 AGCTTTTCCAGAGAAAGTTCATAATGAGAATAACTTATCTGAAGAAGAAGAA-GTTCATAATGAG
1 AGCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGGTTCATAATAAG
*
1208280 AAGAGCTTGTTCAACCTTT
66 AAGAACTTGTTCAACCTTT
1208299 GTATGACTCT
Statistics
Matches: 176, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
109 28 0.16
112 6 0.03
113 139 0.79
114 2 0.01
115 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (110 bp):
AGCATTGCCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGGTTCATAATAAG
AAGAACTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATT
Found at i:1210297 original size:15 final size:15
Alignment explanation
Indices: 1210271--1210309 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1210261 ATTAATAATT
1210271 TATTTAATTATTTATG
1 TATTT-ATTATTTATG
1210287 TATTTATTATTTATG
1 TATTTATTATTTATG
*
1210302 TTTTTATT
1 TATTTATT
1210310 CACTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (15 bp):
TATTTATTATTTATG
Found at i:1212622 original size:21 final size:21
Alignment explanation
Indices: 1212596--1212646 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1212586 TGGGAGCGTC
1212596 AGTGCATCGATGCATACCCTA
1 AGTGCATCGATGCATACCCTA
1212617 AGTGCATCGATGCATACCCTA
1 AGTGCATCGATGCATACCCTA
*
1212638 GGTGCATCG
1 AGTGCATCG
1212647 GTGTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
AGTGCATCGATGCATACCCTA
Found at i:1212735 original size:18 final size:17
Alignment explanation
Indices: 1212681--1212729 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1212671 TTGGACTCTC
* *
1212681 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1212699 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1212717 AGTGCATTCGATG
1 AGTGCA-TCGATG
1212730 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1212798 original size:46 final size:45
Alignment explanation
Indices: 1212700--1212805 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
1212690 GTGCACTAAG
* *
1212700 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* * *
1212745 AGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
1212791 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
1212806 GGTATCTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:1228034 original size:14 final size:14
Alignment explanation
Indices: 1228017--1228049 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1228007 AATTTCTCTA
1228017 TTAAAATATT-AATT
1 TTAAAAT-TTAAATT
1228031 TTAAAATTTAAATT
1 TTAAAATTTAAATT
1228045 TTAAA
1 TTAAA
1228050 TGAATGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATTTAAATT
Found at i:1228795 original size:20 final size:20
Alignment explanation
Indices: 1228770--1228807 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228760 GAGTCATTGG
1228770 GAACACAATGCGTCTTCCAA
1 GAACACAATGCGTCTTCCAA
*
1228790 GAACACAATGTGTCTTCC
1 GAACACAATGCGTCTTCC
1228808 CCGTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (20 bp):
GAACACAATGCGTCTTCCAA
Found at i:1228884 original size:19 final size:19
Alignment explanation
Indices: 1228860--1228901 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1228850 TCTCGGTGAC
*
1228860 TTTCCGATGACACACTGTG
1 TTTCCGAAGACACACTGTG
**
1228879 TTTCCGAAGATGCACTGTG
1 TTTCCGAAGACACACTGTG
1228898 TTTC
1 TTTC
1228902 TTGCAACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (19 bp):
TTTCCGAAGACACACTGTG
Found at i:1229056 original size:33 final size:33
Alignment explanation
Indices: 1229014--1229077 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1229004 AAATCAACCC
*
1229014 AGTTTGGTATGTTGTTGAAGAAAGAAAACCTGA
1 AGTTTGGTATGTTGGTGAAGAAAGAAAACCTGA
1229047 AGTTTGGTATGTTGGTGAAGAAAGAAAACCT
1 AGTTTGGTATGTTGGTGAAGAAAGAAAACCT
1229078 TTCAGGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (33 bp):
AGTTTGGTATGTTGGTGAAGAAAGAAAACCTGA
Found at i:1238592 original size:47 final size:46
Alignment explanation
Indices: 1238482--1238605 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 46
1238472 TTATGTTCGT
* * * * *
1238482 TTTCCATTTCTTTGTGTTCCCATTATTTGTGAGTTGTCTTTTGGTCTA
1 TTTCCATTTCTTTTTGTTCCCATTA-TT-TGAGTTGTCTATAGCTCAA
*
1238530 TTTCCATTTCCTTTTGTTCCCATTATTTGAGTCCTGT-TATAGCTCAA
1 TTTCCATTTCTTTTTGTTCCCATTATTTGAGT--TGTCTATAGCTCAA
1238577 TTTCCATTTCTTTTTGCTT-CCATTATTTG
1 TTTCCATTTCTTTTTG-TTCCCATTATTTG
1238606 GGAGTCTGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
46 5 0.08
47 33 0.50
48 28 0.42
ACGTcount: A:0.13, C:0.20, G:0.12, T:0.55
Consensus pattern (46 bp):
TTTCCATTTCTTTTTGTTCCCATTATTTGAGTTGTCTATAGCTCAA
Found at i:1242054 original size:18 final size:17
Alignment explanation
Indices: 1242028--1242063 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1242018 GAAATTTTAT
*
1242028 TTATTTATTTATTTTAAA
1 TTATGTATTT-TTTTAAA
1242046 TTATGTATTTTTTTAAA
1 TTATGTATTTTTTTAAA
1242063 T
1 T
1242064 ACAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATGTATTTTTTTAAA
Found at i:1243449 original size:21 final size:20
Alignment explanation
Indices: 1243413--1243466 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 20
1243403 TTAAATAATT
1243413 TTAATATTATTTAAATTAAATTAA
1 TTAATATTA--TAAATTAAA-T-A
1243437 TTAAT-TTATAAATTAAATA
1 TTAATATTATAAATTAAATA
1243456 TTAATATTATA
1 TTAATATTATA
1243467 TAAAGGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 9 0.31
23 3 0.10
24 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATATTATAAATTAAATA
Found at i:1244593 original size:21 final size:21
Alignment explanation
Indices: 1244567--1244608 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244557 AATAAAATTG
1244567 TTAATAAAATTTATATTATTT
1 TTAATAAAATTTATATTATTT
1244588 TTAATAAAATTTATATTATTT
1 TTAATAAAATTTATATTATTT
1244609 ATTATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATAAAATTTATATTATTT
Found at i:1244631 original size:13 final size:13
Alignment explanation
Indices: 1244611--1244642 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1244601 TATTATTTAT
1244611 TATT-TTAAATTA
1 TATTATTAAATTA
1244623 TATTATTAAATTA
1 TATTATTAAATTA
1244636 TATTATT
1 TATTATT
1244643 TATGTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTAAATTA
Found at i:1244656 original size:18 final size:16
Alignment explanation
Indices: 1244596--1244658 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 16
1244586 TTTTAATAAA
1244596 ATTTATATTATTTATT
1 ATTTATATTATTTATT
*
1244612 ATTTTAAATTATATTATT
1 A-TTTATATTAT-TTATT
*
1244630 AAATTATATTATTTATGT
1 -ATTTATATTATTTAT-T
1244648 ATTTAATATTA
1 ATTT-ATATTA
1244659 ATATAATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 16 0.42
18 20 0.53
19 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTATATTATTTATT
Found at i:1244836 original size:14 final size:14
Alignment explanation
Indices: 1244817--1244887 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
1244807 TATAAAACTA
*
1244817 TAAAAATGATATTT
1 TAAAAATAATATTT
*
1244831 TAAAAATAATATTGA
1 TAAAAATAATATT-T
*
1244846 TATAAATAATATTT
1 TAAAAATAATATTT
* *
1244860 TAATAATAATATTG
1 TAAAAATAATATTT
*
1244874 AAATAAATAATATT
1 TAA-AAATAATATT
1244888 AAATACATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
14 25 0.54
15 21 0.46
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (14 bp):
TAAAAATAATATTT
Found at i:1244857 original size:29 final size:29
Alignment explanation
Indices: 1244820--1244887 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
1244810 AAAACTATAA
* *
1244820 AAATGATATTTTAAAAATAATATTGATAT
1 AAATAATATTTTAAAAATAATATTGAAAT
*
1244849 AAATAATATTTTAATAATAATATTGAAAT
1 AAATAATATTTTAAAAATAATATTGAAAT
1244878 AAATAATATT
1 AAATAATATT
1244888 AAATACATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
AAATAATATTTTAAAAATAATATTGAAAT
Found at i:1244891 original size:14 final size:15
Alignment explanation
Indices: 1244834--1244892 Score: 77
Period size: 15 Copynumber: 4.1 Consensus size: 15
1244824 GATATTTTAA
*
1244834 AAATAATATTGATAT
1 AAATAATATTGAAAT
**
1244849 AAATAATATTTTAAT
1 AAATAATATTGAAAT
1244864 -AATAATATTGAAAT
1 AAATAATATTGAAAT
1244878 AAATAATATT-AAAT
1 AAATAATATTGAAAT
1244892 A
1 A
1244893 CATTATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
14 17 0.45
15 21 0.55
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATAATATTGAAAT
Found at i:1245717 original size:22 final size:22
Alignment explanation
Indices: 1245692--1245740 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1245682 ATATATTTCT
1245692 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
1245714 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
1245736 AAATA
1 TAATA
1245741 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:1245839 original size:31 final size:30
Alignment explanation
Indices: 1245753--1245840 Score: 72
Period size: 31 Copynumber: 2.8 Consensus size: 30
1245743 CAATTATATT
* * *
1245753 ATAA-TAATATAAGATATAATATTTTTAACAT
1 ATAATTAATATAA-CTATAATA-CTTTAACAA
* *
1245784 ATAATATAATATAAC-ACTATTACTTTAATAA
1 ATAAT-TAATATAACTA-TAATACTTTAACAA
1245815 ATAATTAATATAATCTATAATACTTT
1 ATAATTAATATAA-CTATAATACTTT
1245841 TATTTAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
30 8 0.17
31 25 0.54
32 5 0.11
33 8 0.17
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (30 bp):
ATAATTAATATAACTATAATACTTTAACAA
Found at i:1247223 original size:12 final size:13
Alignment explanation
Indices: 1247196--1247230 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1247186 TAAGATTTTC
*
1247196 TTTGAAAATAAGT
1 TTTGAAATTAAGT
1247209 TTTGAAATTAA-T
1 TTTGAAATTAAGT
1247221 TTTGAAATTA
1 TTTGAAATTA
1247231 CTCCCCCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (13 bp):
TTTGAAATTAAGT
Found at i:1248434 original size:23 final size:23
Alignment explanation
Indices: 1248404--1248485 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
1248394 GCATGACCCT
1248404 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
1248427 GTGCATCGGTGCATCA-GCAA-GA
1 GTGCATCGATGCA-CATTCAAGGA
**
1248449 -TAAATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
1248471 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
1248486 TATTAAGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 4 0.09
23 16 0.36
24 13 0.29
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:1252281 original size:20 final size:19
Alignment explanation
Indices: 1252239--1252281 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1252229 TTATTTTCAT
1252239 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAACA-CA
1252259 TTTTTATATTTTAGAAACA-A
1 TTTTTA-ATTTT-GAAACACA
1252279 TTT
1 TTT
1252282 CTCATAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.48
21 5 0.24
22 6 0.29
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTTAATTTTGAAACACA
Found at i:1254663 original size:14 final size:14
Alignment explanation
Indices: 1254641--1254675 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1254631 TAAACATCGT
*
1254641 AAAACGTTTTCCAA
1 AAAATGTTTTCCAA
*
1254655 AAAATGTTTTTCAA
1 AAAATGTTTTCCAA
1254669 AAAATGT
1 AAAATGT
1254676 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (14 bp):
AAAATGTTTTCCAA
Found at i:1258426 original size:35 final size:35
Alignment explanation
Indices: 1258328--1258427 Score: 128
Period size: 35 Copynumber: 2.8 Consensus size: 35
1258318 TGAGAATGGA
* * * *
1258328 TTATGAATTTGGGGTTGAGTATGTAATTAAAGTATT
1 TTAT-AATTTGGGGTTTAGAATATAATTGAAGTATT
** *
1258364 TTGGAATTTAGGGTTTAGAATATAATTGAAGTATT
1 TTATAATTTGGGGTTTAGAATATAATTGAAGTATT
1258399 TTATAATTTGGGGTTTAGAATATAATTGA
1 TTATAATTTGGGGTTTAGAATATAATTGA
1258428 TGAATGTGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 52 0.96
36 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
TTATAATTTGGGGTTTAGAATATAATTGAAGTATT
Found at i:1259271 original size:23 final size:23
Alignment explanation
Indices: 1259234--1259280 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1259224 GTTAAACGAT
* *
1259234 AAAAAACGTACCATAAAGACATA
1 AAAAAACATACCATAAAAACATA
*
1259257 AAAAAACATATCATAAAAACATA
1 AAAAAACATACCATAAAAACATA
1259280 A
1 A
1259281 TTGTTAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.15, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAAAACATACCATAAAAACATA
Found at i:1260541 original size:25 final size:25
Alignment explanation
Indices: 1260507--1260568 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
1260497 ATCATAACGT
* *
1260507 AATTACAATTATATTCATAATTTAA
1 AATTATAATTATATTCATAAATTAA
1260532 AATTATAATTATATTCATAAATTAA
1 AATTATAATTATATTCATAAATTAA
1260557 AATTATAATTAT
1 AATTATAATTAT
1260569 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTATAATTATATTCATAAATTAA
Found at i:1265991 original size:19 final size:20
Alignment explanation
Indices: 1265967--1266008 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1265957 TATTATATAT
1265967 ATATTTATGAATAT-ATAAA
1 ATATTTATGAATATAATAAA
**
1265986 ATATTTATTCATATAATAAA
1 ATATTTATGAATATAATAAA
1266006 ATA
1 ATA
1266009 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATTTATGAATATAATAAA
Found at i:1267408 original size:3 final size:3
Alignment explanation
Indices: 1267400--1267517 Score: 173
Period size: 3 Copynumber: 39.3 Consensus size: 3
1267390 TTAATATATT
*
1267400 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1267448 TAA TGA TGA TGA TGA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1267496 TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1267518 GATATGGGTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 107 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1268093 original size:113 final size:113
Alignment explanation
Indices: 1267841--1268512 Score: 1157
Period size: 113 Copynumber: 6.0 Consensus size: 113
1267831 AGAATTATGC
* * * *
1267841 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
1267906 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
1267953 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1268018 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
1268066 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1268131 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
1268179 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1268244 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
1268292 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **
1268357 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
1268405 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
1268470 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
1268513 TGAATCTTTG
Statistics
Matches: 543, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
112 68 0.13
113 475 0.87
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:1269456 original size:82 final size:82
Alignment explanation
Indices: 1269351--1269891 Score: 933
Period size: 82 Copynumber: 6.6 Consensus size: 82
1269341 CATACCAAAC
1269351 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269416 GTTCTGTCCAACCAGAT
66 GTTCTGTCCAACCAGAT
*
1269433 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
*
1269498 GATTCTGTCCAATCAGAT
66 G-TTCTGTCCAACCAGAT
*
1269516 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269581 GTTCTGTCCAACCAGAT
66 GTTCTGTCCAACCAGAT
1269598 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269663 GTTCTGTCCAACCAGAT
66 GTTCTGTCCAACCAGAT
1269680 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269745 GTTCTGTCCAACCAGAT
66 GTTCTGTCCAACCAGAT
* ** *
1269762 CAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCCAATTCAATGAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCAATGAT
* *
1269826 TGGTTCTG-CTAAACCAGGT
65 T-GTTCTGTC-CAACCAGAT
**
1269845 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1269892 TTGTTCTATT
Statistics
Matches: 439, Mismatches: 15, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
81 2 0.00
82 302 0.69
83 134 0.31
84 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (82 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
GTTCTGTCCAACCAGAT
Found at i:1269623 original size:165 final size:164
Alignment explanation
Indices: 1269351--1269891 Score: 933
Period size: 165 Copynumber: 3.3 Consensus size: 164
1269341 CATACCAAAC
1269351 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269416 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
66 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
* *
1269481 TTCTAAACTCAATGCTTGATTCTGTCCAATCAGAT
131 TTCTAAACTCAATGATTG-TTCTGTCCAACCAGAT
*
1269516 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1269581 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
66 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
1269646 TTCTAAACTCAATGATTGTTCTGTCCAACCAGAT
131 TTCTAAACTCAATGATTGTTCTGTCCAACCAGAT
1269680 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
*
1269745 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCAT
66 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCAT
** * * *
1269809 CTTCCCAATTCAATGATTGGTTCTG-CTAAACCAGGT
130 CTTCTAAACTCAATGATT-GTTCTGTC-CAACCAGAT
**
1269845 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1269892 TTGTTCTATT
Statistics
Matches: 361, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
163 2 0.01
164 155 0.43
165 204 0.57
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (164 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATC
TTCTAAACTCAATGATTGTTCTGTCCAACCAGAT
Found at i:1269850 original size:247 final size:247
Alignment explanation
Indices: 1269300--1269891 Score: 965
Period size: 247 Copynumber: 2.4 Consensus size: 247
1269290 TTTACTATGA
* * * *
1269300 GCAAATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATAACTCAAAG
1 GCAAATTCATCTTCCAAATTCAATGATT-G--TTCT--G-TCAAACCAGATCAGATAACTCAAAG
1269365 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCA
60 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCA
1269430 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATG
125 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATG
* *
1269495 CTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
190 ATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* *
1269553 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACT
1269618 TCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAG
66 TCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAG
1269683 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTG-T
131 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGAT
1269747 TCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG
196 TCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* * *
1269798 AGCACATTCATCTTCCCAATTCAATGATTGGTTCTG-CTAAACCAGGTCAGATAACTCAAAGAAC
1 -GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGTC-AAACCAGATCAGATAACTCAAAGAAC
**
1269862 ACTTCCAGAAGATGCTATTAACAAATTCAT
63 ACTTCCAGAAGATGCTATTGGCAAATTCAT
1269892 TTGTTCTATT
Statistics
Matches: 321, Mismatches: 15, Indels: 12
0.92 0.04 0.03
Matches are distributed among these distances:
245 2 0.01
246 75 0.23
247 212 0.66
248 1 0.00
250 3 0.01
252 1 0.00
253 27 0.08
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (247 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGAT
TCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
Found at i:1278333 original size:14 final size:15
Alignment explanation
Indices: 1278314--1278346 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1278304 ATTATTTTTC
1278314 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
1278328 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
1278343 AAAT
1 AAAT
1278347 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:1283844 original size:3 final size:3
Alignment explanation
Indices: 1283836--1283962 Score: 209
Period size: 3 Copynumber: 42.3 Consensus size: 3
1283826 TTAATATATT
* * *
1283836 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1283884 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1283932 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1283963 GATATGGGTA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 116 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1287766 original size:60 final size:61
Alignment explanation
Indices: 1287667--1287808 Score: 153
Period size: 60 Copynumber: 2.3 Consensus size: 61
1287657 ATATAAGGAT
* * ****
1287667 AAAGTATAC-AAATGGTCACTCGATTATAAGATGTTATTTTATTAAGT-TTTTCGACTATTA
1 AAAGT-TACAAAATGGTCACTCAATTATAAGATGTCATTTTATTAAGTCCCCCCGACTATTA
* * * * *
1287727 AAAGTTACAAAATAGTCATTCAATTATAGGGTGTCATTTTATTGAGTCCCCCCGACTATTA
1 AAAGTTACAAAATGGTCACTCAATTATAAGATGTCATTTTATTAAGTCCCCCCGACTATTA
*
1287788 AAAGTTATAAAATGGTCACTC
1 AAAGTTACAAAATGGTCACTC
1287809 GACTATTTTC
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
59 3 0.05
60 36 0.55
61 27 0.41
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (61 bp):
AAAGTTACAAAATGGTCACTCAATTATAAGATGTCATTTTATTAAGTCCCCCCGACTATTA
Found at i:1306241 original size:2 final size:2
Alignment explanation
Indices: 1306234--1306270 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1306224 AAATATTAGG
1306234 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1306271 GCATAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1308678 original size:110 final size:108
Alignment explanation
Indices: 1308317--1308678 Score: 420
Period size: 103 Copynumber: 3.4 Consensus size: 108
1308307 TGTATTGTTC
* ** * * * *
1308317 TGAGTCTAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTG---GAACTAGGAAATTATTTGTTG
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAATT-TTTGTTG
* * *
1308379 ACAGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTATCT
65 ACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
* * * *
1308423 CGAGTCTAATATCCTT--TTCCGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAA-----GTT
1 TGAGTCCAATATCCTTCGTT--GTGAAGTTGAAATTGACTCTGAATGAAATTGAAAATTTTTGTT
*
1308481 GACAATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCT
64 GACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
*
1308526 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACACTGAATGAAATTGAAAAGTTGTTTGTT
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAA-TT-TTTGTT
* * *
1308591 GATAATCAGCCGCCCATTCGTCGTGAAGTTGAGCTTGTGTTGTCT
64 GACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
* *
1308636 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA
1308679 ATTGGAAAGC
Statistics
Matches: 217, Mismatches: 25, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
103 90 0.41
105 2 0.01
106 34 0.16
109 7 0.03
110 84 0.39
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (108 bp):
TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAATTTTTGTTGA
CAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
Found at i:1309814 original size:23 final size:23
Alignment explanation
Indices: 1309771--1309815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1309761 CCCACCTTAT
* *
1309771 TTTTTCTTTTCTTTTTTCTTTTG
1 TTTTTCTTCTCTTTTTCCTTTTG
1309794 TTTTTC-TCTCTTTTTCCCTTTT
1 TTTTTCTTCTCTTTTT-CCTTTT
1309816 TTTCAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTCTTCTCTTTTTCCTTTTG
Found at i:1312663 original size:5 final size:5
Alignment explanation
Indices: 1312653--1312684 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1312643 TAGGGGTGTA
1312653 TTCGG TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TTCGG TT
1312685 TTTTACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:1312798 original size:19 final size:18
Alignment explanation
Indices: 1312774--1312833 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
1312764 AACCGAAAAT
1312774 GGTTTTTTCGGTTCGGTTC
1 GGTTTTTT-GGTTCGGTTC
*
1312793 GGTTTTTT--TAACGGTTC
1 GGTTTTTTGGT-TCGGTTC
1312810 GGGTTTTTTGGTTCGGTTC
1 -GGTTTTTTGGTTCGGTTC
1312829 GGTTT
1 GGTTT
1312834 ATCGGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 13 0.37
19 14 0.40
20 1 0.03
ACGTcount: A:0.03, C:0.12, G:0.32, T:0.53
Consensus pattern (18 bp):
GGTTTTTTGGTTCGGTTC
Found at i:1317073 original size:21 final size:21
Alignment explanation
Indices: 1317049--1317088 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1317039 ACGAATGTAA
1317049 AAACATGGAAA-ATATAAAAAT
1 AAACAT-GAAATATATAAAAAT
1317070 AAACATGAAATATATAAAA
1 AAACATGAAATATATAAAA
1317089 TGCAAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACATGAAATATATAAAAAT
Found at i:1320481 original size:26 final size:26
Alignment explanation
Indices: 1320426--1320486 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
1320416 GAAAAAGGAA
* *
1320426 AAAATAAAGATAAAATAGAATAAGAT
1 AAAATAAAGAAAAAATAAAATAAGAT
1320452 -AAATAAAGAAAAAATACAAATAA-AT
1 AAAATAAAGAAAAAATA-AAATAAGAT
1320477 AAAATAAAGA
1 AAAATAAAGA
1320487 TAAAGGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (26 bp):
AAAATAAAGAAAAAATAAAATAAGAT
Found at i:1322694 original size:20 final size:20
Alignment explanation
Indices: 1322671--1322715 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1322661 TGTCTGTAAC
*
1322671 TGTCTTAC-TTTGTTGTTTAT
1 TGTCTTACATTT-TTGTTGAT
*
1322691 TGTCTTCCATTTTTGTTGAT
1 TGTCTTACATTTTTGTTGAT
1322711 TGTCT
1 TGTCT
1322716 CTTCTCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.09, C:0.13, G:0.16, T:0.62
Consensus pattern (20 bp):
TGTCTTACATTTTTGTTGAT
Found at i:1323577 original size:30 final size:30
Alignment explanation
Indices: 1323543--1323599 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1323533 AAATTCCATG
* *
1323543 TTTAGTAGTTAAATTATCAATTT-TTTTCAT
1 TTTAGTACTTAAACTATC-ATTTGTTTTCAT
1323573 TTTAGTACTTAAACTATCATTTGTTTT
1 TTTAGTACTTAAACTATCATTTGTTTT
1323600 AAAACCATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTAGTACTTAAACTATCATTTGTTTTCAT
Found at i:1327931 original size:10 final size:9
Alignment explanation
Indices: 1327913--1328024 Score: 55
Period size: 10 Copynumber: 10.9 Consensus size: 9
1327903 ATCAAAGGGG
1327913 AAAAAATAA
1 AAAAAATAA
1327922 AAAAACATAA
1 AAAAA-ATAA
1327932 AAAATAATAA
1 AAAA-AATAA
1327942 ATAATAAATAA
1 A-AA-AAATAA
1327953 AAGGAAAA-AA
1 AA--AAAATAA
*
1327963 AATAAAAAAA
1 AA-AAAATAA
1327973 GAAATAAATAGA
1 -AAA-AAATA-A
*
1327985 AATAAATCAA
1 AAAAAAT-AA
*
1327995 AGGAAAGAATGA
1 A--AAA-AATAA
1328007 AAAAAATATA
1 AAAAAATA-A
1328017 AAAAAATA
1 AAAAAATA
1328025 TTAAATAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 29
0.70 0.05 0.25
Matches are distributed among these distances:
9 12 0.15
10 39 0.48
11 21 0.26
12 7 0.09
13 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1327950 original size:46 final size:43
Alignment explanation
Indices: 1327898--1328068 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 43
1327888 ATAAATGTTA
1327898 AATAAATCAAAGGGGAAAAAATAAAAAAACATAAAAAATAATAAAT
1 AATAAATCAAA--GGAAAAAATAAAAAAA-ATAAAAAATAATAAAT
* * * *
1327944 AATAAATAAAAGGAAAAAA-AATAAAAA-AAGAAATAAATAGA-
1 AATAAATCAAAGGAAAAAATAAAAAAAATAAAAAAT-AATAAAT
* * *
1327985 AATAAATCAAAGGAAAGAATGAAAAAAATATAAAAA-AAT-ATT
1 AATAAATCAAAGGAAAAAATAAAAAAAATA-AAAAATAATAAAT
1328027 AAATAAATCAAAGGTTAATAAAAAATAAAATAAAATAAAAAA
1 -AATAAATCAAAGG-----AAAAAATAAAA-AAAATAAAAAA
1328069 GTTAAAATTT
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
41 23 0.23
42 15 0.15
43 20 0.20
44 12 0.12
46 10 0.10
48 14 0.14
49 6 0.06
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (43 bp):
AATAAATCAAAGGAAAAAATAAAAAAAATAAAAAATAATAAAT
Found at i:1327976 original size:17 final size:17
Alignment explanation
Indices: 1327913--1327976 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
1327903 ATCAAAGGGG
*
1327913 AAAAAATAAAAAAACATA
1 AAAAAAGAAAAAAA-ATA
* *
1327931 AAAAATA-ATAAATAATA
1 AAAAA-AGAAAAAAAATA
1327948 AATAAAAGGAAAAAAAATA
1 AA-AAAA-GAAAAAAAATA
1327967 AAAAAAGAAA
1 AAAAAAGAAA
1327977 TAAATAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
17 10 0.26
18 17 0.45
19 11 0.29
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATA
Found at i:1328090 original size:9 final size:9
Alignment explanation
Indices: 1328078--1328151 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
1328068 AGTTAAAATT
1328078 TAAAAATAA
1 TAAAAATAA
1328087 T-AAAATAA
1 TAAAAATAA
*
1328095 -AACAAT-A
1 TAAAAATAA
*
1328102 T-GAAATAA
1 TAAAAATAA
1328110 -AATAAATAA
1 TAA-AAATAA
* **
1328119 TAATAATTT
1 TAAAAATAA
1328128 TAAAAAATAA
1 T-AAAAATAA
1328138 TAAAAATAA
1 TAAAAATAA
1328147 TAAAA
1 TAAAA
1328152 TAAAAATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
7 4 0.08
8 12 0.25
9 24 0.50
10 8 0.17
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (9 bp):
TAAAAATAA
Found at i:1328090 original size:16 final size:16
Alignment explanation
Indices: 1328045--1328154 Score: 68
Period size: 17 Copynumber: 6.6 Consensus size: 16
1328035 CAAAGGTTAA
1328045 TAAAAAATAAAATAAAA-
1 TAAAAAAT--AATAAAAT
1328062 TAAAAAAGT--TAAAAT
1 TAAAAAA-TAATAAAAT
*
1328077 TTAAAAATAATAAAA-
1 TAAAAAATAATAAAAT
*
1328092 TAAAACAAT-ATGAAAT
1 TAAAA-AATAATAAAAT
*
1328108 AAAATAAATAATAATAATTT
1 TAAA-AAATAATAA-AA--T
*
1328128 TAAAAAATAATAAAAA
1 TAAAAAATAATAAAAT
1328144 TAATAAAATAA
1 TAA-AAAATAA
1328155 AAATTTAGAG
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
14 6 0.08
15 15 0.20
16 17 0.23
17 18 0.24
18 5 0.07
19 9 0.12
20 4 0.05
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (16 bp):
TAAAAAATAATAAAAT
Found at i:1328130 original size:50 final size:47
Alignment explanation
Indices: 1328043--1328156 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 47
1328033 ATCAAAGGTT
1328043 AATAAAAAATAAAATAAAATAAAAAAGTTAAAATTT-AAAAATAATAA
1 AATAAAAAATAAAATAAAATAAAAAAG-TAAAATTTAAAAAATAATAA
*
1328090 AATAAAACAATATGAAATAAAATAAATAA-TAATAATTTTAAAAAATAATAAA
1 AATAAAA-AATA--AAATAAAATAAAAAAGTAA-AA-TTTAAAAAATAAT-AA
1328142 AATAATAAAATAAAA
1 AATAA-AAAATAAAA
1328157 ATTTAGAGGA
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
47 7 0.12
48 7 0.12
49 2 0.03
50 20 0.34
51 9 0.16
52 11 0.19
53 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.25
Consensus pattern (47 bp):
AATAAAAAATAAAATAAAATAAAAAAGTAAAATTTAAAAAATAATAA
Found at i:1328150 original size:19 final size:19
Alignment explanation
Indices: 1328104--1328151 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
1328094 AAACAATATG
*
1328104 AAATAA-AATAAATAATAA
1 AAATAATAAAAAATAATAA
* **
1328122 TAATTTTAAAAAATAATAA
1 AAATAATAAAAAATAATAA
1328141 AAATAATAAAA
1 AAATAATAAAA
1328152 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAATAAAAAATAATAA
Found at i:1329484 original size:37 final size:37
Alignment explanation
Indices: 1329443--1329578 Score: 168
Period size: 37 Copynumber: 3.6 Consensus size: 37
1329433 AAATATTTTC
*
1329443 AAAACTTATATATTATATATA-TTTAAAAATGTTATAA
1 AAAAC-TATATATTATATATATTTTAAAAATGTTTTAA
* * **
1329480 AAAACTATATATCATATA-AGTTTTCAAAATGTTTTTTT
1 AAAACTATATATTATATATA-TTTTAAAAATG-TTTTAA
* *
1329518 TAAACTATATATTATATACATTTTAAAAATGTTTTAA
1 AAAACTATATATTATATATATTTTAAAAATGTTTTAA
1329555 AAAACTATATATTATATATATTTT
1 AAAACTATATATTATATATATTTT
1329579 TTCAAAAACC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
35 1 0.01
36 12 0.14
37 40 0.48
38 29 0.35
39 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTAAAAATGTTTTAA
Found at i:1330555 original size:85 final size:85
Alignment explanation
Indices: 1330292--1330884 Score: 744
Period size: 85 Copynumber: 7.0 Consensus size: 85
1330282 CATGTAGTTA
* * * * * *
1330292 ATATGTCATCGAGCTGAATGGAATCGAACTCGATA-GTTTTTTTTGACAGATATCCCTTCTCGCC
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGA-AGGTTTTTGTTGACAGATAGCCCTTCTCACC
*
1330356 TTGAGCTATGCTATAAATTTG
65 TTGAGCTATGCTGTAAATTTG
* * * * * *
1330377 ATATGCCCTTGAGATGGATGTAATTGAACTCGAAGG--TTTGTTAACAGATAGCCCTTTTCACCT
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
1330440 TGAGCTATGCTGTAAATTTG
66 TGAGCTATGCTGTAAATTTG
* * * * * *
1330460 ATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTATTGACAAATAACCCTTCTCGCTT
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
* *
1330525 TGAGTTATGTTGTAAATTTG
66 TGAGCTATGCTGTAAATTTG
* * *
1330545 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGCTTTTGGTTGACAGATAGGCCTTCTCACCT
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
*
1330610 TGAGCTATGCTATAAATTTG
66 TGAGCTATGCTGTAAATTTG
* * *
1330630 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGATTTTGGTTGACAGATAGCCCTTCTCGCCT
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
*
1330695 TGAGCTATGTTGTAAATTTG
66 TGAGCTATGCTGTAAATTTG
* * *
1330715 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATATCCTTTCTCACCT
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
*
1330780 TGAGCTATGTTGTAAATTTG
66 TGAGCTATGCTGTAAATTTG
* * * * *
1330800 ATATGTCATTGAGTTGACTGTAATCGAACTCGAAGGTTTTTTTTGTTGGCAGATAACCC-TCATC
1 ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG---TTTTTGTTGACAGATAGCCCTTC-TC
* * *
1330864 GCCTTAAGCTATGCTGCAAAT
62 ACCTTGAGCTATGCTGTAAAT
1330885 AGTTCCTTTA
Statistics
Matches: 444, Mismatches: 57, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
83 74 0.17
84 1 0.00
85 332 0.75
87 2 0.00
88 35 0.08
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (85 bp):
ATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCT
TGAGCTATGCTGTAAATTTG
Found at i:1339083 original size:9 final size:9
Alignment explanation
Indices: 1339069--1339175 Score: 52
Period size: 9 Copynumber: 10.2 Consensus size: 9
1339059 AAGGGGAAAG
1339069 TAAAAAAAA
1 TAAAAAAAA
1339078 TAAAAAAACA
1 TAAAAAAA-A
*
1339088 TAAAAATAA
1 TAAAAAAAA
1339097 TAAATAATAAA
1 TAAA-AA-AAA
1339108 TCAAAGGAAAAAA
1 T--AA--AAAAAA
1339121 TAAAATAATAA
1 TAAAA-AA-AA
*
1339132 TAGAAATAAA
1 TA-AAAAAAA
1339142 TCAAAGGAAAAAA
1 T--AA--AAAAAA
*
1339155 TGAAAAAATA
1 T-AAAAAAAA
1339165 TAAAAAAAA
1 TAAAAAAAA
1339174 TA
1 TA
1339176 TTAAATAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
9 24 0.31
10 21 0.27
11 11 0.14
12 6 0.08
13 12 0.16
14 2 0.03
15 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1339084 original size:8 final size:8
Alignment explanation
Indices: 1339071--1339172 Score: 51
Period size: 8 Copynumber: 11.9 Consensus size: 8
1339061 GGGGAAAGTA
1339071 AAAAAAAT
1 AAAAAAAT
*
1339079 AAAAAAAC
1 AAAAAAAT
*
1339087 ATAAAAAT
1 AAAAAAAT
1339095 AATAAATAAT
1 AA-AAA-AAT
* *
1339105 AAATCAAAG
1 AAA-AAAAT
*
1339114 GAAAAAAT
1 AAAAAAAT
*
1339122 AAAATAAT
1 AAAAAAAT
*
1339130 AATAGAAAT
1 AA-AAAAAT
* *
1339139 AAATCAAAG
1 AAA-AAAAT
*
1339148 GAAAAAAT
1 AAAAAAAT
1339156 GAAAAAATAT
1 -AAAAAA-AT
1339166 AAAAAAA
1 AAAAAAA
1339173 ATATTAAATA
Statistics
Matches: 68, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
8 30 0.44
9 30 0.44
10 8 0.12
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1339119 original size:34 final size:35
Alignment explanation
Indices: 1339081--1339161 Score: 114
Period size: 34 Copynumber: 2.3 Consensus size: 35
1339071 AAAAAAATAA
*
1339081 AAAAACATAAAAATAATAA-A-TAATAAATCAAAGG
1 AAAAA-ATAAAAATAATAATAGAAATAAATCAAAGG
1339115 AAAAAAT-AAAATAATAATAGAAATAAATCAAAGG
1 AAAAAATAAAAATAATAATAGAAATAAATCAAAGG
1339149 AAAAAATGAAAAA
1 AAAAAAT-AAAAA
1339162 ATATAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 10 0.24
33 3 0.07
34 25 0.60
36 4 0.10
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (35 bp):
AAAAAATAAAAATAATAATAGAAATAAATCAAAGG
Found at i:1339119 original size:35 final size:34
Alignment explanation
Indices: 1339080--1339174 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 34
1339070 AAAAAAAATA
1339080 AAAAAACATAAA-AATAATAAATAATAAATCAAAGG
1 AAAAAACA-AAATAATAATAAA-AATAAATCAAAGG
* *
1339115 AAAAAATAAAATAATAATAGAAATAAATCAAAGG
1 AAAAAACAAAATAATAATAAAAATAAATCAAAGG
*
1339149 AAAAAATGAAAA-AAT-ATAAAAA-AAAT
1 AAAAAA-CAAAATAATAATAAAAATAAAT
1339175 ATTAAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.07
33 6 0.11
34 25 0.46
35 19 0.35
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (34 bp):
AAAAAACAAAATAATAATAAAAATAAATCAAAGG
Found at i:1339124 original size:17 final size:17
Alignment explanation
Indices: 1339102--1339155 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1339092 AATAATAAAT
1339102 AATAAATCAAAGGAAAA
1 AATAAATCAAAGGAAAA
*
1339119 AATAAAAT-AATA--ATAGA
1 AAT-AAATCAA-AGGA-AAA
1339136 AATAAATCAAAGGAAAA
1 AATAAATCAAAGGAAAA
1339153 AAT
1 AAT
1339156 GAAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAATCAAAGGAAAA
Found at i:1339161 original size:77 final size:75
Alignment explanation
Indices: 1339072--1339216 Score: 186
Period size: 77 Copynumber: 1.9 Consensus size: 75
1339062 GGGAAAGTAA
*
1339072 AAAAAATAAAAAAACATAAAAATAATAA-ATAATAAATCAAAGG-AAAAAATAAAATAATAATAG
1 AAAAAATAAAAAAACATAAAAAAAATAATA-AATAAATCAAAGGTAAAAAA-AAAATAA-AATA-
1339135 AAATAAATCAAAGG
62 AAATAAATCAAAGG
* * * * *
1339149 AAAAAATGAAAAAATATAAAAAAAATATTAAATAAATCAAAGGTCAAGAAAAAATAAAATAAAAT
1 AAAAAATAAAAAAACATAAAAAAAATAATAAATAAATCAAAGGTAAAAAAAAAATAAAATAAAAT
1339214 AAA
66 AAA
1339217 AAAGTTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
75 7 0.12
76 4 0.07
77 44 0.73
78 5 0.08
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.17
Consensus pattern (75 bp):
AAAAAATAAAAAAACATAAAAAAAATAATAAATAAATCAAAGGTAAAAAAAAAATAAAATAAAAT
AAATCAAAGG
Found at i:1339211 original size:43 final size:42
Alignment explanation
Indices: 1339110--1339226 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 42
1339100 ATAATAAATC
* *
1339110 AAAGGAAAAAATAAAATAATAATA-GAAATAAATCAAAGGAAA
1 AAAGAAAAAAATAAAATAA-AATATTAAATAAATCAAAGGAAA
1339152 AAATGAAAAAATATAAAA-AAAATATTAAATAAATCAAAGGTCAAGA
1 AAA-GAAAAAA-ATAAAATAAAATATTAAATAAATCAAAGG--AA-A
* *
1339198 AAA-AATAAAATAAAATAAAAAAGTTAAAT
1 AAAGAAAAAAATAAAATAAAATA-TTAAAT
1339227 TTTTAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
42 7 0.11
43 28 0.44
44 16 0.25
45 8 0.13
46 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (42 bp):
AAAGAAAAAAATAAAATAAAATATTAAATAAATCAAAGGAAA
Found at i:1339253 original size:16 final size:17
Alignment explanation
Indices: 1339233--1339273 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1339223 AAATTTTTAA
1339233 AAATAATAAAATAAAA-
1 AAATAATAAAATAAAAG
* *
1339249 TAAT-ATGAAATAAAAG
1 AAATAATAAAATAAAAG
1339265 AAATAATAA
1 AAATAATAA
1339274 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 3
0.73 0.15 0.12
Matches are distributed among these distances:
15 10 0.53
16 6 0.32
17 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AAATAATAAAATAAAAG
Found at i:1340541 original size:13 final size:14
Alignment explanation
Indices: 1340507--1340556 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1340497 CCTAAAAGTG
*
1340507 AAATAAATAAATAAA
1 AAATAAAT-AATGAA
1340522 TAAATAAA-AATGAA
1 -AAATAAATAATGAA
*
1340536 AAATAAATAATTAA
1 AAATAAATAATGAA
1340550 AAA-AAAT
1 AAATAAAT
1340557 TTAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 11 0.35
14 13 0.42
16 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
AAATAAATAATGAA
Found at i:1340668 original size:36 final size:35
Alignment explanation
Indices: 1340609--1340789 Score: 150
Period size: 36 Copynumber: 4.9 Consensus size: 35
1340599 AAAATTTCAA
* *
1340609 AAAACGTTTTCAAAACTTATATATTATATATATTT-
1 AAAATGTTTTAAAAAC-TATATATTATATATATTTC
** *
1340644 AATTTTTTTTAAAAAAACTATATATTATATAT-TTTC
1 AAAATGTTTT--AAAAACTATATATTATATATATTTC
* *
1340680 AAAATGTTTTCAAAACTATATATTATATATACATTTTT
1 AAAATGTTTTAAAAACTATATATTATATAT--A-TTTC
*
1340718 AAAATGTTTTAGAAACTATATTATATATATATATATATTC
1 AAAATGTTTTAAAAAC--TA-TATAT-TATATATAT-TTC
** *
1340758 AAAATGTTTTAAAAGTTATATAATATATATAT
1 AAAATGTTTTAAAAACTATATATTATATATAT
1340790 ATATATATAT
Statistics
Matches: 117, Mismatches: 17, Indels: 23
0.75 0.11 0.15
Matches are distributed among these distances:
34 19 0.16
35 9 0.08
36 30 0.26
37 9 0.08
38 19 0.16
39 1 0.01
40 18 0.15
41 5 0.04
42 7 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATATTATATATATTTC
Found at i:1340762 original size:40 final size:39
Alignment explanation
Indices: 1340662--1340903 Score: 177
Period size: 38 Copynumber: 6.3 Consensus size: 39
1340652 TTAAAAAAAC
*
1340662 TATATAT-TATATATTTTCAAAATGTTTTCAAAACTATA-
1 TATATATATATATATATTCAAAATGTTTT-AAAACTATAT
* * *
1340700 TAT-TATATATACATTTTTAAAATGTTTTAGAAACTATAT
1 TATATATATATATATATTCAAAATGTTTTA-AAACTATAT
*
1340739 TATATATATATATATATTCAAAATGTTTTAAAAGTTATAT
1 TATATATATATATATATTCAAAATGTTTTAAAA-CTATAT
* * *
1340779 AATATATATATATATATATAT-ATATATGTTTTCAAAA-TGTTT
1 --TATATATATATATATAT-TCA-AAATGTTTT-AAAACTATAT
* * * * *
1340821 TAGAAACTATA-ATATA-T--ATATATTTTCAAACTATA-
1 TATATA-TATATATATATTCAAAATGTTTTAAAACTATAT
*
1340856 TAT-TATATACAT-T-TTCAAAATGTTTTAAAAACTATAT
1 TATATATATATATATATTCAAAATGTTTT-AAAACTATAT
1340893 TATATATATAT
1 TATATATATAT
1340904 TTTTTCAAAA
Statistics
Matches: 164, Mismatches: 21, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
33 6 0.04
34 3 0.02
35 12 0.07
36 18 0.11
37 7 0.04
38 37 0.23
39 6 0.04
40 37 0.23
41 4 0.02
42 21 0.13
43 9 0.05
44 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (39 bp):
TATATATATATATATATTCAAAATGTTTTAAAACTATAT
Found at i:1340785 original size:2 final size:2
Alignment explanation
Indices: 1340774--1340805 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1340764 TTTTAAAAGT
1340774 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1340806 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1340851 original size:24 final size:24
Alignment explanation
Indices: 1340824--1340874 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1340814 AATGTTTTAG
*
1340824 AAACTATA-ATATATATATATTTTC
1 AAACTATATAT-TATATACATTTTC
1340848 AAACTATATATTATATACATTTTC
1 AAACTATATATTATATACATTTTC
1340872 AAA
1 AAA
1340875 ATGTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (24 bp):
AAACTATATATTATATACATTTTC
Found at i:1340873 original size:60 final size:57
Alignment explanation
Indices: 1340739--1340906 Score: 193
Period size: 60 Copynumber: 2.9 Consensus size: 57
1340729 GAAACTATAT
* * * *
1340739 TATATA-TATATATATATTCAAAATGTTTTAAAAGT-T-ATATA-ATATA-TATATA
1 TATATATTATATATATTTTCAAAATGTTTTAAAACTATAATATATATATATTTTAAA
*
1340791 TATATATATATATATGTTTTCAAAATGTTTTAGAAACTATAATATATATATATTTTCAAA
1 TATATAT-TATATATATTTTCAAAATGTTTTA-AAACTATAATATATATATATTTT-AAA
* *
1340851 CTATATATTATATACATTTTCAAAATGTTTTAAAAACTATATTATATATATATTTT
1 -TATATATTATATATATTTTCAAAATGTTTT-AAAACTATAATATATATATATTTT
1340907 TTCAAAAATC
Statistics
Matches: 98, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
52 6 0.06
54 22 0.22
55 4 0.04
56 1 0.01
57 5 0.05
58 5 0.05
59 2 0.02
60 45 0.46
61 8 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (57 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAACTATAATATATATATATTTTAAA
Done.