Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 3 of 226
Found at i:844950 original size:5 final size:5
Alignment explanation
Indices: 844937--844966 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
844927 AAGCTTACAA
*
844937 AAAAG AAAAT AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
844967 TGGGTTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:857796 original size:18 final size:18
Alignment explanation
Indices: 857773--857865 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
857763 CCCAACTACT
*
857773 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
857791 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
857809 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
857827 ATATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
857845 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
857863 GTA
1 GTA
857866 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:861133 original size:2 final size:2
Alignment explanation
Indices: 861126--861153 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
861116 TTAGAAGTGA
861126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
861154 TTTATCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:865427 original size:20 final size:20
Alignment explanation
Indices: 865402--865445 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
865392 TTTTTATTTG
*
865402 TAAAAAAATT-ATAATATAA
1 TAAAAAAATTCATAAAATAA
*
865421 TTAAAAAATTCATAAAATAA
1 TAAAAAAATTCATAAAATAA
865441 TAAAA
1 TAAAA
865446 GTACTAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAATTCATAAAATAA
Found at i:865428 original size:19 final size:19
Alignment explanation
Indices: 865404--865445 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
865394 TTTATTTGTA
*
865404 AAAAAATT-ATAATATAATT
1 AAAAAATTCATAAAATAA-T
865423 AAAAAATTCATAAAATAAT
1 AAAAAATTCATAAAATAAT
865442 AAAA
1 AAAA
865446 GTACTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTCATAAAATAAT
Found at i:867387 original size:31 final size:31
Alignment explanation
Indices: 867349--867410 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
867339 ATCGGCGACC
867349 CTAACCACGGATCCATGTGTGAGGAACGAAT
1 CTAACCACGGATCCATGTGTGAGGAACGAAT
867380 CTAACCACGGATCCATGTGTGAGGAACGAAT
1 CTAACCACGGATCCATGTGTGAGGAACGAAT
867411 TGGGGTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (31 bp):
CTAACCACGGATCCATGTGTGAGGAACGAAT
Found at i:877145 original size:16 final size:18
Alignment explanation
Indices: 877120--877156 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
877110 ATTGACCCAC
*
877120 TATTTTATATT-A-AAAA
1 TATTTCATATTGATAAAA
877136 TATTTCATATTGATAAAA
1 TATTTCATATTGATAAAA
877154 TAT
1 TAT
877157 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTCATATTGATAAAA
Found at i:896770 original size:32 final size:32
Alignment explanation
Indices: 896734--896805 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
896724 AAAAAACAAT
* **
896734 AATTTAACTT-TTTTTCAAAAGATTGATGGTCA
1 AATTTAACTTCTTTTT-AAAAGATTGAAGACCA
* *
896766 AATTTGA-TTCTTTTTAAAAGGTTGAAGACCA
1 AATTTAACTTCTTTTTAAAAGATTGAAGACCA
896797 AATTTAACT
1 AATTTAACT
896806 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (32 bp):
AATTTAACTTCTTTTTAAAAGATTGAAGACCA
Found at i:899500 original size:11 final size:11
Alignment explanation
Indices: 899486--899542 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
899476 ATATTCAAAT
899486 AATAATAACAA
1 AATAATAACAA
899497 AATAATAACAA
1 AATAATAACAA
* ***
899508 TATAATAGTGA
1 AATAATAACAA
*
899519 AATAACAACAA
1 AATAATAACAA
*
899530 AATAGTAACAA
1 AATAATAACAA
899541 AA
1 AA
899543 AAGAACAATT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.67, C:0.09, G:0.05, T:0.19
Consensus pattern (11 bp):
AATAATAACAA
Found at i:899512 original size:22 final size:22
Alignment explanation
Indices: 899487--899551 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
899477 TATTCAAATA
*
899487 ATAATAACAAAATAATAACAAT
1 ATAATAACAAAATAACAACAAT
*** *
899509 ATAATAGTGAAATAACAACAAA
1 ATAATAACAAAATAACAACAAT
* *
899531 ATAGTAACAAAA-AAGAACAAT
1 ATAATAACAAAATAACAACAAT
899552 TTTTGTTTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.18
Consensus pattern (22 bp):
ATAATAACAAAATAACAACAAT
Found at i:900311 original size:11 final size:11
Alignment explanation
Indices: 900297--900322 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
900287 AAAAAAGGAG
900297 ATATATTTTAT
1 ATATATTTTAT
900308 ATATATTTTAT
1 ATATATTTTAT
900319 ATAT
1 ATAT
900323 GGAAAGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATATTTTAT
Found at i:907858 original size:20 final size:20
Alignment explanation
Indices: 907833--907882 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
907823 TGGCTTAAAA
907833 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
907853 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
907870 GTGGTAGTGGATT
1 TTGGTAGTGGATT
907883 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:912489 original size:20 final size:20
Alignment explanation
Indices: 912464--912513 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
912454 TGGCTTAAAA
912464 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
912484 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
912501 GTGGTAGTGGATT
1 TTGGTAGTGGATT
912514 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:942605 original size:4 final size:4
Alignment explanation
Indices: 942596--942624 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
942586 CTCCCAGTAC
942596 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
942625 TCTCAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:945634 original size:19 final size:19
Alignment explanation
Indices: 945610--945651 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
945600 TAAGGACAAG
945610 TTTTAAAGTTATATAT-TAA
1 TTTTAAAGTTA-ATATGTAA
*
945629 TTTT-AATTTAATATGTAA
1 TTTTAAAGTTAATATGTAA
945647 TTTTA
1 TTTTA
945652 TACCAACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAGTTAATATGTAA
Found at i:945923 original size:158 final size:154
Alignment explanation
Indices: 945545--945948 Score: 394
Period size: 152 Copynumber: 2.6 Consensus size: 154
945535 TTGATAGGAA
* ** *
945545 TTAGTTTCTCACTTTGATTTTCAACTTTTACAAAATAATACATTTTTTTAATATTTAAGG-ACAA
1 TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAAT-A-ACATTTTTTTAATATTTAAGGTA-AA
* * * * * *
945609 GTTTTAAAGTTATATATTAATTTTAATTTAATATGTAATTTTATACCAACTCAATAATGAGTTCT
63 -TTTTAAAATTATACATGAATTTTAATTTAATATATAATTTTATACCAACTCAATAATAAATTCT
*
945674 ATTAATAGTATAGATATTTCAAGAAAAG
127 ATTAATAGTATAGATATTTCAACAAAAG
* * * * *
945702 ---GTTTCTCA-TGTCAATTTAGAATTTTCATAAAATGATACA--TTTTTAATATTTAAAGATAA
1 TTAGTTTCTCACTCT-GATTTAGAATTTTTACAAAAT-A-ACATTTTTTTAATATTT-AAGGTAA
**
945761 ATTTTAAAATTATACATGAATTTTAATTTAATATATAATTTTATATACCAACTCGGTTAATAAAT
62 ATTTTAAAATTATACATGAATTTTAATTTAATATATAA-TTT-TATACCAACTC-AATAATAAAT
*
945826 T-TATT-ATAGTATAGATATTTCAACAAGAG
124 TCTATTAATAGTATAGATATTTCAACAAAAG
* * *
945855 TTAGTTTTTCACTCTGATTTAGAATTTTTACAAAATAAGCATTTTTTTTAATGTTTAACGGTGAA
1 TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAATAA-CA-TTTTTTTAATATTTAA-GGTAAA
* * *
945920 TTTTAAAATTTTACATGATTTTTTATTTA
63 TTTTAAAATTATACATGAATTTTAATTTA
945949 TCAAGGTATC
Statistics
Matches: 202, Mismatches: 30, Indels: 29
0.77 0.11 0.11
Matches are distributed among these distances:
152 45 0.22
153 32 0.16
154 45 0.22
155 10 0.05
156 25 0.12
157 4 0.02
158 41 0.20
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (154 bp):
TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAATAACATTTTTTTAATATTTAAGGTAAATTT
TAAAATTATACATGAATTTTAATTTAATATATAATTTTATACCAACTCAATAATAAATTCTATTA
ATAGTATAGATATTTCAACAAAAG
Found at i:956583 original size:21 final size:21
Alignment explanation
Indices: 956557--956597 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
956547 AGACGAGCAA
* *
956557 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
956578 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
956598 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:959758 original size:40 final size:40
Alignment explanation
Indices: 959703--959784 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
959693 TAGAAATCTC
*
959703 CACTTGATATTATAAATTTGGAAGCCTTACTATGAGTAGA
1 CACTTGATATTATAAATTTGGAAGCCTTACTATAAGTAGA
959743 CACTTGATATTATAAATTTGGAAGCCTTACTATAAGTAGA
1 CACTTGATATTATAAATTTGGAAGCCTTACTATAAGTAGA
959783 CA
1 CA
959785 ATCATAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (40 bp):
CACTTGATATTATAAATTTGGAAGCCTTACTATAAGTAGA
Found at i:960217 original size:20 final size:17
Alignment explanation
Indices: 960189--960231 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
960179 AAATTCCAGG
960189 AAAAAAACATAATATTTTA
1 AAAAAAACA-AA-ATTTTA
960208 AAAAATAACAAAATTTTA
1 AAAAA-AACAAAATTTTA
960226 AAAAAA
1 AAAAAA
960232 CTATATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 7 0.30
20 4 0.17
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAAACAAAATTTTA
Found at i:965523 original size:14 final size:14
Alignment explanation
Indices: 965500--965530 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
965490 GAAATGAGAA
965500 TATGAACCCACATG
1 TATGAACCCACATG
*
965514 TATGATCCCACATG
1 TATGAACCCACATG
965528 TAT
1 TAT
965531 TTTAGCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (14 bp):
TATGAACCCACATG
Found at i:972551 original size:40 final size:40
Alignment explanation
Indices: 972496--972592 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
972486 CCACGTCAGT
972496 GCGATTTGCTGACGTGGACACAAATAGCGCCCTCTAAGAC
1 GCGATTTGCTGACGTGGACACAAATAGCGCCCTCTAAGAC
* *
972536 GCGATTTACTGACGTGGACACAAATAGCGCCCTCTAGGAC
1 GCGATTTGCTGACGTGGACACAAATAGCGCCCTCTAAGAC
972576 GCGATTTGCTGACGTGG
1 GCGATTTGCTGACGTGG
972593 CATGAACAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.22
Consensus pattern (40 bp):
GCGATTTGCTGACGTGGACACAAATAGCGCCCTCTAAGAC
Found at i:974344 original size:20 final size:20
Alignment explanation
Indices: 974321--974360 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
974311 TATTTTTCGA
974321 AAAATGATTTACTTTTCTGG
1 AAAATGATTTACTTTTCTGG
974341 AAAATGATTTACTTTTCTGG
1 AAAATGATTTACTTTTCTGG
974361 TGTTTGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (20 bp):
AAAATGATTTACTTTTCTGG
Found at i:974468 original size:20 final size:20
Alignment explanation
Indices: 974443--974480 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
974433 GTTTTTACAT
974443 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
974463 ATATTAATAATTTTATAT
1 ATATTAATAAATTTATAT
974481 TTTAAATTAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:974681 original size:41 final size:43
Alignment explanation
Indices: 974635--974715 Score: 148
Period size: 41 Copynumber: 1.9 Consensus size: 43
974625 TATATTTGCA
974635 TTAATAATTTTTTGAGAAA-T-TAAGCTACTTTCTTTGTAATT
1 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTAATT
974676 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTA
1 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTA
974716 TCAATACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 19 0.50
42 1 0.03
43 18 0.47
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (43 bp):
TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTAATT
Found at i:974696 original size:21 final size:21
Alignment explanation
Indices: 974635--974696 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
974625 TATATTTGCA
974635 TTAATAATTTTTTGAGAAA--
1 TTAATAATTTTTTGAGAAATT
* *
974654 TTAAGCTACTTTCTTT--GTAATT
1 TTAA--TAATTT-TTTGAGAAATT
974676 TTAATAATTTTTTGAGAAATT
1 TTAATAATTTTTTGAGAAATT
974697 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
19 7 0.22
20 8 0.25
21 10 0.31
22 7 0.22
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (21 bp):
TTAATAATTTTTTGAGAAATT
Found at i:976892 original size:17 final size:17
Alignment explanation
Indices: 976870--976903 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
976860 ATCCACTAAT
*
976870 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
976887 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
976904 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:981531 original size:17 final size:17
Alignment explanation
Indices: 981509--981542 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
981499 ATCCACTAAT
*
981509 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
981526 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
981543 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:987530 original size:47 final size:47
Alignment explanation
Indices: 987472--987562 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
987462 ATCCGGTGAG
*
987472 TTAGTACCCATCAAAAAGTAGAAAAATCCTAAGTCAATTCGACACTA
1 TTAGTACCCATCAAAAAGTAGAAAAATCATAAGTCAATTCGACACTA
* *
987519 TTAGTATCCATCAAAAAGTAGAAGAATCATAAGTCAATTCGACA
1 TTAGTACCCATCAAAAAGTAGAAAAATCATAAGTCAATTCGACA
987563 GTTAGTGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (47 bp):
TTAGTACCCATCAAAAAGTAGAAAAATCATAAGTCAATTCGACACTA
Found at i:989978 original size:22 final size:23
Alignment explanation
Indices: 989950--990018 Score: 90
Period size: 22 Copynumber: 3.1 Consensus size: 23
989940 TATGCACTAT
989950 TAAACAGAGAGCACTAAA-GTGC
1 TAAACAGAGAGCACTAAATGTGC
*
989972 TATACAGAGAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAATGTGC
* *
989994 TAAACGGAGAGCACT-AATATGC
1 TAAACAGAGAGCACTAAATGTGC
990016 TAA
1 TAA
990019 TAATCGAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.07
22 38 0.93
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:993458 original size:23 final size:23
Alignment explanation
Indices: 993405--993459 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
993395 AATTCAATTT
*
993405 AACTTACATTTTGTAAGTTATCA
1 AACTTACCTTTTGTAAGTTATCA
993428 AACTTACCTTTTGTAAGTTATCA
1 AACTTACCTTTTGTAAGTTATCA
993451 AACTTACCT
1 AACTTACCT
993460 CAACACATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (23 bp):
AACTTACCTTTTGTAAGTTATCA
Found at i:993601 original size:22 final size:22
Alignment explanation
Indices: 993575--993641 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
993565 TGCACTATTG
993575 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* * * *
993597 TACAGAGAACACGAATGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
993619 AAC-GAAGAGCACTAATA-TGCTA
1 AACAG-AGAGCACTAA-AGTGCTA
993641 A
1 A
993642 TAATCGAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:995137 original size:15 final size:15
Alignment explanation
Indices: 995117--995148 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
995107 TTCTTACAAA
995117 AGTCATTTCCAAATT
1 AGTCATTTCCAAATT
*
995132 AGTCATTTTCAAATT
1 AGTCATTTCCAAATT
995147 AG
1 AG
995149 GTACATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (15 bp):
AGTCATTTCCAAATT
Found at i:1001686 original size:22 final size:24
Alignment explanation
Indices: 1001661--1001706 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1001651 AATATATGTA
1001661 AATAATTAGGAT-AAA-AATATAT
1 AATAATTAGGATGAAATAATATAT
* *
1001683 AATATTTAGGTTGAAATAATATAT
1 AATAATTAGGATGAAATAATATAT
1001707 TCTTTCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (24 bp):
AATAATTAGGATGAAATAATATAT
Found at i:1010041 original size:24 final size:24
Alignment explanation
Indices: 1010013--1010066 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1010003 ATGGATGAGC
* *
1010013 CCCGTAAGGTGCCGGTTGAGGG-G
1 CCCGTAAGGAGCCGATTGAGGGTG
1010036 CTCCGTAAGGAGCCGATTGAGGGTG
1 C-CCGTAAGGAGCCGATTGAGGGTG
1010061 CCCGTA
1 CCCGTA
1010067 TGAAGGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.89
25 2 0.07
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.19
Consensus pattern (24 bp):
CCCGTAAGGAGCCGATTGAGGGTG
Found at i:1011668 original size:24 final size:24
Alignment explanation
Indices: 1011640--1011697 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1011630 GCCTGAACTT
* *
1011640 GGTGGAGGAGCCCCTTATGGTGCC
1 GGTGGAGGAGCCCCATACGGTGCC
*
1011664 GGTGGAGCAGCCCCATACGGTGCC
1 GGTGGAGGAGCCCCATACGGTGCC
* *
1011688 GATGAAGGAG
1 GGTGGAGGAG
1011698 GTGCATATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.41, T:0.16
Consensus pattern (24 bp):
GGTGGAGGAGCCCCATACGGTGCC
Found at i:1013875 original size:34 final size:33
Alignment explanation
Indices: 1013817--1013885 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 33
1013807 TAAACACCAG
1013817 AAAATATTTTCCAGTAAATCATTTTACAGAAAAAT
1 AAAATATTTTCCAG-AAATCATTTTAC-GAAAAAT
1013852 AAAATATTTTCCCA-AAATCATTTTACGAAAAAT
1 AAAATATTTT-CCAGAAATCATTTTACGAAAAAT
1013885 A
1 A
1013886 TGTTACTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 8 0.24
34 12 0.36
35 10 0.30
36 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (33 bp):
AAAATATTTTCCAGAAATCATTTTACGAAAAAT
Found at i:1016386 original size:32 final size:32
Alignment explanation
Indices: 1016349--1016412 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1016339 GTTGCTTGCC
1016349 TGCATTGCTTTTGGTTG-ATTTGCCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTG-CTTCCTATT
* *
1016381 TGCATTGGTTTTGGTTGTTTTTGCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
1016413 ATATGCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (32 bp):
TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
Found at i:1016740 original size:218 final size:218
Alignment explanation
Indices: 1016362--1016790 Score: 750
Period size: 218 Copynumber: 2.0 Consensus size: 218
1016352 ATTGCTTTTG
* * * **
1016362 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTGCTTCCTATTATATGCATATGATG
1 GTTGATTTGCCTTCCAATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
* *
1016427 AACTCTACTTGGATTCCCCTTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
66 AACTCTACTTGGATTCCCCTTCAAGACATCATGGGAGATGCTAACTCGAGTTTCTGATGCAAACA
1016492 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
*
1016557 TCATTCTTTCTTCAATTTGGTTT
196 TCATTCATTCTTCAATTTGGTTT
1016580 GTTGATTTGCCTTCCAATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
1 GTTGATTTGCCTTCCAATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
* * *
1016645 AACTCTACTTGGATTCCTCTTCAAGACATCATGGGAGATGCTAACTTGAGTTTCTGATGGAAACA
66 AACTCTACTTGGATTCCCCTTCAAGACATCATGGGAGATGCTAACTCGAGTTTCTGATGCAAACA
*
1016710 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGGAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
1016775 TCATTCATTCTTCAAT
196 TCATTCATTCTTCAAT
1016791 CCTCTAATAA
Statistics
Matches: 199, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
218 199 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (218 bp):
GTTGATTTGCCTTCCAATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
AACTCTACTTGGATTCCCCTTCAAGACATCATGGGAGATGCTAACTCGAGTTTCTGATGCAAACA
TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
TCATTCATTCTTCAATTTGGTTT
Found at i:1019357 original size:14 final size:15
Alignment explanation
Indices: 1019335--1019411 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1019325 CAATCAAACA
1019335 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1019349 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1019364 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
*
1019384 CCCG-AAATCATTTT
1 CCAGAAAATCATTTT
*
1019398 ACAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
1019412 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 15 0.31
16 1 0.02
18 1 0.02
19 3 0.06
20 8 0.16
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1019394 original size:34 final size:35
Alignment explanation
Indices: 1019339--1019405 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1019329 CAAACACCAG
*
1019339 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1019374 AAAACATTTTCCCG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1019406 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1019772 original size:24 final size:24
Alignment explanation
Indices: 1019745--1019798 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1019735 TGAATCAAAT
1019745 CAAAATTTCATGCATTAAATGGAA
1 CAAAATTTCATGCATTAAATGGAA
1019769 CAAAATTTCATGCATTAAATGGAA
1 CAAAATTTCATGCATTAAATGGAA
1019793 CAAAAT
1 CAAAAT
1019799 CAAACTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (24 bp):
CAAAATTTCATGCATTAAATGGAA
Found at i:1020290 original size:29 final size:29
Alignment explanation
Indices: 1020206--1020294 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 29
1020196 GATTAAATCA
* *
1020206 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAG-TTCAAGTATACAATTGCACC
* * * *
1020236 ACAATTAGAATTTCATGTGTATAATTGCACC
1 A-AATTA-AAGTTCAAGTATACAATTGCACC
*
1020267 AAATTAAAGTTCACGTATACAATTGCAC
1 AAATTAAAGTTCAAGTATACAATTGCAC
1020295 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 18 0.38
30 6 0.13
31 21 0.45
32 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (29 bp):
AAATTAAAGTTCAAGTATACAATTGCACC
Found at i:1024052 original size:29 final size:30
Alignment explanation
Indices: 1024019--1024077 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1024009 TCAAAATTTT
*
1024019 ATAAAATTGCACA-AAAGCAAAGTTCATAC
1 ATAAAATTACACATAAAGCAAAGTTCATAC
*
1024048 ATAAAATTACACATTAAATCAAAGTTCATA
1 ATAAAATTACACA-TAAAGCAAAGTTCATA
1024078 AGTTTGGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
31 14 0.54
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (30 bp):
ATAAAATTACACATAAAGCAAAGTTCATAC
Found at i:1024749 original size:13 final size:13
Alignment explanation
Indices: 1024731--1024755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1024721 AGTTTGATAA
1024731 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1024744 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1024756 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1025425 original size:3 final size:3
Alignment explanation
Indices: 1025417--1025445 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1025407 ATAGGAAAAA
1025417 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1025446 AATCTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1045798 original size:31 final size:30
Alignment explanation
Indices: 1045741--1045798 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
1045731 CATAAAAAAG
* * *
1045741 GTTTAAACCTCAATATCAGAACAATTGGCT
1 GTTTAAACCCCAAAATAAGAACAATTGGCT
*
1045771 GTTTCAAACCCCAAAATAAGAATAATTG
1 GTTT-AAACCCCAAAATAAGAACAATTG
1045799 TCAAACCCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 4 0.17
31 19 0.83
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (30 bp):
GTTTAAACCCCAAAATAAGAACAATTGGCT
Found at i:1050155 original size:19 final size:18
Alignment explanation
Indices: 1050114--1050157 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1050104 TAGTTAAGAA
*
1050114 ATTATTAAAATAAATTTT
1 ATTATTAAAATAAATTAT
* *
1050132 TTTATATAAAATAAGTTAT
1 ATTAT-TAAAATAAATTAT
1050151 ATTATTA
1 ATTATTA
1050158 CAAGTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTATTAAAATAAATTAT
Found at i:1054751 original size:25 final size:25
Alignment explanation
Indices: 1054721--1054770 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1054711 TTCCACTCTT
1054721 GAAATCATTTTTTTTCTTCAATTGC
1 GAAATCATTTTTTTTCTTCAATTGC
1054746 GAAATCATTTTTTTTCTTCAATTGC
1 GAAATCATTTTTTTTCTTCAATTGC
1054771 ATCCAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (25 bp):
GAAATCATTTTTTTTCTTCAATTGC
Found at i:1067069 original size:21 final size:22
Alignment explanation
Indices: 1067040--1067086 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1067030 CAGAAGGAGT
*
1067040 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1067062 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1067083 GAGT
1 GAGT
1067087 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1078788 original size:30 final size:28
Alignment explanation
Indices: 1078753--1078818 Score: 69
Period size: 31 Copynumber: 2.2 Consensus size: 28
1078743 TACTTGAGGT
* * **
1078753 TTTTTTTTTGTTCCAATTTGGTACCTAATT
1 TTTTTTTTTATCCCAATTAAGTACCT--TT
1078783 TTTTTTCTTTATCCCAATTAAGTACCTTT
1 TTTTTT-TTTATCCCAATTAAGTACCTTT
1078812 TTTTTTT
1 TTTTTTT
1078819 ACTAAAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 8 0.26
30 6 0.19
31 16 0.52
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (28 bp):
TTTTTTTTTATCCCAATTAAGTACCTTT
Found at i:1083044 original size:29 final size:28
Alignment explanation
Indices: 1083011--1083067 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1083001 TTAGATTTTT
1083011 TTTAATAGTATAA-GAACTAAATTGATCCA
1 TTTAATA--ATAATGAACTAAATTGATCCA
* *
1083040 TTTAATAATAATGGACTAATTTGATCCA
1 TTTAATAATAATGAACTAAATTGATCCA
1083068 ATCCCTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
TTTAATAATAATGAACTAAATTGATCCA
Found at i:1087443 original size:2 final size:2
Alignment explanation
Indices: 1087436--1087487 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1087426 TTCAGAGTCT
1087436 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1087478 TC TC TC TC TC
1 TC TC TC TC TC
1087488 GCACACACGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1088719 original size:21 final size:21
Alignment explanation
Indices: 1088694--1088738 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1088684 TGAATCAAGT
*
1088694 AAAATTATACAAGTT-AAATTA
1 AAAATTA-AAAAGTTCAAATTA
*
1088715 AAAATTAAAAATTTCAAATTA
1 AAAATTAAAAAGTTCAAATTA
1088736 AAA
1 AAA
1088739 TATTGTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTAAAAAGTTCAAATTA
Found at i:1091827 original size:24 final size:24
Alignment explanation
Indices: 1091799--1091858 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1091789 TGTCAAGATG
*
1091799 AAAATTTTCAAA-TCTGAAATATAA
1 AAAATTTT-AAATTCTGAAAAATAA
* *
1091823 AAAATTTTAAATTTTTAAAAATAA
1 AAAATTTTAAATTCTGAAAAATAA
1091847 AAAA-TTTAAATT
1 AAAATTTTAAATT
1091859 TAAATGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATTTTAAATTCTGAAAAATAA
Found at i:1094577 original size:40 final size:39
Alignment explanation
Indices: 1094494--1094579 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
1094484 TATTTTTTTA
* * *
1094494 ATTTTT-AAATTTAAAAACCTTTAAAAATTATAAAACTT
1 ATTTTTAAAACTTAAAAAACATTAAAAATTATAAAACTT
* ** *
1094532 GTTTTTAAAACTTAAAAAACATTAAATTTTATAAAAATTT
1 ATTTTTAAAACTTAAAAAACATTAAAAATTAT-AAAACTT
1094572 ATTTTTAA
1 ATTTTTAA
1094580 TACAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
38 5 0.13
39 20 0.53
40 13 0.34
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (39 bp):
ATTTTTAAAACTTAAAAAACATTAAAAATTATAAAACTT
Found at i:1096913 original size:22 final size:22
Alignment explanation
Indices: 1096871--1096913 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1096861 ATCTAAATTT
*
1096871 AGATGATTAATTAGTTAGTTAG
1 AGATGATTAATTAATTAGTTAG
1096893 AGATGAGTTAATTAATT-GTTA
1 AGATGA-TTAATTAATTAGTTA
1096914 AAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (22 bp):
AGATGATTAATTAATTAGTTAG
Found at i:1098021 original size:17 final size:16
Alignment explanation
Indices: 1097990--1098025 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1097980 CCGAATATAA
1097990 TAAATATTTTTATTTT
1 TAAATATTTTTATTTT
* *
1098006 TAAATTTTTTTAATTT
1 TAAATATTTTTATTTT
1098022 TAAA
1 TAAA
1098026 ATACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAAATATTTTTATTTT
Found at i:1098027 original size:17 final size:16
Alignment explanation
Indices: 1097991--1098034 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1097981 CGAATATAAT
*
1097991 AAATATTTTTATTTTT
1 AAATATTTTTATTTTA
*
1098007 AAATTTTTTTAATTTTA
1 AAATATTTTT-ATTTTA
1098024 AAATACTTTTT
1 AAATA-TTTTT
1098035 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
AAATATTTTTATTTTA
Found at i:1100801 original size:47 final size:47
Alignment explanation
Indices: 1100750--1100845 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
1100740 ACATAATTTA
1100750 CTTAAACTAATTTATTTTTGTTGTATTTAATTTCTAGTTTGTAACAC
1 CTTAAACTAATTTATTTTTGTTGTATTTAATTTCTAGTTTGTAACAC
*
1100797 CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
1 CTTAAACTAATTTATTTTTGTTGTATTTAATTTCTAGTTTGTAACAC
1100844 CT
1 CT
1100846 CTATATCCGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (47 bp):
CTTAAACTAATTTATTTTTGTTGTATTTAATTTCTAGTTTGTAACAC
Found at i:1101534 original size:22 final size:22
Alignment explanation
Indices: 1101509--1101550 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1101499 CACTATTAAG
*
1101509 CAGATAGCACTAAA-GTGCTATA
1 CAGAAAGCAC-AAATGTGCTATA
1101531 CAGAAAGCACAAATGTGCTA
1 CAGAAAGCACAAATGTGCTA
1101551 ATAATCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
CAGAAAGCACAAATGTGCTATA
Found at i:1101587 original size:25 final size:25
Alignment explanation
Indices: 1101509--1101588 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
1101499 CACTATTAAG
*
1101509 CAGATAGCACTAAAGTGCT-AT-A-
1 CAGAGAGCACTAAAGTGCTAATAAT
*
1101531 CAGAAAGCAC-AAATGTGCTAATAAT
1 CAGAGAGCACTAAA-GTGCTAATAAT
* *
1101556 CATAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAAAGTGCTAATAAT
1101581 CAGAGAGC
1 CAGAGAGC
1101589 GCGCTAAGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.06
22 14 0.29
23 2 0.04
24 1 0.02
25 26 0.54
26 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (25 bp):
CAGAGAGCACTAAAGTGCTAATAAT
Found at i:1105206 original size:18 final size:19
Alignment explanation
Indices: 1105162--1105213 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1105152 CTTCAAATTT
* *
1105162 TATATAATAATTTAT-TAA
1 TATAAAATAATTTTTATAA
*
1105180 TATATAATAATTTTTATAA
1 TATAAAATAATTTTTATAA
*
1105199 TA-AAAATAATGTTTA
1 TATAAAATAATTTTTA
1105214 ATATTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATAAAATAATTTTTATAA
Found at i:1109636 original size:49 final size:48
Alignment explanation
Indices: 1109560--1109823 Score: 207
Period size: 49 Copynumber: 5.4 Consensus size: 48
1109550 AAAACAAAAA
* * * *
1109560 ACAAAAAAAAAA-TTAGGTGCTGGCTTGTCAGTGGCCAGCACCAGTAT
1 ACAAAAAAAAAATTTTGGTGCTGCCTTGTCAATGGCCAGCACCAATAT
*
1109607 ACAAAAAAAAAAATTTTGGTGCTACCTTGTCAATGGCC-GTCACCAATAT
1 AC-AAAAAAAAAATTTTGGTGCTGCCTTGTCAATGGCCAG-CACCAATAT
* * *
1109656 ACGAAAAAAAAATTTGGGGTGCTGGCC-TGTCAATGGCTAGCACCACCA-AT
1 ACAAAAAAAAAATTT-TGGTGCT-GCCTTGTCAATGGCCAGCACCA--ATAT
* * *
1109706 ACGAAAAAAAAAATTTTGGGTGTTGGCC-TGTCAATGGCCGGCACCAACAAT
1 AC-AAAAAAAAAATTTT-GGTGCT-GCCTTGTCAATGGCCAGCACCAA-TAT
* * * * * * *
1109757 ACGAAAAAGAAATTTAGGTGTTGGCC-TGTCAATGACCAACACCAGTAT
1 ACAAAAAAAAAATTTTGGTGCT-GCCTTGTCAATGGCCAGCACCAATAT
1109805 ACGAAAAAAAATAATTTTG
1 AC-AAAAAAAA-AATTTTG
1109824 AGAGAGCCAT
Statistics
Matches: 178, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
47 2 0.01
48 27 0.15
49 83 0.47
50 24 0.13
51 42 0.24
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (48 bp):
ACAAAAAAAAAATTTTGGTGCTGCCTTGTCAATGGCCAGCACCAATAT
Found at i:1109764 original size:100 final size:99
Alignment explanation
Indices: 1109554--1109823 Score: 309
Period size: 100 Copynumber: 2.7 Consensus size: 99
1109544 AAATTAAAAA
* * * * *
1109554 CAAAAAAC-AAAAAA-AAAATTAGGTGCTGGCTTGTCAGTGGCCAGCACCAGTATACAAAAAAAA
1 CAAAATACGAAAAAAGAAATTTAGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACGAAAAAAA
*
1109617 AAATTTT-GGTGCTACCTTGTCAATGGCCGTCAC
66 AAATTTTGGGTGCTACCTTGTCAATGGCCGGCAC
* * * **
1109650 CAATATACGAAAAAA-AAATTTGGGGTGCTGGCCTGTCAATGGCTAGCACCACCAATACGAAAAA
1 CAAAATACGAAAAAAGAAATTT-AGGTGCTGGCCTGTCAATGGCCAGCACCA-GTATACGAAAAA
* *
1109714 AAAAATTTTGGGTGTTGGCC-TGTCAATGGCCGGCAC
64 AAAAATTTTGGGTGCT-ACCTTGTCAATGGCCGGCAC
* * *
1109750 CAACAATACG-AAAAAGAAATTTAGGTGTTGGCCTGTCAATGACCAACACCAGTATACGAAAAAA
1 CAA-AATACGAAAAAAGAAATTTAGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACGAAAAAA
1109814 AATAATTTTG
65 AA-AATTTTG
1109824 AGAGAGCCAT
Statistics
Matches: 145, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
96 6 0.04
97 11 0.08
98 25 0.17
99 31 0.21
100 59 0.41
101 13 0.09
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (99 bp):
CAAAATACGAAAAAAGAAATTTAGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACGAAAAAAA
AAATTTTGGGTGCTACCTTGTCAATGGCCGGCAC
Found at i:1110701 original size:9 final size:9
Alignment explanation
Indices: 1110687--1110714 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1110677 AATTAATATT
1110687 AAAAAATAA
1 AAAAAATAA
1110696 AAAAAATAA
1 AAAAAATAA
1110705 AAAAAATAA
1 AAAAAATAA
1110714 A
1 A
1110715 TATTTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1112803 original size:33 final size:33
Alignment explanation
Indices: 1112761--1112839 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1112751 ATAGAGTGAT
*
1112761 CGACGGTCGTCGGTGGTGGTTGAGGGTGAATAG
1 CGACGGTCGTCGGTGGTGGTTAAGGGTGAATAG
*
1112794 CGACGGTCGTTGGTGGTGGTTAAGGGTGAATAG
1 CGACGGTCGTCGGTGGTGGTTAAGGGTGAATAG
* *
1112827 CGGCAGTCGTCGG
1 CGACGGTCGTCGG
1112840 CAATGGTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.14, G:0.47, T:0.24
Consensus pattern (33 bp):
CGACGGTCGTCGGTGGTGGTTAAGGGTGAATAG
Found at i:1112847 original size:33 final size:33
Alignment explanation
Indices: 1112777--1112856 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
1112767 TCGTCGGTGG
* * ***
1112777 TGGTTGAGGGTGAATAGCGACGGTCGTTGGTGG
1 TGGTTGAGGGTGAATAGCGACAGTCGTCGGCAA
* *
1112810 TGGTTAAGGGTGAATAGCGGCAGTCGTCGGCAA
1 TGGTTGAGGGTGAATAGCGACAGTCGTCGGCAA
*
1112843 TGGTTGAGAGTGAA
1 TGGTTGAGGGTGAA
1112857 CCGCGGTGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.21, C:0.10, G:0.44, T:0.25
Consensus pattern (33 bp):
TGGTTGAGGGTGAATAGCGACAGTCGTCGGCAA
Found at i:1113204 original size:13 final size:14
Alignment explanation
Indices: 1113179--1113214 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1113169 AATTTCATTT
1113179 TTTTCATTT-AATA
1 TTTTCATTTAAATA
1113192 TTTT-ATTTAAATA
1 TTTTCATTTAAATA
1113205 TTTTCATTTA
1 TTTTCATTTA
1113215 TTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 12 0.57
14 5 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCATTTAAATA
Found at i:1113220 original size:14 final size:14
Alignment explanation
Indices: 1113179--1113220 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1113169 AATTTCATTT
1113179 TTTTCATTTA-ATA
1 TTTTCATTTATATA
*
1113192 TTTT-ATTTAAATA
1 TTTTCATTTATATA
*
1113205 TTTTCATTTATTTA
1 TTTTCATTTATATA
1113219 TT
1 TT
1113221 ATTTTTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 9 0.36
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTCATTTATATA
Found at i:1113354 original size:12 final size:11
Alignment explanation
Indices: 1113329--1113353 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1113319 TTTCAAATTT
1113329 AAAGGCAAAAA
1 AAAGGCAAAAA
1113340 AAAGGCAAAAA
1 AAAGGCAAAAA
1113351 AAA
1 AAA
1113354 AAAGGCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGGCAAAAA
Found at i:1113354 original size:14 final size:14
Alignment explanation
Indices: 1113335--1113362 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1113325 ATTTAAAGGC
1113335 AAAAAAAAGGCAAA
1 AAAAAAAAGGCAAA
1113349 AAAAAAAAGGCAAA
1 AAAAAAAAGGCAAA
1113363 TGAGTCATTT
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:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGCAAA
Found at i:1113395 original size:5 final size:5
Alignment explanation
Indices: 1113385--1113479 Score: 73
Period size: 5 Copynumber: 17.6 Consensus size: 5
1113375 ACCTCTTTTT
* * *
1113385 TTTCA TTTCA TTTCCT TTTCA TTTTCA TTTCA TTTTA TTTTTA TTTCA
1 TTTCA TTTCA TTT-CA TTTCA -TTTCA TTTCA TTTCA -TTTCA TTTCA
* * *
1113433 TTTCA TTCTAA TTTCA TTTCCA TTACCA TTTCCC TTTCA TTTCA TTT
1 TTTCA TT-TCA TTTCA TTT-CA TT-TCA TTT-CA TTTCA TTTCA TTT
1113480 AAAAAAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
5 43 0.59
6 30 0.41
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:1113405 original size:16 final size:16
Alignment explanation
Indices: 1113384--1113479 Score: 70
Period size: 17 Copynumber: 5.9 Consensus size: 16
1113374 AACCTCTTTT
1113384 TTTTCATTTCATTTCC
1 TTTTCATTTCATTTCC
*
1113400 TTTTCATTTTCATTTCA
1 TTTTCA-TTTCATTTCC
*
1113417 TTTT-ATTTTTATTT-C
1 TTTTCA-TTTCATTTCC
* * *
1113432 ATTTCATTCTAATTTCA
1 TTTTCATT-TCATTTCC
* *
1113449 TTTCCATTACCATTTCC
1 TTTTCATT-TCATTTCC
*
1113466 CTTTCATTTCATTT
1 TTTTCATTTCATTT
1113480 AAAAAAAATA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
15 5 0.08
16 26 0.43
17 30 0.49
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCATTTCATTTCC
Found at i:1113531 original size:22 final size:22
Alignment explanation
Indices: 1113490--1113538 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
1113480 AAAAAAAATA
1113490 TTTTTCAATTTCAATTTATT-T
1 TTTTTCAATTTCAATTTATTAT
*
1113511 TTTTCTCAA-TTCATTTATATTAT
1 TTTT-TCAATTTCAATT-TATTAT
1113534 TTTTT
1 TTTTT
1113539 AATGTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTCAATTTCAATTTATTAT
Found at i:1115619 original size:91 final size:91
Alignment explanation
Indices: 1115464--1115645 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
1115454 AGACTGTGTT
1115464 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1115529 TTTTTTGTTATCAAATTGTTGTCTTA
66 TTTTTTGTTATCAAATTGTTGTCTTA
*
1115555 GACTTCGTTACTTTATATTCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1115620 TTTTTTGTTATCAAATTGTTGTCTTA
66 TTTTTTGTTATCAAATTGTTGTCTTA
1115646 CACACAACTT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (91 bp):
GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
TTTTTTGTTATCAAATTGTTGTCTTA
Found at i:1116513 original size:11 final size:11
Alignment explanation
Indices: 1116497--1116535 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
1116487 TTGATTTTTG
1116497 ATAAATGGAAC
1 ATAAATGGAAC
1116508 ATAAATGGAAC
1 ATAAATGGAAC
1116519 ATAAAATGGAAC
1 AT-AAATGGAAC
1116531 ATAAA
1 ATAAA
1116536 AAGGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (11 bp):
ATAAATGGAAC
Found at i:1116527 original size:12 final size:12
Alignment explanation
Indices: 1116499--1116541 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
1116489 GATTTTTGAT
1116499 AAATGGAACAT-
1 AAATGGAACATA
1116510 AAATGGAACATA
1 AAATGGAACATA
1116522 AAATGGAACATA
1 AAATGGAACATA
*
1116534 AAAAGGAA
1 AAATGGAA
1116542 AAAAAATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.60, C:0.07, G:0.19, T:0.14
Consensus pattern (12 bp):
AAATGGAACATA
Found at i:1116547 original size:23 final size:23
Alignment explanation
Indices: 1116499--1116548 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1116489 GATTTTTGAT
* *
1116499 AAATGGAACATAAATGGAACATA
1 AAATGGAACATAAAAGGAACAAA
1116522 AAATGGAACATAAAAAGGAA-AAA
1 AAATGGAACAT-AAAAGGAACAAA
1116545 AAAT
1 AAAT
1116549 TCAAACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.64, C:0.06, G:0.16, T:0.14
Consensus pattern (23 bp):
AAATGGAACATAAAAGGAACAAA
Found at i:1119247 original size:49 final size:50
Alignment explanation
Indices: 1119159--1119300 Score: 137
Period size: 49 Copynumber: 2.8 Consensus size: 50
1119149 TTTTCGTAGA
* * * * * *
1119159 CTGGTGCCGCCCATTGACAAGCTAGCACCCCAAGA-TTTTTTTTCCGTACTG
1 CTGGTGTCGACCATTGACAGGCCAACA-CCCAA-ATTTTTTTTTCCATACTG
* * * *
1119210 CTGGTGTCGGCCATTTTA-AGGCCAACA-CCAATTTTTTTTTTTCATACTG
1 CTGGTGTCGACCA-TTGACAGGCCAACACCCAAATTTTTTTTTCCATACTG
*
1119259 CTGGTGTCGACCATTGACAGGCCAGCACCCAAATTTTTTTTT
1 CTGGTGTCGACCATTGACAGGCCAACACCCAAATTTTTTTTT
1119301 AAATTTTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
48 3 0.04
49 38 0.51
50 13 0.18
51 17 0.23
52 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (50 bp):
CTGGTGTCGACCATTGACAGGCCAACACCCAAATTTTTTTTTCCATACTG
Found at i:1123911 original size:16 final size:15
Alignment explanation
Indices: 1123890--1123925 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
1123880 ATTTGAATTG
1123890 AAAATATTGAGCGAA
1 AAAATATTGAGCGAA
1123905 TAAAATATTGAGCGAA
1 -AAAATATTGAGCGAA
1123921 AAAAT
1 AAAAT
1123926 TAAACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (15 bp):
AAAATATTGAGCGAA
Found at i:1124154 original size:7 final size:8
Alignment explanation
Indices: 1124137--1124208 Score: 71
Period size: 8 Copynumber: 9.1 Consensus size: 8
1124127 AATTTATTTT
1124137 AAAAATAA
1 AAAAATAA
1124145 AAAAATAA
1 AAAAATAA
*
1124153 AAAAAGTATTT
1 AAAAA-TA--A
*
1124164 TAAAAT--
1 AAAAATAA
1124170 AAAAATAA
1 AAAAATAA
1124178 AAAAATAA
1 AAAAATAA
1124186 AAAAAT-A
1 AAAAATAA
1124193 AAAAAT-A
1 AAAAATAA
1124200 AAAAATAA
1 AAAAATAA
1124208 A
1 A
1124209 TATTTATTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.09
7 14 0.25
8 29 0.53
9 2 0.04
10 1 0.02
11 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:1124190 original size:22 final size:22
Alignment explanation
Indices: 1124165--1124208 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1124155 AAAGTATTTT
1124165 AAAAT-AAAAATAAAAAAATAAA
1 AAAATAAAAAAT-AAAAAATAAA
1124187 AAAATAAAAAATAAAAAATAAA
1 AAAATAAAAAATAAAAAATAAA
1124209 TATTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAATAAAAAATAAA
Found at i:1128093 original size:23 final size:22
Alignment explanation
Indices: 1128066--1128120 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
1128056 ATTTTTATAA
1128066 TTTAAAATATCACA-ATAAAAAAT
1 TTTAAAATAT-A-ATATAAAAAAT
*
1128089 TTTAAAAAAAATAATATAAAAAAT
1 TTT--AAAATATAATATAAAAAAT
1128113 TTTAAAAT
1 TTTAAAAT
1128121 GTAAGTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 13 0.48
25 6 0.22
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATATAATATAAAAAAT
Found at i:1137492 original size:16 final size:17
Alignment explanation
Indices: 1137461--1137505 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1137451 AATTTAAAAT
1137461 AATATATATAAAAATCA
1 AATATATATAAAAATCA
*
1137478 AATATA-ATCAAAATCA
1 AATATATATAAAAATCA
*
1137494 AGTAT-TATAAAA
1 AATATATATAAAA
1137506 CACAAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (17 bp):
AATATATATAAAAATCA
Found at i:1139023 original size:30 final size:29
Alignment explanation
Indices: 1138961--1139024 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1138951 ACGATAAAGA
* *
1138961 AAATTTTTTTCCATAATAAAATAAAAATT
1 AAATTTTTTTCCATAAAAAAATAAAAACT
* **
1138990 AAATTTTTTTCACCTAAAAAAATTGAAACT
1 AAATTTTTTTC-CATAAAAAAATAAAAACT
1139020 AAATT
1 AAATT
1139025 AAAAAAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATTTTTTTCCATAAAAAAATAAAAACT
Found at i:1143834 original size:112 final size:113
Alignment explanation
Indices: 1143649--1143855 Score: 294
Period size: 112 Copynumber: 1.8 Consensus size: 113
1143639 GACGTGAGCT
* *
1143649 AGAACCCCACTAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCG
1 AGAACCCCACCAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCA
* * *
1143714 ATGTACTCTCAATTTTGTAAACCAAGCCCTCACAAAGGGATGTGGGCG
66 AGGTACTCTCAATTCTGTAAACCAAACCCTCACAAAGGGATGTGGGCG
* * * *
1143762 AGAACCCCACCAGGGGCGAGATGCTTATGT-CCCTTGGTGGGTGG-TGTGTGCTC-ATGTACGGT
1 AGAACCCCACCA-GGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGC-CAATGTACGGT
1143824 CAAGGTACTCTCAATTCTGTAAACCAAACCCT
64 CAAGGTACTCTCAATTCTGTAAACCAAACCCT
1143856 TAAGGCAACT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
112 44 0.53
113 25 0.30
114 14 0.17
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (113 bp):
AGAACCCCACCAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCA
AGGTACTCTCAATTCTGTAAACCAAACCCTCACAAAGGGATGTGGGCG
Found at i:1144528 original size:32 final size:31
Alignment explanation
Indices: 1144483--1144578 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
1144473 CTTAGATAAT
1144483 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1144514 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
* *
1144546 TTGAAAGAGTTGTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1144577 TT
1 TT
1144579 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 32 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:1151864 original size:13 final size:13
Alignment explanation
Indices: 1151846--1151881 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1151836 TCATTTCAGT
1151846 AGCTCGTTTGACC
1 AGCTCGTTTGACC
1151859 AGCTCGTTTGACC
1 AGCTCGTTTGACC
*
1151872 AACTCGTTTG
1 AGCTCGTTTG
1151882 GTTTATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (13 bp):
AGCTCGTTTGACC
Found at i:1152429 original size:12 final size:12
Alignment explanation
Indices: 1152412--1152452 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1152402 TTCCCACTCA
*
1152412 TAATAATAATAC
1 TAATAATAATAT
*
1152424 TAATAATTATAT
1 TAATAATAATAT
*
1152436 TAATACTAATAT
1 TAATAATAATAT
1152448 TAATA
1 TAATA
1152453 TTTACTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:1152453 original size:18 final size:19
Alignment explanation
Indices: 1152412--1152454 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1152402 TTCCCACTCA
*
1152412 TAATAATAATACTAATAAT
1 TAATATTAATACTAATAAT
1152431 T-ATATTAATACTAAT-AT
1 TAATATTAATACTAATAAT
1152448 TAATATT
1 TAATATT
1152455 TACTTCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTAATACTAATAAT
Found at i:1153219 original size:19 final size:19
Alignment explanation
Indices: 1153174--1153213 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1153164 TTTGTTTTGT
*
1153174 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
1153192 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
1153211 TTT
1 TTT
1153214 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:1153370 original size:5 final size:5
Alignment explanation
Indices: 1153362--1153413 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
1153352 TATTTAATTT
* * *
1153362 ATATA ATATA ATACA ATATA ATATA ATATA TTATATA ATAAA ATATC ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA
1153414 TAAAACATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 34 0.87
7 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1153397 original size:17 final size:16
Alignment explanation
Indices: 1153361--1153416 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
1153351 CTATTTAATT
*
1153361 TATATAATATAATACA
1 TATATAATATAATATA
1153377 -ATATAATATAATATA
1 TATATAATATAATATA
*
1153392 TTATATAATAAAATATCA
1 -TATATAATATAATAT-A
1153410 TATATAA
1 TATATAA
1153417 AACATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 14 0.40
17 20 0.57
18 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
TATATAATATAATATA
Found at i:1153820 original size:19 final size:20
Alignment explanation
Indices: 1153779--1153824 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1153769 AATTACAAAA
* *
1153779 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATCTAT
1153799 AAAAATTCAAAAT-ATCTAT
1 AAAAATTCAAAATAATCTAT
1153818 AAAAATT
1 AAAAATT
1153825 TCAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTCAAAATAATCTAT
Found at i:1155364 original size:6 final size:6
Alignment explanation
Indices: 1155353--1155388 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1155343 AATGAGTACA
*
1155353 TATATT TATATT TATATG TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
1155389 GAATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:1155376 original size:18 final size:18
Alignment explanation
Indices: 1155353--1155387 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1155343 AATGAGTACA
1155353 TATATTTATATTTATATG
1 TATATTTATATTTATATG
1155371 TATATTTATATTTATAT
1 TATATTTATATTTATAT
1155388 TGAATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATATTTATATTTATATG
Found at i:1158420 original size:26 final size:27
Alignment explanation
Indices: 1158390--1158447 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1158380 CTTTAACAGG
1158390 TTCTTGCAAAGTTTG-TTTCCCCATTT
1 TTCTTGCAAAGTTTGTTTTCCCCATTT
*
1158416 TTCTTGCCAAGTTTGTTTTCCCCATTT
1 TTCTTGCAAAGTTTGTTTTCCCCATTT
1158443 TTCTT
1 TTCTT
1158448 TGTTGAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.53
Consensus pattern (27 bp):
TTCTTGCAAAGTTTGTTTTCCCCATTT
Found at i:1161518 original size:28 final size:29
Alignment explanation
Indices: 1161472--1161526 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1161462 GAATTTTAAG
* *
1161472 TTATTTTCATTATTTTAAATATAAAATAT
1 TTATTTTCATTATTATAAAAATAAAATAT
*
1161501 TTATTTTTA-TATTATAAAAATAAAAT
1 TTATTTTCATTATTATAAAAATAAAAT
1161527 TACTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTTCATTATTATAAAAATAAAATAT
Found at i:1161533 original size:29 final size:29
Alignment explanation
Indices: 1161472--1161533 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1161462 GAATTTTAAG
* * *
1161472 TTATTTTCATTATTTTAAATATAAAATAT
1 TTATTTTCATTATTATAAAAATAAAATAC
*
1161501 TTATTTTTA-TATTATAAAAATAAAATTAC
1 TTATTTTCATTATTATAAAAATAAAA-TAC
1161530 TTAT
1 TTAT
1161534 AAATTAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTTCATTATTATAAAAATAAAATAC
Found at i:1162677 original size:13 final size:13
Alignment explanation
Indices: 1162659--1162684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1162649 AGCCCTCCCT
1162659 TAATAAACAAAAA
1 TAATAAACAAAAA
1162672 TAATAAACAAAAA
1 TAATAAACAAAAA
1162685 GAGATTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
TAATAAACAAAAA
Found at i:1171768 original size:21 final size:21
Alignment explanation
Indices: 1171742--1171782 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1171732 ATCTGCTCAA
* *
1171742 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1171763 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1171783 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1191301 original size:236 final size:232
Alignment explanation
Indices: 1190783--1191447 Score: 736
Period size: 236 Copynumber: 2.8 Consensus size: 232
1190773 CACGATATAT
* * ** *
1190783 AAGGAAACTAAGACATGGATCATGAAAACCAGTCATTTCTCCTAGAACCTTATGGAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAG-ACAGTATGAAGCCAAAAGA
* * *
1190848 GAAAGAAAACGGAGTAACAGTAAAGAATCTGAGCATGCCATTAAA-CGAAATTACTCTCTGATAA
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACT-TCTGCTAA
* * ** * *** * *
1190912 TCATGAAAATGCAGGTA-GA-C-AGGATCC-TAAT--C-ATCCGTCCAAACCTCGAGCATAAAGC
129 TCAAGAAAATGCAGATAGGATCTAACATCCATGATGACTATGTATCCAAATCTCAAGCATAAAGC
*
1190970 ACATGTTAAAATTATTTCATGCATCCCCAACATGATATA
194 ACATGTTAAAATTATTTCATGCATCCCCAACATGATACA
* * * * * *
1191009 AAGAAAACCAAGTCATGGATCATGAAAACCGGTTATTCCTCCCAGATAGGTATGAAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGACA-GTATGAAGCCAAAAGA
*
1191074 GAAAGGAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTATCTGCTAA
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACT-TCTGCTAA
*
1191139 TCAAGAAAATGCAGATAGGATCTTAATCATCCATGATGACTATGTATCCTAATCTCAAGCATAAA
129 TCAAGAAAATGCAGATAGGATC-TAA-CATCCATGATGACTATGTATCCAAATCTCAAGCATAAA
* * ** * * *
1191204 GCGCATGTTACAATTATTTTGTGCATTCCCGACATGCTACA
192 GCACATGTTAAAATTATTTCATGCATCCCCAACATGATACA
* * *
1191245 AAGGAAACTAACTCATGGATCATGAAAATCAATTATTTCTCCTAGAGCAGTATGAAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGA-CAGTATGAAGCCAAAAGA
* * * *
1191310 GAAAGAAAACACAGCAACAGTAAAGAATCCAAGTATGCCATTAAACCGAAATTAC-TCTGCTAAT
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTTCTGCTAAT
* * * * *
1191374 CAAGAAAGTGCAGGTAGATAGAATCCTAACTATCCATGACGATTATGTATCCGAATCTCAAGCAT
130 CAAGAAAATGC----AGATAGGAT-CTAAC-ATCCATGATGACTATGTATCCAAATCTCAAGCAT
1191439 AAAGCACAT
189 AAAGCACAT
1191448 CTTGCAAAAT
Statistics
Matches: 366, Mismatches: 55, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
225 1 0.00
226 94 0.26
227 32 0.09
228 2 0.01
229 1 0.00
231 1 0.00
232 4 0.01
233 3 0.01
234 19 0.05
235 1 0.00
236 155 0.42
237 2 0.01
238 50 0.14
239 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (232 bp):
AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGACAGTATGAAGCCAAAAGAG
AAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTTCTGCTAATC
AAGAAAATGCAGATAGGATCTAACATCCATGATGACTATGTATCCAAATCTCAAGCATAAAGCAC
ATGTTAAAATTATTTCATGCATCCCCAACATGATACA
Found at i:1192201 original size:13 final size:12
Alignment explanation
Indices: 1192185--1192219 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1192175 ACAAAATTAG
1192185 AAAAAAAATGAAA
1 AAAAAAAAT-AAA
*
1192198 AAAAAAAGTAAA
1 AAAAAAAATAAA
1192210 AAAAAAAATA
1 AAAAAAAATA
1192220 TTTTTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:1200529 original size:10 final size:10
Alignment explanation
Indices: 1200514--1200540 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1200504 ATTAATTTTT
1200514 AATATTTAAA
1 AATATTTAAA
1200524 AATATTTAAA
1 AATATTTAAA
1200534 AATATTT
1 AATATTT
1200541 TTATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATTTAAA
Found at i:1201367 original size:12 final size:11
Alignment explanation
Indices: 1201348--1201377 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1201338 GGTATACAAC
1201348 ATAATTATAAT
1 ATAATTATAAT
1201359 ATGAATTATAAT
1 AT-AATTATAAT
1201371 ATAATTA
1 ATAATTA
1201378 GGGTGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
ATAATTATAAT
Found at i:1202480 original size:18 final size:18
Alignment explanation
Indices: 1202454--1202496 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1202444 TTTAACCATT
*
1202454 TAAAATATTATAAA-AATA
1 TAAATTATTA-AAATAATA
1202472 TAAATTATTAAAATAATA
1 TAAATTATTAAAATAATA
1202490 -AAATTAT
1 TAAATTAT
1202497 ATTTTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATTATTAAAATAATA
Found at i:1202484 original size:15 final size:17
Alignment explanation
Indices: 1202460--1202497 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1202450 CATTTAAAAT
1202460 ATTATAAAAAT-AT-AA
1 ATTATAAAAATAATAAA
*
1202475 ATTATTAAAATAATAAA
1 ATTATAAAAATAATAAA
1202492 ATTATA
1 ATTATA
1202498 TTTTAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATAAAAATAATAAA
Found at i:1202942 original size:26 final size:26
Alignment explanation
Indices: 1202911--1203038 Score: 171
Period size: 26 Copynumber: 5.2 Consensus size: 26
1202901 ATAATAATTC
1202911 GAATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
1202937 GAATGCAATGGATATAATTGTAGTT-
1 GAATGCAATGGATATAATTGTAGTTA
*
1202962 --A-G-AATGGATATAATTG-A-TCA
1 GAATGCAATGGATATAATTGTAGTTA
**
1202982 TCATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
1203008 GAATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
*
1203034 AAATG
1 GAATG
1203039 GATATAATTG
Statistics
Matches: 90, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 14 0.16
22 2 0.02
23 2 0.02
24 14 0.16
25 1 0.01
26 55 0.61
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (26 bp):
GAATGCAATGGATATAATTGTAGTTA
Found at i:1202990 original size:71 final size:71
Alignment explanation
Indices: 1202913--1203069 Score: 305
Period size: 71 Copynumber: 2.2 Consensus size: 71
1202903 AATAATTCGA
*
1202913 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
1 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAAAATGGATATAATTG
1202978 ATCATC
66 ATCATC
1202984 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAAAATGGATATAATTG
1 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAAAATGGATATAATTG
1203049 ATCATC
66 ATCATC
1203055 ATGCAATGGATATAA
1 ATGCAATGGATATAA
1203070 CATGATGATC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 85 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (71 bp):
ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAAAATGGATATAATTG
ATCATC
Found at i:1207851 original size:43 final size:42
Alignment explanation
Indices: 1207773--1207929 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 42
1207763 ACCGAGATTA
* *
1207773 CGTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGACTT
1 CGTGTAAGACCATGTCT-GGATATTGGCATCGATATGAGAATT
* *
1207815 CGTGTAAGACCATGTCTAGGACATTGGCATCGATATGTGAATT
1 CGTGTAAGACCATGTCT-GGATATTGGCATCGATATGAGAATT
* **
1207858 CGTGTAAGACCATGGCTGGAATATTGGCATCGATACAAG-ATT
1 CGTGTAAGACCATGTCTGG-ATATTGGCATCGATATGAGAATT
* *
1207900 ACATGTAAGACCATATCTGGGATA-TGGCAT
1 -CGTGTAAGACCATGTCT-GGATATTGGCAT
1207930 TGTTACGGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
42 31 0.32
43 65 0.66
44 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGATATTGGCATCGATATGAGAATT
Found at i:1212866 original size:11 final size:11
Alignment explanation
Indices: 1212839--1212888 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1212829 AAATTAATCC
1212839 TCTCTCAAATTT
1 TCTCTC-AATTT
*
1212851 CCTCTCAATTT
1 TCTCTCAATTT
1212862 TCTCTCAATTT
1 TCTCTCAATTT
* * *
1212873 GCTCTTAAATT
1 TCTCTCAATTT
1212884 TCTCT
1 TCTCT
1212889 TAAATCCCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:1212877 original size:22 final size:23
Alignment explanation
Indices: 1212839--1212893 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1212829 AAATTAATCC
*
1212839 TCTCTCAAATTTCCTCTCAATTT
1 TCTCTCAAATTTCCTCTCAAATT
* *
1212862 TCTCTC-AATTTGCTCTTAAATT
1 TCTCTCAAATTTCCTCTCAAATT
*
1212884 TCTCTTAAAT
1 TCTCTCAAAT
1212894 CCCTATTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.24, C:0.25, G:0.02, T:0.49
Consensus pattern (23 bp):
TCTCTCAAATTTCCTCTCAAATT
Found at i:1218247 original size:29 final size:30
Alignment explanation
Indices: 1218188--1218245 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1218178 TCTGAGCCTT
*
1218188 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1218218 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1218246 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1218475 original size:13 final size:13
Alignment explanation
Indices: 1218457--1218488 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1218447 TTTCCAGCAA
1218457 TTATGAATTTATT
1 TTATGAATTTATT
1218470 TTATGAATTTATT
1 TTATGAATTTATT
*
1218483 TGATGA
1 TTATGA
1218489 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1218696 original size:50 final size:50
Alignment explanation
Indices: 1218583--1218824 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
1218573 ATTTGGGTAA
* * *
1218583 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1218639 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1218689 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1218739 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1218789 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1218825 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1218772 original size:100 final size:103
Alignment explanation
Indices: 1218583--1218832 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
1218573 ATTTGGGTAA
1218583 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
1218648 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
1218689 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
1218751 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
1218789 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1218833 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:1221086 original size:14 final size:15
Alignment explanation
Indices: 1221067--1221109 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1221057 TTGATTGCCA
1221067 GTAAAATGTTTTAC-
1 GTAAAATGTTTTACT
*
1221081 GTAAAATGATTT-CT
1 GTAAAATGTTTTACT
*
1221095 GGAAAATGTTTTACT
1 GTAAAATGTTTTACT
1221110 TTTCTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 21 0.88
15 2 0.08
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (15 bp):
GTAAAATGTTTTACT
Found at i:1221115 original size:20 final size:20
Alignment explanation
Indices: 1221090--1221129 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1221080 CGTAAAATGA
*
1221090 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1221110 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1221130 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1222118 original size:31 final size:32
Alignment explanation
Indices: 1222058--1222122 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
1222048 TGCAATAGTT
1222058 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGTG-AAAGAGGAGCTGTGGAA
* *
1222091 AGGGTGAAGAGAGTG-GAGATGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAGAGGAGCTGTGGAA
1222122 A
1 A
1222123 ATGTCTTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.37, C:0.03, G:0.46, T:0.14
Consensus pattern (32 bp):
AGGGTGAAGAGAGTGAAAGAGGAGCTGTGGAA
Found at i:1225916 original size:18 final size:18
Alignment explanation
Indices: 1225895--1225935 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1225885 TGAGCGTGAT
1225895 CGTGACCATGATAGAGAC
1 CGTGACCATGATAGAGAC
* *
1225913 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAC
1225931 CGTGA
1 CGTGA
1225936 GCGTTATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAC
Done.