Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 8 of 328
Found at i:2452162 original size:18 final size:17
Alignment explanation
Indices: 2452138--2452185 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2452128 ACATGTTGAA
2452138 TAATTATATTTTAAT-TT
1 TAATTAT-TTTTAATATT
*
2452155 TAAATTATTTTTTACTATT
1 T-AATTA-TTTTTAATATT
2452174 TAATTATTTTTA
1 TAATTATTTTTA
2452186 GTTGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTATTTTTAATATT
Found at i:2454948 original size:20 final size:20
Alignment explanation
Indices: 2454925--2454966 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2454915 AAAAAATTAA
2454925 ATTATTTTTTAAACGAAAAT
1 ATTATTTTTTAAACGAAAAT
2454945 ATTATTTTTTAAACGAAAAT
1 ATTATTTTTTAAACGAAAAT
2454965 AT
1 AT
2454967 AAAGTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTATTTTTTAAACGAAAAT
Found at i:2457837 original size:8 final size:8
Alignment explanation
Indices: 2457826--2457899 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
2457816 TTTTAATTTT
2457826 TAAAAATA
1 TAAAAATA
*
2457834 TAAAAGTCA
1 TAAAAAT-A
2457843 -AAAAA-A
1 TAAAAATA
2457849 T-AAAAT-
1 TAAAAATA
2457855 TAAAAA-A
1 TAAAAATA
*
2457862 TAGAAATA
1 TAAAAATA
*
2457870 TTAAAATGA
1 TAAAAAT-A
2457879 TTAAAAATGA
1 -TAAAAAT-A
2457889 TAAAAATA
1 TAAAAATA
2457897 TAA
1 TAA
2457900 CATTTATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
7 9 0.17
8 20 0.38
9 9 0.17
10 8 0.15
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.24
Consensus pattern (8 bp):
TAAAAATA
Found at i:2464847 original size:17 final size:17
Alignment explanation
Indices: 2464823--2464856 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2464813 ATTCATTGAC
2464823 CTAACCAATTC-AAAAA
1 CTAACCAATTCTAAAAA
2464839 CTAATCCAATTCTAAAAA
1 CTAA-CCAATTCTAAAAA
2464857 TTTTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAACCAATTCTAAAAA
Found at i:2466193 original size:23 final size:23
Alignment explanation
Indices: 2466149--2466202 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2466139 ATCAACAAAT
* **
2466149 TTAATAAAAGAATTTTTGCAGTA
1 TTAACAAAAGAATTTTAACAGTA
2466172 TTAACAAAAGAATTTTAACAGTA
1 TTAACAAAAGAATTTTAACAGTA
*
2466195 TGAACAAA
1 TTAACAAA
2466203 TTGACCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (23 bp):
TTAACAAAAGAATTTTAACAGTA
Found at i:2466580 original size:24 final size:24
Alignment explanation
Indices: 2466528--2466582 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
2466518 GTATTTAATT
*
2466528 TTTTTGTCTAATTTGACACCTGATA
1 TTTTT-TCTAATTTGACACCTGAAA
2466553 TTTTTTCTAATTTGACACCT-AAA
1 TTTTTTCTAATTTGACACCTGAAA
2466576 CTTTTTT
1 -TTTTTT
2466583 TTACTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 21 0.75
25 5 0.18
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (24 bp):
TTTTTTCTAATTTGACACCTGAAA
Found at i:2466605 original size:28 final size:26
Alignment explanation
Indices: 2466526--2466605 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 26
2466516 TAGTATTTAA
* *
2466526 TTTTTTTGTCTAATTTGACACCT-GA-
1 TTTTTTT-TCTAATTTGACACATAAAC
* *
2466551 TATTTTTTCTAATTTGACACCTAAAC
1 TTTTTTTTCTAATTTGACACATAAAC
* *
2466577 TTTTTTTTACTCAATTTGGCACATGAAC
1 TTTTTTTT-CT-AATTTGACACATAAAC
2466605 T
1 T
2466606 AGGCATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 15 0.33
25 7 0.16
26 7 0.16
27 2 0.04
28 14 0.31
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (26 bp):
TTTTTTTTCTAATTTGACACATAAAC
Found at i:2469120 original size:29 final size:29
Alignment explanation
Indices: 2469065--2469121 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2469055 TAAAATAATG
*
2469065 ATATGTACAAAAAATATATATATATATAC
1 ATATGTACAAAAAATATACATATATATAC
*
2469094 ATATGTACATAAAATATACACTA-ATATA
1 ATATGTACAAAAAATATACA-TATATATA
2469122 ATAATAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATGTACAAAAAATATACATATATATAC
Found at i:2469247 original size:34 final size:33
Alignment explanation
Indices: 2469184--2469335 Score: 94
Period size: 34 Copynumber: 4.5 Consensus size: 33
2469174 ACACAATATG
* *
2469184 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTATATATAATA
*
2469217 GTATTTAAGAATATATACATAAGATGATATAAAATA
1 GTATTTAA-AATATATACATAAG-T-ATATATAATA
* ** * * * *
2469253 CATACATAGAATAGTATA-AGAAATATATAACTAATG
1 -GTATTTAAAATA-TATACATAAGTATAT-A-TAATA
*
2469289 GTATTAAAAATATATACATAA-TATATATAA-A
1 GTATTTAAAATATATACATAAGTATATATAATA
* * *
2469320 ATATATATAATATATA
1 GTATTTAAAATATATA
2469336 TACGTATTAG
Statistics
Matches: 89, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
31 12 0.13
32 3 0.03
33 9 0.10
34 25 0.28
35 13 0.15
36 19 0.21
37 8 0.09
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.36
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTATATATAATA
Found at i:2469247 original size:36 final size:33
Alignment explanation
Indices: 2469184--2469338 Score: 98
Period size: 36 Copynumber: 4.5 Consensus size: 33
2469174 ACACAATATG
* * *
2469184 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTATATAAAATA
2469217 GTATTTAAGAATATATACATAAGATGATATAAAATA
1 GTATTTAA-AATATATACATAAG-T-ATATAAAATA
* ** * * * *
2469253 CATACATAGAATAGTATA-AGAAATATATAACTAATG
1 -GTATTTAAAATA-TATACATAAGTATATAA--AATA
* *
2469289 GTATTAAAAATATATACATAATATATATAAAATA
1 GTATTTAAAATATATACATAA-GTATATAAAATA
* *
2469323 -TATATAATATATATAC
1 GTATTTAAAATATATAC
2469339 GTATTAGAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
33 21 0.23
34 25 0.27
35 12 0.13
36 27 0.29
37 8 0.09
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTATATAAAATA
Found at i:2469310 original size:23 final size:23
Alignment explanation
Indices: 2469206--2469328 Score: 85
Period size: 23 Copynumber: 5.2 Consensus size: 23
2469196 TATATATATG
* *
2469206 TATATATAATAGTATTTAAGAATA
1 TATACATAATAGTA-TTAAAAATA
*
2469230 TATACATAAGA-TGA-TATAAAATA
1 TATACATAATAGT-ATTA-AAAATA
*
2469253 CATACATAGAATAGTA-TAAGAAATA
1 TATACAT--AATAGTATTAA-AAATA
*
2469278 TATA-ACTAATGGTATTAAAAATA
1 TATACA-TAATAGTATTAAAAATA
2469301 TATACATAATA-TATATAAAATATA
1 TATACATAATAGTAT-TAAAA-ATA
2469325 TATA
1 TATA
2469329 ATATATATAC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
22 5 0.06
23 36 0.45
24 23 0.29
25 15 0.19
26 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (23 bp):
TATACATAATAGTATTAAAAATA
Found at i:2469336 original size:11 final size:11
Alignment explanation
Indices: 2469297--2469337 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2469287 TGGTATTAAA
*
2469297 AATATATACAT
1 AATATATATAT
2469308 AATATATATA-
1 AATATATATAT
2469318 AA-ATATATAT
1 AATATATATAT
2469328 AATATATATA
1 AATATATATA
2469338 CGTATTAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 7 0.26
10 4 0.15
11 16 0.59
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATATATAT
Found at i:2470466 original size:17 final size:17
Alignment explanation
Indices: 2470446--2470480 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2470436 TTTTTTTTGA
2470446 GTTAGGTTTTTCTTTTT
1 GTTAGGTTTTTCTTTTT
*
2470463 GTTAGGTTTTTTTTTTT
1 GTTAGGTTTTTCTTTTT
2470480 G
1 G
2470481 GGTTTAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.20, T:0.71
Consensus pattern (17 bp):
GTTAGGTTTTTCTTTTT
Found at i:2471164 original size:2 final size:2
Alignment explanation
Indices: 2471159--2471191 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2471149 ATAAAAAAAC
2471159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2471192 CATAGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2471919 original size:21 final size:22
Alignment explanation
Indices: 2471891--2472004 Score: 72
Period size: 23 Copynumber: 4.9 Consensus size: 22
2471881 TTCTAATACG
*
2471891 TATATATATAT-TATATGTATTTT
1 TATATAT-TATGTATATAT-TTTT
2471914 TATATATTATGTATATATTTTT
1 TATATATTATGTATATATTTTT
*
2471936 TA-ATGCCATTA-GTTATATATTTCT
1 TATAT---ATTATG-TATATATTTTT
* *
2471960 TATACTATTCCATGTATGTATTTTA
1 TATA-TATT--ATGTATATATTTTT
*
2471985 TATCATCTTATGTATATATT
1 TAT-ATATTATGTATATATT
2472005 CTTAAATACT
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
21 2 0.03
22 9 0.12
23 27 0.37
24 16 0.22
25 16 0.22
26 3 0.04
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (22 bp):
TATATATTATGTATATATTTTT
Found at i:2473346 original size:8 final size:8
Alignment explanation
Indices: 2473312--2473363 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
2473302 TAGTGATGTG
*
2473312 AATAATAA
1 AATATTAA
*
2473320 AGTATATAA
1 AATAT-TAA
2473329 AATA-TAA
1 AATATTAA
2473336 AATATTAA
1 AATATTAA
*
2473344 AATATCAA
1 AATATTAA
*
2473352 AATATTAG
1 AATATTAA
2473360 AATA
1 AATA
2473364 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 23 0.64
9 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:2473353 original size:16 final size:15
Alignment explanation
Indices: 2473316--2473363 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2473306 GATGTGAATA
*
2473316 ATAAAGTATATAAAAT
1 ATAAAATAT-TAAAAT
2473332 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
2473347 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
2473363 A
1 A
2473364 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2473569 original size:22 final size:24
Alignment explanation
Indices: 2473506--2473602 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
2473496 GTGATAATAT
* *
2473506 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
* *
2473530 TAAAAAATACATAGATAATATAAT-
1 T-AAAAATATATACATAATATAATG
*
2473554 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
*
2473579 TAGAAAAATATATATATAA-ATAAT
1 T--AAAAATATATACATAATATAAT
2473603 ATAGTATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
22 15 0.26
23 1 0.02
24 4 0.07
25 21 0.36
26 1 0.02
27 2 0.03
28 14 0.24
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:2473626 original size:25 final size:25
Alignment explanation
Indices: 2473590--2473723 Score: 102
Period size: 25 Copynumber: 5.6 Consensus size: 25
2473580 AGAAAAATAT
*
2473590 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
2473615 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
2473640 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
2473664 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
2473686 AATATATATATAATATAATATT-AAG
1 -ATATATACATAATATAGTATTAAAG
*
2473711 AAATATA-ATAATA
1 ATATATACATAATA
2473724 ACAAAAAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 20 0.23
24 23 0.27
25 38 0.44
26 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:2473630 original size:27 final size:27
Alignment explanation
Indices: 2473519--2473630 Score: 85
Period size: 28 Copynumber: 4.2 Consensus size: 27
2473509 AAATATGTAC
*
2473519 ATAATATAGT-GTAAAA-A-ATACATA
1 ATAATATAGTATTAAAATATATACATA
2473543 GATAATATA--ATTAAAATATATACATAA
1 -ATAATATAGTATTAAAATATATACAT-A
* ** *
2473570 GATAACAT-GTAGAAAAATATATATATAA
1 -ATAATATAGTATTAAAATATATACAT-A
2473598 ATAATATAGTATTAAAGATATATACATA
1 ATAATATAGTATTAAA-ATATATACATA
2473626 A-AATA
1 ATAATA
2473631 GTATAATATA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
24 5 0.07
25 9 0.13
26 6 0.09
27 18 0.26
28 23 0.33
29 9 0.13
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (27 bp):
ATAATATAGTATTAAAATATATACATA
Found at i:2473699 original size:24 final size:23
Alignment explanation
Indices: 2473672--2473723 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2473662 AGAATATACC
*
2473672 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
2473696 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
2473719 TAATA
1 TAATA
2473724 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:2474132 original size:17 final size:15
Alignment explanation
Indices: 2474110--2474164 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 15
2474100 CTTTCTCCCC
2474110 CAAAAAAAAAACTTCTT
1 CAAAAAAAAAAC-TC-T
2474127 CAAAAAAAAAA-TCT
1 CAAAAAAAAAACTCT
2474141 CAAAAAAAAAAACTCCT
1 C-AAAAAAAAAACT-CT
2474158 CAAAAAA
1 CAAAAAA
2474165 CCCCATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.06
15 12 0.34
16 7 0.20
17 14 0.40
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (15 bp):
CAAAAAAAAAACTCT
Found at i:2474133 original size:15 final size:14
Alignment explanation
Indices: 2474110--2474151 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 14
2474100 CTTTCTCCCC
2474110 CAAAAAAAAAACTTCTT
1 CAAAAAAAAAA--TC-T
2474127 CAAAAAAAAAATCT
1 CAAAAAAAAAATCT
2474141 CAAAAAAAAAA
1 CAAAAAAAAAA
2474152 ACTCCTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
17 11 0.44
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
CAAAAAAAAAATCT
Found at i:2475920 original size:32 final size:33
Alignment explanation
Indices: 2475879--2475951 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
2475869 CAGTTTTCCT
2475879 AAAATATTTT-CA-AGAAATC-TGCCAAACAACAG
1 AAAATATTTTACACAG-AATCAT-CCAAACAACAG
* *
2475911 AAAATATTTTACACAGATTCATCCAAACACCAG
1 AAAATATTTTACACAGAATCATCCAAACAACAG
2475944 AAAATATT
1 AAAATATT
2475952 AACTTTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 10 0.28
33 23 0.64
34 3 0.08
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.25
Consensus pattern (33 bp):
AAAATATTTTACACAGAATCATCCAAACAACAG
Found at i:2476765 original size:13 final size:13
Alignment explanation
Indices: 2476747--2476774 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2476737 GGATTATGGG
2476747 TAATTCTAGGTAT
1 TAATTCTAGGTAT
2476760 TAATTCTAGGTAT
1 TAATTCTAGGTAT
2476773 TA
1 TA
2476775 TGTCAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
TAATTCTAGGTAT
Found at i:2478471 original size:4 final size:4
Alignment explanation
Indices: 2478464--2478488 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2478454 TACACTTATG
2478464 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
2478489 AAATTTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:2479180 original size:27 final size:28
Alignment explanation
Indices: 2479150--2479203 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
2479140 TTTTTAAATA
2479150 TTCAA-AATGTAGT-TTCTTTATTTTTAT
1 TTCAACAATGTAGTCTT-TTTATTTTTAT
*
2479177 TTCAACGAATTTAGTCTTTTTATTTTT
1 TTCAAC-AATGTAGTCTTTTTATTTTT
2479204 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
29 16 0.70
30 2 0.09
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.59
Consensus pattern (28 bp):
TTCAACAATGTAGTCTTTTTATTTTTAT
Found at i:2479463 original size:10 final size:10
Alignment explanation
Indices: 2479444--2479476 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2479434 TATTTGTAAC
2479444 ATTT-TAATA
1 ATTTATAATA
2479453 ATTTATAATA
1 ATTTATAATA
2479463 ATTTATAAT-
1 ATTTATAATA
2479472 ATTTA
1 ATTTA
2479477 ATGATGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTATAATA
Found at i:2482546 original size:13 final size:13
Alignment explanation
Indices: 2482530--2482580 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
2482520 TGGTGCTAAT
*
2482530 ATACTATATATTC
1 ATACAATATATTC
*
2482543 ATACAATATATTA
1 ATACAATATATTC
*
2482556 ATATAATATATTC
1 ATACAATATATTC
2482569 ATACAATATATT
1 ATACAATATATT
2482581 AATATTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (13 bp):
ATACAATATATTC
Found at i:2482571 original size:26 final size:27
Alignment explanation
Indices: 2482526--2482585 Score: 104
Period size: 26 Copynumber: 2.2 Consensus size: 27
2482516 TATATGGTGC
2482526 TAATATACTATATATTCATACAATATAT
1 TAATATAC-ATATATTCATACAATATAT
2482554 TAATATA-ATATATTCATACAATATAT
1 TAATATACATATATTCATACAATATAT
2482580 TAATAT
1 TAATAT
2482586 TTGAAGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 25 0.78
28 7 0.22
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATATACATATATTCATACAATATAT
Found at i:2482621 original size:11 final size:11
Alignment explanation
Indices: 2482605--2482629 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2482595 TATTTCACTT
2482605 TCATATCATAA
1 TCATATCATAA
2482616 TCATATCATAA
1 TCATATCATAA
2482627 TCA
1 TCA
2482630 CATGTAATAA
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:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
TCATATCATAA
Found at i:2483411 original size:28 final size:29
Alignment explanation
Indices: 2483379--2483434 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
2483369 ATTAAAATTC
*
2483379 TAATTCAATTGATTTA-ATTATTTTTTTT
1 TAATTCAATTGATTTATATTAATTTTTTT
2483407 TAATTCAATTGATTTATATTAATTTTTT
1 TAATTCAATTGATTTATATTAATTTTTT
2483435 GGTCAATCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (29 bp):
TAATTCAATTGATTTATATTAATTTTTTT
Found at i:2488051 original size:64 final size:65
Alignment explanation
Indices: 2487947--2488076 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 65
2487937 GTCCTAACAA
*
2487947 CACTCATCAATCCATCACATTTGACAGATTCCTAATCTAATCCCTTCAAGTCGACTCTAATAATG
1 CACTCATCAATCCATCACATTTAACAGATTCCTAATCTAATCCCTTCAAGTCGACTCTAATAATG
* * * *
2488012 CACTCATCAATCCATTATA-TTAATAGATTCCTCATCTAATCCCTTCAAGTCGACTCTAATAATG
1 CACTCATCAATCCATCACATTTAACAGATTCCTAATCTAATCCCTTCAAGTCGACTCTAATAATG
2488076 C
1 C
2488077 CCTAACATCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 43 0.72
65 17 0.28
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (65 bp):
CACTCATCAATCCATCACATTTAACAGATTCCTAATCTAATCCCTTCAAGTCGACTCTAATAATG
Found at i:2493525 original size:27 final size:27
Alignment explanation
Indices: 2493495--2493548 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2493485 TTTGTTGAGC
2493495 ATAATACTAGTTATATATAGTTTTCAA
1 ATAATACTAGTTATATATAGTTTTCAA
2493522 ATAATACTAGTTATATATAGTTTTCAA
1 ATAATACTAGTTATATATAGTTTTCAA
2493549 TTATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (27 bp):
ATAATACTAGTTATATATAGTTTTCAA
Found at i:2502072 original size:21 final size:21
Alignment explanation
Indices: 2502046--2502089 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2502036 CTAGTTTTCT
*
2502046 TTTTTTTAATTA-TTATTATAA
1 TTTTTTTAATAATTTATT-TAA
2502067 TTTTTTTAATAATTTATTTAA
1 TTTTTTTAATAATTTATTTAA
2502088 TT
1 TT
2502090 AAAATCGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTTTAATAATTTATTTAA
Found at i:2502368 original size:7 final size:7
Alignment explanation
Indices: 2502356--2502388 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2502346 TCTTTCAAAT
2502356 TTTTAAA
1 TTTTAAA
2502363 TTTTAAA
1 TTTTAAA
2502370 TTTTAAA
1 TTTTAAA
*
2502377 -TTTAAT
1 TTTTAAA
2502383 TTTTAA
1 TTTTAA
2502389 CATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:2502386 original size:13 final size:14
Alignment explanation
Indices: 2502353--2502401 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
2502343 TAATCTTTCA
2502353 AATTTTTAAATTTT
1 AATTTTTAAATTTT
*
2502367 AAATTTTAAA-TTT
1 AATTTTTAAATTTT
2502380 AATTTTTAACATTATT
1 AATTTTTAA-ATT-TT
2502396 -ATTTTT
1 AATTTTT
2502402 TGTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.37
14 10 0.33
15 7 0.23
16 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTAAATTTT
Found at i:2506478 original size:22 final size:22
Alignment explanation
Indices: 2506432--2506487 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2506422 TAGCTCAAAT
** *
2506432 TTTTC-TACTATTTTCTTGTTG
1 TTTTCTTACTATTTTCTCATTA
2506453 TTTTCTTACTATTTTCTCATTA
1 TTTTCTTACTATTTTCTCATTA
* *
2506475 TTTTGTTATTATT
1 TTTTCTTACTATT
2506488 GTTTGTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTCTTACTATTTTCTCATTA
Found at i:2508675 original size:13 final size:13
Alignment explanation
Indices: 2508623--2508675 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2508613 AGTTTGACAA
2508623 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
2508636 CGCTTTTGAAGAG
1 TGCTTTTGAAAAG
*
2508649 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
2508662 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
2508675 T
1 T
2508676 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:2510164 original size:20 final size:22
Alignment explanation
Indices: 2510141--2510183 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2510131 ATGTTTTTTT
2510141 AATAATTTTT-AAA-TTTTAAA
1 AATAATTTTTAAAATTTTTAAA
*
2510161 AATATTTTTTAAAATTTTTAAA
1 AATAATTTTTAAAATTTTTAAA
2510183 A
1 A
2510184 CTTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATTTTTAAAATTTTTAAA
Found at i:2512883 original size:30 final size:30
Alignment explanation
Indices: 2512847--2512906 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2512837 TATTTTATTA
2512847 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
2512877 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
2512907 CTTATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:2513798 original size:16 final size:15
Alignment explanation
Indices: 2513779--2513818 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2513769 TAATTTTTAC
*
2513779 AATTTTTGTTTTTTGT
1 AATTTTTATTTTTT-T
*
2513795 AATTTATATTTTTTT
1 AATTTTTATTTTTTT
2513810 AATTTTTAT
1 AATTTTTAT
2513819 AAAATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
AATTTTTATTTTTTT
Found at i:2525286 original size:22 final size:22
Alignment explanation
Indices: 2525235--2525294 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
2525225 AAGAAATGAG
*
2525235 TAAAAAATAATATACATAATAA
1 TAAAAAATATTATACATAATAA
*
2525257 TAAGAAAATATTATA-ATAAGTAC
1 TAA-AAAATATTATACATAA-TAA
2525280 TAAAAAATATCTATA
1 TAAAAAATAT-TATA
2525295 TTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAAAATATTATACATAATAA
Found at i:2526675 original size:16 final size:16
Alignment explanation
Indices: 2526656--2526713 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2526646 TAGATTGTAA
2526656 TGGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
*** **
2526672 TGGGTTTTATTTGTAAA
1 TGGG-TTTAGGGGTATT
*
2526689 TAGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
2526705 TGGGTTTAG
1 TGGGTTTAG
2526714 AGGTTGTTTA
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (16 bp):
TGGGTTTAGGGGTATT
Found at i:2526696 original size:33 final size:32
Alignment explanation
Indices: 2526650--2526711 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
2526640 ATGGGTTAGA
*
2526650 TTGTAATGGGTTTAGGGGTATTTGGGTTTTAT
1 TTGTAATAGGTTTAGGGGTATTTGGGTTTTAT
2526682 TTGTAAATAGGTTTAGGGGTATTTGGGTTT
1 TTGT-AATAGGTTTAGGGGTATTTGGGTTT
2526712 AGAGGTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (32 bp):
TTGTAATAGGTTTAGGGGTATTTGGGTTTTAT
Found at i:2527388 original size:21 final size:22
Alignment explanation
Indices: 2527346--2527389 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2527336 CGATTATATC
* *
2527346 AATTAATTCATTTTATTATTAA
1 AATTAATTAATTTAATTATTAA
*
2527368 AATT-ATTAATTTAATTGTTAA
1 AATTAATTAATTTAATTATTAA
2527389 A
1 A
2527390 TAATATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTAATTAATTTAATTATTAA
Found at i:2528048 original size:3 final size:3
Alignment explanation
Indices: 2528015--2528091 Score: 67
Period size: 3 Copynumber: 27.3 Consensus size: 3
2528005 CTTGAACAGT
* * *
2528015 AGA AGA AAA AG- AGA A-A AAA AGA ATA AG- AGA AGA A-A CAG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
*
2528056 AGA AGA AGA AGA AGA AGA AGA AG- AGG AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2528092 TTAAGAGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
2 11 0.18
3 50 0.82
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:2528100 original size:26 final size:27
Alignment explanation
Indices: 2528015--2528100 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 27
2528005 CTTGAACAGT
* *
2528015 AGAAGAAAAAGAGAA-AAAAAGAATAAG
1 AGAAG-AACAGAGAAGAAGAAGAATAAG
*
2528042 AGAAGAAACAGAGAAGAAGAAGAAGAAG
1 AGAAG-AACAGAGAAGAAGAAGAATAAG
*
2528070 AAGAAG-A-AGAGGAGAAGAAGAATTAAG
1 -AGAAGAACAGAGAAGAAGAAGAA-TAAG
2528097 AGAA
1 AGAA
2528101 AATGGCAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 18 0.35
27 18 0.35
28 10 0.20
29 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.29, T:0.03
Consensus pattern (27 bp):
AGAAGAACAGAGAAGAAGAAGAATAAG
Found at i:2528225 original size:2 final size:2
Alignment explanation
Indices: 2528218--2528246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2528208 CAACTTCTGT
2528218 TA TA 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 T
2528247 TCCTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2528419 original size:12 final size:12
Alignment explanation
Indices: 2528402--2528427 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2528392 TCTAAAAAAG
2528402 ACTTAATTTTGC
1 ACTTAATTTTGC
2528414 ACTTAATTTTGC
1 ACTTAATTTTGC
2528426 AC
1 AC
2528428 CAGCAGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (12 bp):
ACTTAATTTTGC
Found at i:2536322 original size:43 final size:43
Alignment explanation
Indices: 2536273--2536430 Score: 289
Period size: 43 Copynumber: 3.7 Consensus size: 43
2536263 TAAAAAAAAT
2536273 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
2536316 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
* *
2536359 GCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTTTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
*
2536402 GCCGCTAAAAGTCACGGCCTTTAGCGGCG
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCG
2536431 ATTTAGCGGC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 111 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
Found at i:2536615 original size:31 final size:31
Alignment explanation
Indices: 2536561--2536641 Score: 65
Period size: 31 Copynumber: 2.6 Consensus size: 31
2536551 TTCCTGCATT
* * * * *
2536561 AAAATCCAACCAAATACAACAAATATAA-TA
1 AAAATACAACCAAAAATAGCAAATATACATA
* * *
2536591 TAAAATGCAGCCAAAAATAGCAAATTTAGCATA
1 -AAAATACAACCAAAAATAGCAAATATA-CATA
2536624 AAAATACAACCAAAAATA
1 AAAATACAACCAAAAATA
2536642 TTAATTCTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
31 21 0.54
32 16 0.41
33 2 0.05
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (31 bp):
AAAATACAACCAAAAATAGCAAATATACATA
Found at i:2536911 original size:21 final size:21
Alignment explanation
Indices: 2536885--2536961 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2536875 GCTGCTGCTT
2536885 CTGCCTCTGCCTCCCTCGCT-
1 CTGCCTCTGCCTCCCTCGCTG
2536905 CGTGCCTCTGCCTCCCTCGCTG
1 C-TGCCTCTGCCTCCCTCGCTG
* * *
2536927 CTGTCGCTGCCTCCCTCGCTA
1 CTGCCTCTGCCTCCCTCGCTG
2536948 CTG-CTGCTGCCTCC
1 CTGCCT-CTGCCTCC
2536962 GCTCTAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 2 0.04
21 47 0.94
22 1 0.02
ACGTcount: A:0.01, C:0.51, G:0.19, T:0.29
Consensus pattern (21 bp):
CTGCCTCTGCCTCCCTCGCTG
Found at i:2538427 original size:56 final size:56
Alignment explanation
Indices: 2538367--2538585 Score: 313
Period size: 56 Copynumber: 4.0 Consensus size: 56
2538357 AAAGTTATGA
*
2538367 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATATT
*
2538423 TATGATATATATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
1 TATGATATATATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATATT
* *
2538480 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATATT
* * * *
2538536 TATG-TAT-TATGTAAGT-TT-TGTAAGTTATGTAAGTTATTATATGATATATA
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATA
2538586 ATAAATATTA
Statistics
Matches: 149, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
52 29 0.19
53 2 0.01
54 7 0.05
55 3 0.02
56 56 0.38
57 51 0.34
58 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (56 bp):
TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATATT
Found at i:2538541 original size:43 final size:43
Alignment explanation
Indices: 2538480--2538564 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
2538470 GATACATATT
*
2538480 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGA
* *
2538523 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATG
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATG
2538565 TAAGTTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.51
Consensus pattern (43 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGA
Found at i:2538559 original size:9 final size:9
Alignment explanation
Indices: 2538499--2538572 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 9
2538489 TATTTATGTA
*
2538499 TTATGTTAG
1 TTATGTAAG
*
2538508 TTGTGTAAG
1 TTATGTAAG
*
2538517 TTATGATATG
1 TTATG-TAAG
* * *
2538527 ATATAT-AT
1 TTATGTAAG
2538535 TTATGT-A-
1 TTATGTAAG
2538542 TTATGTAAG
1 TTATGTAAG
*
2538551 TTTTGTAAG
1 TTATGTAAG
2538560 TTATGTAAG
1 TTATGTAAG
2538569 TTAT
1 TTAT
2538573 TATATGATAT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 32 0.64
10 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:2538577 original size:43 final size:43
Alignment explanation
Indices: 2538486--2538577 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
2538476 TATTTATGAA
* *
2538486 ATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGAT
1 ATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGAT
* *
2538529 ATATATTTATGTATTATGTAAGTTTTGTAAGTTATG-TAAGTT
1 ATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGAT
2538571 ATTATAT
1 A-TATAT
2538578 GATATATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 5 0.11
43 39 0.89
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (43 bp):
ATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGAT
Found at i:2538582 original size:113 final size:113
Alignment explanation
Indices: 2538367--2538581 Score: 332
Period size: 113 Copynumber: 1.9 Consensus size: 113
2538357 AAAGTTATGA
*
2538367 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
* * *
2538432 TATTTGGAGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
66 TATGTGAAGTATTATGTAAGTTATGTAAGTTATGATATGATACATATT
* *
2538480 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATG-TAT-
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
*
2538543 TATGT-AAGT-TT-TGTAAGTTATGTAAGTTATTATATGATA
66 TATGTGAAGTATTATGTAAGTTATGTAAGTTATGATATGATA
2538582 TATAATAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
108 26 0.27
109 2 0.02
110 3 0.03
111 4 0.04
112 3 0.03
113 57 0.60
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (113 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
TATGTGAAGTATTATGTAAGTTATGTAAGTTATGATATGATACATATT
Found at i:2538683 original size:25 final size:21
Alignment explanation
Indices: 2538654--2538721 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 21
2538644 TATGTAATTT
2538654 AAAAAATTGTGTCGTGATTAA
1 AAAAAATTGTGTCGTGATTAA
* *
2538675 ATTGCAAAATATGTGTCGTAATTTAA
1 A---AAAAAT-TGTGTCGTGA-TTAA
*
2538701 AAAAAATTGTGTCCTGATTAA
1 AAAAAATTGTGTCGTGATTAA
2538722 TCCAAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.14
22 8 0.22
23 5 0.14
24 5 0.14
25 9 0.24
26 5 0.14
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.35
Consensus pattern (21 bp):
AAAAAATTGTGTCGTGATTAA
Found at i:2539024 original size:37 final size:37
Alignment explanation
Indices: 2538980--2539070 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 37
2538970 AAATTATATT
*
2538980 AATTGATAAATATTGAAATAT-TG-AAAT-ATATTTAA
1 AATTGATAAATATTGAAATATAAGCAAATCAT-TTTAA
2539015 AATGTTGAT-AA-A-TGAAATATAAGCAAATCATTTTAA
1 AA--TTGATAAATATTGAAATATAAGCAAATCATTTTAA
2539051 AATTGATAAATATTGAAATA
1 AATTGATAAATATTGAAATA
2539071 CATTAAAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
34 13 0.28
35 6 0.13
36 14 0.30
37 14 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (37 bp):
AATTGATAAATATTGAAATATAAGCAAATCATTTTAA
Found at i:2541040 original size:59 final size:59
Alignment explanation
Indices: 2540969--2541098 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 59
2540959 TTTCAAATTG
* * ** * *
2540969 GAGAGAAAGGGGTAATTATTTTAGGGTTTCGAATTAGGGAAAATGGATGG-AATAAACTA
1 GAGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAATGG-GGGAAATAAACCA
*
2541028 GAGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAATGGGGGAAATAAACCA
1 GAGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAATGGGGGAAATAAACCA
*
2541087 GGGAGAAGGGGG
1 GAGAGAAGGGGG
2541099 AACTCGGTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 2 0.03
59 60 0.97
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.21
Consensus pattern (59 bp):
GAGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAATGGGGGAAATAAACCA
Found at i:2541297 original size:114 final size:114
Alignment explanation
Indices: 2541167--2541705 Score: 468
Period size: 114 Copynumber: 4.7 Consensus size: 114
2541157 TAACATTTGA
2541167 GGCG-TTTTCACCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACAT-AAACGCCACTA
1 GGCGTTTTTCA-CTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAAACGCCACTA
*
2541230 AAAAAACAAACAAAACGACACCGTTTTGATATAAACAGAATAAACTTTAGT
65 AAAAACCAAA-AAAACGACACCGTTTTGATATAAACAGAATAAACTTTAGT
* * * * *
2541281 GGCGTTTTTCAGTAGCGCCGCTAAAGGCAAATCAATTGCGGCGTTTCACCCTAAAACGCCACTAA
1 GGCGTTTTTCACTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAAACGCCACTAA
* * * *
2541346 AAATCCAAAAAAACGACGA-TGTTTTCATATGAACAGAAT-AACATTTAGT
66 AAAACCAAAAAAACGAC-ACCGTTTTGATATAAACAGAATAAAC-TTTAGT
* * * * *
2541395 GGCGTTTTATCACCAAGCGCCGCTAAAGGCGAAA-CTATTTCGGCGTTTTACCCTAAAACGCCAC
1 GGCGTTTT-TCA-CTAGCGCCGCTAAAGGC-AAACCAATTGCGGCGTTTTAACATAAAACGCCAC
* * * * * * * *
2541459 TAATAATCGAATAAAACTACATCGTTTTGATATAAACA-AATTAACCATTAGT
63 TAAAAAACCAAAAAAACGACACCGTTTTGATATAAACAGAA-TAAACTTTAGT
* * * * *
2541511 GGCGTTTAT-ACCTTAGCGCCGCTAAA-TCAAACCTATTGTGGCGTTTGAACCA-AAAACGCCAC
1 GGCGTTTTTCA-C-TAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAA-CATAAAACGCCAC
* * * * * * *
2541573 TAAAAATCCATAAAAACTACACCGTTTTGATCTAAACAAAATAACCCTTAGT
63 TAAAAAACCAAAAAAACGACACCGTTTTGATATAAACAGAATAAACTTTAGT
* * * * * * * * ** *
2541625 GGCGTTTATAACCTTGCGACGCTAAA-TCGACCCTATTATGGCGTTTTAACCTAAAACGCCACTA
1 GGCGTTTTTCA-CTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAAACGCCACTA
*
2541689 AAAATCCAAAGAAAACG
65 AAAAACCAAA-AAAACG
2541706 GTGTCGTCTT
Statistics
Matches: 360, Mismatches: 48, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
113 7 0.02
114 208 0.58
115 56 0.16
116 84 0.23
117 5 0.01
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (114 bp):
GGCGTTTTTCACTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAAACGCCACTAA
AAAACCAAAAAAACGACACCGTTTTGATATAAACAGAATAAACTTTAGT
Found at i:2541626 original size:230 final size:229
Alignment explanation
Indices: 2541167--2541705 Score: 599
Period size: 230 Copynumber: 2.4 Consensus size: 229
2541157 TAACATTTGA
* * *
2541167 GGCGTTT-TCACCTAGCGCCGCTAAAGGC-AAACCAATTGCGGCGTTTTAACAT-AAACGCCACT
1 GGCGTTTATCACCTAGCGCCGCTAAAGGCGAAA-CTATTTCGGCGTTTTAACCTAAAACGCCACT
* * *
2541229 AAAAAAACAAACAAAACGACACCGTTTTGATATAAACAGAATAAACTTTAGTGGCGTTTTTCAGT
65 -AAAAATCAAACAAAACGACACCGTTTTGATATAAACAGAATAAACATTAGTGGCGTTTTACAGT
* * *
2541294 AGCGCCGCTAAAGGCAAATCAATTGCGGCGTTTCACCCTAAAACGCCACTAAAAATCCAAAAAAA
129 AGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACCAAAAACGCCACTAAAAATCCAAAAAAA
* * * *
2541359 CGACGATGTTTTCATATGAACAGAATAACATTTAGT
194 CGACGACGTTTTCATATAAACAAAATAACACTTAGT
* *
2541395 GGCGTTTTATCACCAAGCGCCGCTAAAGGCGAAACTATTTCGGCGTTTTACCCTAAAACGCCACT
1 GGCG-TTTATCACCTAGCGCCGCTAAAGGCGAAACTATTTCGGCGTTTTAACCTAAAACGCCACT
* * * * * * **
2541460 AATAATCGAATAAAACTACATCGTTTTGATATAAACA-AATTAACCATTAGTGGCGTTTATACCT
65 AAAAATCAAACAAAACGACACCGTTTTGATATAAACAGAA-TAAACATTAGTGGCGTTT-TACAG
* * * * *
2541524 TAGCGCCGCTAAA-TCAAACCTATTGTGGCGTTTGAACCAAAAACGCCACTAAAAATCCATAAAA
128 TAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACCAAAAACGCCACTAAAAATCCAAAAAA
* * * *
2541588 ACTAC-ACCGTTTTGATCTAAACAAAATAACCCTTAGT
193 ACGACGA-CGTTTTCATATAAACAAAATAACACTTAGT
* * * * **
2541625 GGCGTTTATAACCTTGCGACGCTAAA-TCGACCCTATTAT-GGCGTTTTAACCTAAAACGCCACT
1 GGCGTTTATCACCTAGCGCCGCTAAAGGCGAAACTATT-TCGGCGTTTTAACCTAAAACGCCACT
*
2541688 AAAAATCCAAAGAAAACG
65 AAAAAT-CAAACAAAACG
2541706 GTGTCGTCTT
Statistics
Matches: 258, Mismatches: 44, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
228 40 0.16
229 33 0.13
230 157 0.61
231 28 0.11
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (229 bp):
GGCGTTTATCACCTAGCGCCGCTAAAGGCGAAACTATTTCGGCGTTTTAACCTAAAACGCCACTA
AAAATCAAACAAAACGACACCGTTTTGATATAAACAGAATAAACATTAGTGGCGTTTTACAGTAG
CGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACCAAAAACGCCACTAAAAATCCAAAAAAACG
ACGACGTTTTCATATAAACAAAATAACACTTAGT
Found at i:2542594 original size:45 final size:45
Alignment explanation
Indices: 2542545--2542638 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
2542535 GGTTTTAAAT
*
2542545 GTTATAGTTTAGTGTTT-TGTGTTTAGGGGGTTTAGTG-TTTTAGGG
1 GTTATAGATTAGTGTTTATGT-TTTAGGGGGTTTAG-GATTTTAGGG
**
2542590 GTTATAGATTAGTGTTTATGTTTTTTGGGGTTTAGGATTTTAGGG
1 GTTATAGATTAGTGTTTATGTTTTAGGGGGTTTAGGATTTTAGGG
2542635 GTTA
1 GTTA
2542639 AATGACTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 1 0.02
45 40 0.91
46 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (45 bp):
GTTATAGATTAGTGTTTATGTTTTAGGGGGTTTAGGATTTTAGGG
Found at i:2542702 original size:41 final size:41
Alignment explanation
Indices: 2542645--2542782 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
2542635 GTTAAATGAC
*
2542645 TTTTAGCGGCGTTTTACCAAAAACGCAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCAGCTAATGCTCTGGT
* * * *
2542686 TTTTAGTGGCGTTTTA-CACAAAGCGCCGCTAATTCTTTGGT
1 TTTTAGCGGCGTTTTACCA-AAAGCGCAGCTAATGCTCTGGT
** *
2542727 TTTTAGTAGCGTTTTACCAAAAGCGCCA-CTAATGCTCTGGC
1 TTTTAGCGGCGTTTTACCAAAAGCG-CAGCTAATGCTCTGGT
2542768 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
2542783 TGGTAAAACG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.02
41 77 0.94
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCAGCTAATGCTCTGGT
Found at i:2542821 original size:82 final size:82
Alignment explanation
Indices: 2542645--2542823 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 82
2542635 GTTAAATGAC
* * *
2542645 TTTTAGCGGCGTTTTACCAAAAACGCAGCTAATGCTCTGGTTTTTAGTGGCGTTTTACACAAAGC
1 TTTTAGCGGCGTTTTACCAAAAACGCAGCTAATGCTCTGGCTTTTAGCGGCGTTTTACACAAAAC
* *
2542710 GCCGCTAATTCTTTGGT
66 GCCACTAATTCTATGGT
** * ****
2542727 TTTTAGTAGCGTTTTACCAAAAGCGCCA-CTAATGCTCTGGCTTTTAGCGGCGTTTTTGGTAAAA
1 TTTTAGCGGCGTTTTACCAAAAACG-CAGCTAATGCTCTGGCTTTTAGCGGCGTTTTACACAAAA
*
2542791 CGCCACT-ATTGCTATGTT
65 CGCCACTAATT-CTATGGT
*
2542809 TTTTGGCGGCGTTTT
1 TTTTAGCGGCGTTTT
2542824 CTGTAAAACG
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
81 3 0.04
82 74 0.94
83 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTACCAAAAACGCAGCTAATGCTCTGGCTTTTAGCGGCGTTTTACACAAAAC
GCCACTAATTCTATGGT
Found at i:2542841 original size:41 final size:41
Alignment explanation
Indices: 2542745--2542858 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
2542735 GCGTTTTACC
* * **
2542745 AAAAGCGCCACTAATGCTCTGGCTTTTAGCGGCGTTTTTGGT
1 AAAA-CGCCACTATTGCTATGTTTTTTAGCGGCGTTTTTGGT
*
2542787 AAAACGCCACTATTGCTATGTTTTTTGGCGGCGTTTTCT-GT
1 AAAACGCCACTATTGCTATGTTTTTTAGCGGCGTTTT-TGGT
* * **
2542828 AAAACGCCGCTATTTCTATAATTTTTAGCGG
1 AAAACGCCACTATTGCTATGTTTTTTAGCGG
2542859 AAAACGCCGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 56 0.92
42 5 0.08
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
AAAACGCCACTATTGCTATGTTTTTTAGCGGCGTTTTTGGT
Found at i:2545122 original size:24 final size:24
Alignment explanation
Indices: 2545090--2545137 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2545080 CAAAGCCTCG
2545090 CTCTTCACGTTGGGTTTGTTCTAC
1 CTCTTCACGTTGGGTTTGTTCTAC
2545114 CTCTTCACGTTGGGTTTGTTCTAC
1 CTCTTCACGTTGGGTTTGTTCTAC
2545138 TTGTTCGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.25, G:0.21, T:0.46
Consensus pattern (24 bp):
CTCTTCACGTTGGGTTTGTTCTAC
Found at i:2546172 original size:34 final size:30
Alignment explanation
Indices: 2546097--2546181 Score: 77
Period size: 34 Copynumber: 2.8 Consensus size: 30
2546087 TCAATTTAAG
2546097 ATTT-TTTATTAA-AAACTAATTAATATAT
1 ATTTATTTATTAATAAACTAATTAATATAT
* *
2546125 ATTTA-TTAATAATAAACTATTATAATCATTAT
1 ATTTATTTATTAATAAACTAAT-TAAT-A-TAT
* *
2546157 ATTTTATTTATTAATATATTAATTA
1 A-TTTATTTATTAATAAACTAATTA
2546182 TGGTTATAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 10 0.23
29 7 0.16
30 4 0.09
31 1 0.02
32 4 0.09
33 6 0.14
34 12 0.27
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTATTTATTAATAAACTAATTAATATAT
Found at i:2547714 original size:2 final size:2
Alignment explanation
Indices: 2547707--2547753 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2547697 TTCTAAGAAA
2547707 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2547749 AC AC A
1 AC AC A
2547754 TATATATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2552826 original size:3 final size:3
Alignment explanation
Indices: 2552820--2552876 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2552810 TTCCTTTCGA
2552820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2552868 TAT TAT TAT
1 TAT TAT TAT
2552877 CTTTTCGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2554045 original size:31 final size:33
Alignment explanation
Indices: 2553979--2554046 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 33
2553969 AAAAGAGTTG
* *
2553979 AAAATATTATTTTTCAATTGTTAAGGGGCCCAA
1 AAAATATTATTTTTCAATTGTTAAGAGGCCAAA
*
2554012 AAAATAATT-TTTTT-AATTTTTAA-AGGCCAAA
1 AAAAT-ATTATTTTTCAATTGTTAAGAGGCCAAA
2554043 AAAA
1 AAAA
2554047 AACTTTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 10 0.32
32 8 0.26
33 10 0.32
34 3 0.10
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (33 bp):
AAAATATTATTTTTCAATTGTTAAGAGGCCAAA
Found at i:2554107 original size:31 final size:33
Alignment explanation
Indices: 2554040--2554107 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
2554030 TTTAAAGGCC
* **
2554040 AAAAAAAAACTTTTACCAACTTTTAAGGGATTT
1 AAAAAAAAACTTCTACCAACTTTTAAGGGACCT
2554073 AAAAAAAAA-TTCT-CCAACTTTTAAGGGACCT
1 AAAAAAAAACTTCTACCAACTTTTAAGGGACCT
2554104 AAAA
1 AAAA
2554108 CTCCATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 20 0.62
32 3 0.09
33 9 0.28
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.28
Consensus pattern (33 bp):
AAAAAAAAACTTCTACCAACTTTTAAGGGACCT
Found at i:2561773 original size:21 final size:21
Alignment explanation
Indices: 2561724--2561782 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2561714 ATAATAAATT
*
2561724 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
2561744 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
2561766 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
2561783 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:2564673 original size:3 final size:3
Alignment explanation
Indices: 2564667--2564718 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2564657 GAACAAAAAA
2564667 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2564715 AAT A
1 AAT A
2564719 TTAGTAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2567939 original size:15 final size:16
Alignment explanation
Indices: 2567907--2567939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2567897 TGCTGCTGTT
*
2567907 AGTTGCCATTCAAATG
1 AGTTGCCAATCAAATG
2567923 AGTTGCCAATC-AATG
1 AGTTGCCAATCAAATG
2567938 AG
1 AG
2567940 CTGTGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (16 bp):
AGTTGCCAATCAAATG
Found at i:2570456 original size:30 final size:28
Alignment explanation
Indices: 2570418--2570477 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2570408 ATTAGACCTG
*
2570418 AATTTTGAAATCTGAAAAGTAGAGG-ATTA
1 AATTTTGAAA-ATG-AAAGTAGAGGTATTA
2570447 AATTCTTGAAAATGAAAGTAGAGGTATTA
1 AATT-TTGAAAATGAAAGTAGAGGTATTA
2570476 AA
1 AA
2570478 CTCCAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
29 12 0.43
30 6 0.21
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (28 bp):
AATTTTGAAAATGAAAGTAGAGGTATTA
Found at i:2571869 original size:13 final size:13
Alignment explanation
Indices: 2571853--2571882 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2571843 CAAAAAGAAC
2571853 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
*
2571866 AAAAAAGAAAAGG
1 AAAAAAAAAAAGG
2571879 AAAA
1 AAAA
2571883 TAATTACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:2575199 original size:16 final size:18
Alignment explanation
Indices: 2575173--2575205 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2575163 TACTCAATTG
2575173 ATTTTTCTTAA-ATAAAT
1 ATTTTTCTTAATATAAAT
2575190 ATTTTT-TTAATATAAA
1 ATTTTTCTTAATATAAA
2575206 ATCAAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTCTTAATATAAAT
Found at i:2576594 original size:20 final size:20
Alignment explanation
Indices: 2576571--2576622 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2576561 AAATCCAAAT
*
2576571 TAAAATACTGAAATTCAGGA
1 TAAAATACTGAAATTCAAGA
*
2576591 TAAAATCCTGAAATTCAAGA
1 TAAAATACTGAAATTCAAGA
2576611 TAAGAATACTGA
1 TAA-AATACTGA
2576623 TGTGACATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (20 bp):
TAAAATACTGAAATTCAAGA
Found at i:2585037 original size:32 final size:31
Alignment explanation
Indices: 2584974--2585040 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
2584964 TTAAAAGTAA
* *
2584974 AAAAAAAAATTTATCAACATTTAGGAGACTT
1 AAAAAAAAATTTATCAACATTTAAGAAACTT
* **
2585005 AAAAAAAAATTTCTCTAATTTTTAAGAAACTT
1 AAAAAAAAATTTATC-AACATTTAAGAAACTT
2585037 AAAA
1 AAAA
2585041 TCTCATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (31 bp):
AAAAAAAAATTTATCAACATTTAAGAAACTT
Found at i:2585358 original size:3 final size:3
Alignment explanation
Indices: 2585350--2585393 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2585340 TTGAAGTACC
2585350 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2585394 ACAATAGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2588542 original size:60 final size:57
Alignment explanation
Indices: 2588473--2588614 Score: 158
Period size: 60 Copynumber: 2.4 Consensus size: 57
2588463 AAATATAATT
* * *
2588473 TAGTGTTTGAACTTGATAATTTTTCTTAACTTGGTCCCTAAATCTTTTTTAATTCACATT
1 TAGT-TTTGAACTTGATAATTTTTCTTAACTTGATCCCTAAATCTTTTTTAA-CCACA-A
* * * * * *
2588533 TAATTTTTGAACTTAACAATTTTTCTTAATTTGATCCCTAATTTTTTTTTAACCACAA
1 T-AGTTTTGAACTTGATAATTTTTCTTAACTTGATCCCTAAATCTTTTTTAACCACAA
2588591 TAGTTTTGAAACTTGATAATTTTT
1 TAGTTTTG-AACTTGATAATTTTT
2588615 TTCCAATGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
57 6 0.09
58 14 0.21
59 4 0.06
60 42 0.62
61 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (57 bp):
TAGTTTTGAACTTGATAATTTTTCTTAACTTGATCCCTAAATCTTTTTTAACCACAA
Found at i:2591602 original size:28 final size:26
Alignment explanation
Indices: 2591571--2591632 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 26
2591561 TTAAATTTAA
2591571 TAAAAAT-AAAATTATATTTTAATCCCTT
1 TAAAAATAAAAATTA-A-TTTAA-CCCTT
*
2591599 TAAAATGATAAAAATTAATTTAACCTTT
1 TAAAA--ATAAAAATTAATTTAACCCTT
2591627 TAAAAA
1 TAAAAA
2591633 ATATAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 1 0.03
28 14 0.47
29 5 0.17
30 3 0.10
31 7 0.23
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAATAAAAATTAATTTAACCCTT
Found at i:2593495 original size:297 final size:300
Alignment explanation
Indices: 2592949--2593543 Score: 720
Period size: 297 Copynumber: 2.0 Consensus size: 300
2592939 CAACTTACTG
* * * * **
2592949 AGATAATAAATTGTGTATATTAAAACAAAATTATATAAATTATATTAAAATGAAGTTTTAGTTGA
1 AGATAATAAATTATGTATATTAAAACAAAAATATATAAATTATATCAAAATAAAACTTTAGTTGA
* * * *
2593014 GTGATAAATCTAAGGTTTTAATAATCCAATTGGTGCGAGTTTGAATTCCACCGTATGCATATTTT
66 ATAATAAATCTAAGGTTTTAAT-ATCCAATTGGCGCGAGTTTAAATTCCACCG-ATGCATATTTT
* * ** * **
2593079 TATTGGTTTTTGTTTTAATAAAAGACTAAAATATTCTCGAATAATATAACTTTTTTTTAATTACA
129 AATTGGGTTTTGTTAAAATAAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTTAATTACA
* * * * *
2593144 AAAGGATATTTTCGTAATTTCTCAACCGAGTTGGTGAGCCAATTGAAAGTGACACCAACTTAGTT
194 AAAGGATATTTTCATAATTTCTCAACCGAGTTAGTGACCCAATTGAAAGTGACACCAACTCAGTC
2593209 AGGAGCTTAATAAAATAGTATAGAT-ATATAAACAATTAATGT
259 AGGAGCTTAAT-AAATAGTATAGATCATATAAACAATTAATGT
* *
2593251 AGATAATAAATTATGTATATTAAAACAAAAAATGTATAAGA-TATATCAAAATAAAACTTTGGTT
1 AGATAATAAATTATGTATATTAAAAC-AAAAATATATAA-ATTATATCAAAATAAAACTTTAGTT
* * *
2593315 GAATAATAAATTTAAGGTTTT-AT-T-CAATTGGCGCGGGTTTAAA-TCTTACC-ATGCATATTT
64 GAATAATAAATCTAAGGTTTTAATATCCAATTGGCGCGAGTTTAAATTC-CACCGATGCATATTT
2593375 TAATTGGGTTTTGTTAAAATAAAAAGACTAAAAAACCCTCGAATAATATAAC-TTTTTTTAATTA
128 TAATTGGGTTTTGTTAAAAT-AAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTTAATTA
*** ** * * * *
2593439 TGGATTGATATTTTCATAATTTCTTAATCGAGTTAGTGACCCAGTTGAAGGTGACACCAACTCAG
192 CAAAAGGATATTTTCATAATTTCTCAACCGAGTTAGTGACCCAATTGAAAGTGACACCAACTCAG
* *
2593504 TCAGGGGCTTAATAAATAGTATAGATGCATATAATCAATT
257 TCAGGAGCTTAATAAATAGTATAGAT-CATATAAACAATT
2593544 GTGTATATTA
Statistics
Matches: 249, Mismatches: 38, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
296 13 0.05
297 101 0.41
298 41 0.16
299 19 0.08
300 1 0.00
302 27 0.11
303 46 0.18
304 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (300 bp):
AGATAATAAATTATGTATATTAAAACAAAAATATATAAATTATATCAAAATAAAACTTTAGTTGA
ATAATAAATCTAAGGTTTTAATATCCAATTGGCGCGAGTTTAAATTCCACCGATGCATATTTTAA
TTGGGTTTTGTTAAAATAAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTTAATTACAAA
AGGATATTTTCATAATTTCTCAACCGAGTTAGTGACCCAATTGAAAGTGACACCAACTCAGTCAG
GAGCTTAATAAATAGTATAGATCATATAAACAATTAATGT
Found at i:2595123 original size:29 final size:26
Alignment explanation
Indices: 2595081--2595139 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
2595071 TAATGATGAA
2595081 AATAATAATAATAACAGTGAAAATAGGAT
1 AATAATAATAATAACAGT-AAAA-A-GAT
*
2595110 AATAATAA-ATATAATAGTAAAAAGAT
1 AATAATAATA-ATAACAGTAAAAAGAT
2595136 AATA
1 AATA
2595140 CTATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.25
27 1 0.04
28 5 0.18
29 15 0.54
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (26 bp):
AATAATAATAATAACAGTAAAAAGAT
Found at i:2595341 original size:3 final size:3
Alignment explanation
Indices: 2595323--2595374 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
2595313 AAACGTATAC
* *
2595323 TAA TACA TAG TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2595369 TAA TAA
1 TAA TAA
2595375 ATAAGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2596440 original size:14 final size:14
Alignment explanation
Indices: 2596421--2596454 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2596411 TGGTTGCAGA
2596421 TGGGCTGGGGTAGT
1 TGGGCTGGGGTAGT
2596435 TGGGCTGGGGTAGT
1 TGGGCTGGGGTAGT
2596449 TGGGCT
1 TGGGCT
2596455 TCGGGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.09, G:0.56, T:0.29
Consensus pattern (14 bp):
TGGGCTGGGGTAGT
Found at i:2596747 original size:26 final size:26
Alignment explanation
Indices: 2596695--2596748 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2596685 CAAGAAATAT
* **
2596695 TTATTATAAATTAGTTTTGCTTTTTA
1 TTATTATAAATGAGTTTTGCTCATTA
*
2596721 TTATTATAAATGAGTTTTTCTCATTA
1 TTATTATAAATGAGTTTTGCTCATTA
2596747 TT
1 TT
2596749 TAACTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (26 bp):
TTATTATAAATGAGTTTTGCTCATTA
Found at i:2600018 original size:6 final size:6
Alignment explanation
Indices: 2600007--2600033 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2599997 AAGATCAGAA
2600007 AGAAAG AGAAAG AGAAAG AGAAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGA
2600034 GAAGCAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:2601077 original size:2 final size:2
Alignment explanation
Indices: 2601070--2601109 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2601060 CTTAGCTTGA
2601070 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2601110 TTGTGTGTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2604576 original size:18 final size:18
Alignment explanation
Indices: 2604553--2604589 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2604543 GTTTACTTTT
2604553 GTTTTGAAAATTGTAGAA
1 GTTTTGAAAATTGTAGAA
2604571 GTTTTGAAAATTGTAGAA
1 GTTTTGAAAATTGTAGAA
2604589 G
1 G
2604590 CAATTCAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
GTTTTGAAAATTGTAGAA
Found at i:2613916 original size:2 final size:2
Alignment explanation
Indices: 2613911--2613954 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2613901 CCAAAAAACC
*
2613911 AT AT AT CT AT AT AT 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 AT AT AT AT AT AT AT
2613953 AT
1 AT
2613955 GTTTCAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2617204 original size:7 final size:7
Alignment explanation
Indices: 2617192--2617218 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2617182 CGATTATTTG
2617192 ATTAATA
1 ATTAATA
2617199 ATTAATA
1 ATTAATA
2617206 ATTAATA
1 ATTAATA
2617213 ATTAAT
1 ATTAAT
2617219 TTAGTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAATA
Found at i:2617807 original size:21 final size:20
Alignment explanation
Indices: 2617776--2617814 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2617766 TTGGTACAAA
*
2617776 AAAATTTAAAATTTATTAAT
1 AAAATTTAAAAGTTATTAAT
2617796 AAAATTTAAAAAGTTATTA
1 AAAATTT-AAAAGTTATTA
2617815 CAATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAATTTAAAAGTTATTAAT
Found at i:2617992 original size:10 final size:10
Alignment explanation
Indices: 2617943--2618012 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
2617933 CCAACCATGG
2617943 TTTTTAATAAA
1 TTTTT-ATAAA
2617954 TTTTTA-AACA
1 TTTTTATAA-A
*
2617964 TTTTTATTAA
1 TTTTTATAAA
*
2617974 TTTTAATAAA
1 TTTTTATAAA
*
2617984 TTTTTATAAC
1 TTTTTATAAA
*
2617994 TTCTTATAATTA
1 TTTTTATAA--A
2618006 TTTTTAT
1 TTTTTAT
2618013 TTTTATTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
9 2 0.04
10 33 0.70
11 6 0.13
12 6 0.13
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:2618045 original size:44 final size:45
Alignment explanation
Indices: 2617973--2618063 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 45
2617963 ATTTTTATTA
*
2617973 ATTTTAATAAATTTTTATAACTTCTTATAAT-TATTTT-TATTTTT
1 ATTTTAATAAATTTTCATAACTTCTTAT-ATGTATTTTGTATTTTT
* * *
2618017 ATTTTAATAAGTTTTCCATAA-TTTTTATATGTTTTTTGTATTTTT
1 ATTTTAATAAATTTT-CATAACTTCTTATATGTATTTTGTATTTTT
2618062 AT
1 AT
2618064 AGTAATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.05
44 25 0.62
45 13 0.32
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (45 bp):
ATTTTAATAAATTTTCATAACTTCTTATATGTATTTTGTATTTTT
Found at i:2618190 original size:12 final size:12
Alignment explanation
Indices: 2618170--2618201 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2618160 CTAGATGCGA
*
2618170 TTTTAAATAATT
1 TTTTTAATAATT
2618182 TTTTTAATAATT
1 TTTTTAATAATT
2618194 TTTTTAAT
1 TTTTTAAT
2618202 TGCTGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTAATAATT
Found at i:2621536 original size:19 final size:20
Alignment explanation
Indices: 2621514--2621554 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2621504 ATAAAGAGTA
2621514 TTTATATAT-AAAAATATAT
1 TTTATATATAAAAAATATAT
2621533 TTTATATATAAAAAATATAT
1 TTTATATATAAAAAATATAT
2621553 TT
1 TT
2621555 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATATATAAAAAATATAT
Found at i:2621555 original size:19 final size:18
Alignment explanation
Indices: 2621512--2621556 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
2621502 TTATAAAGAG
2621512 TATTTATATATAAAAATA
1 TATTTATATATAAAAATA
2621530 TATTTTATATATAAAAAATA
1 TA-TTTATATAT-AAAAATA
2621550 TATTTAT
1 TATTTAT
2621557 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTATATATAAAAATA
Found at i:2621566 original size:20 final size:21
Alignment explanation
Indices: 2621512--2621568 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
2621502 TTATAAAGAG
2621512 TATTTATATATAAAAATATATT
1 TATTTATAT-TAAAAATATATT
* *
2621534 T-TATATATAAAAAATATATT
1 TATTTATATTAAAAATATATT
2621554 TATTTA-ATTAAAAAT
1 TATTTATATTAAAAAT
2621569 TTTGATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 20 0.67
21 9 0.30
22 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTATATTAAAAATATATT
Found at i:2621743 original size:25 final size:27
Alignment explanation
Indices: 2621704--2621757 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
2621694 AATTAATTTC
*
2621704 ATATTAATATATTATCATTTTAAT-TA
1 ATATTAATATATTATCATTCTAATGTA
* *
2621730 ATATTACT-TATTATTATTCTAATGTA
1 ATATTAATATATTATCATTCTAATGTA
2621756 AT
1 AT
2621758 TTAGTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (27 bp):
ATATTAATATATTATCATTCTAATGTA
Found at i:2628267 original size:29 final size:30
Alignment explanation
Indices: 2628208--2628271 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2628198 TTATTTGTTT
*
2628208 ATAAAAAAAAGGAATAAAAGAATAAAGAAC
1 ATAAAAAAAAGGAATAAAAGAATAAAAAAC
*
2628238 ATAAAGAAAAA-GAAT-AAAGTATAAAAAAC
1 ATAAA-AAAAAGGAATAAAAGAATAAAAAAC
2628267 A-AAAA
1 ATAAAA
2628272 CAGAAAAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 1 0.03
28 3 0.10
29 13 0.42
30 9 0.29
31 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (30 bp):
ATAAAAAAAAGGAATAAAAGAATAAAAAAC
Found at i:2631144 original size:20 final size:21
Alignment explanation
Indices: 2631106--2631150 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2631096 AGTATAAATG
2631106 TTAA-ATAATTTTTAAGT-AA
1 TTAATATAATTTTTAAGTAAA
**
2631125 TTAATATAATTTTTTTGTAAA
1 TTAATATAATTTTTAAGTAAA
2631146 TTAAT
1 TTAAT
2631151 GATACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 11 0.50
21 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTAATATAATTTTTAAGTAAA
Found at i:2631203 original size:15 final size:15
Alignment explanation
Indices: 2631185--2631243 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
2631175 TAAATATAAT
2631185 AATAATTTATATTTA
1 AATAATTTATATTTA
* *
2631200 AATAATCTA-ATATA
1 AATAATTTATATTTA
*
2631214 ATGATAAATTATATTTA
1 A--ATAATTTATATTTA
2631231 AATAATTTGATAT
1 AATAATTT-ATAT
2631244 AATGGTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 5 0.15
15 14 0.41
16 10 0.29
17 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (15 bp):
AATAATTTATATTTA
Found at i:2631247 original size:31 final size:31
Alignment explanation
Indices: 2631177--2631247 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
2631167 TAAAAACTTA
* *
2631177 AATATAATAATAATTTATATTTAAATAATCT
1 AATATAATGATAAATTATATTTAAATAATCT
*
2631208 AATATAATGATAAATTATATTTAAATAATTT
1 AATATAATGATAAATTATATTTAAATAATCT
*
2631239 GATATAATG
1 AATATAATG
2631248 GTACATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (31 bp):
AATATAATGATAAATTATATTTAAATAATCT
Found at i:2634380 original size:75 final size:75
Alignment explanation
Indices: 2634261--2634432 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
2634251 CATGGCAAAG
** *
2634261 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
2634320 CCATACTGAGC
65 CCATACCGAGC
2634331 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
2634396 CATACCGAGT
66 CATACCGAGC
***
2634406 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
2634433 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:2634399 original size:35 final size:35
Alignment explanation
Indices: 2634264--2634430 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
2634254 GGCAAAGTGT
* **
2634264 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
2634299 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
2634334 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
2634374 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
2634410 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
2634431 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:2634422 original size:36 final size:35
Alignment explanation
Indices: 2634360--2634430 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
2634350 ATTATCAAAT
* *
2634360 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
2634395 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
2634431 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:2640960 original size:16 final size:16
Alignment explanation
Indices: 2640939--2640970 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2640929 ATATATTCAT
*
2640939 AAGCTAATGAAAAGGC
1 AAGCTAATCAAAAGGC
2640955 AAGCTAATCAAAAGGC
1 AAGCTAATCAAAAGGC
2640971 TTACTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (16 bp):
AAGCTAATCAAAAGGC
Found at i:2649434 original size:36 final size:36
Alignment explanation
Indices: 2649388--2649456 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
2649378 TTTTATTCAC
*
2649388 TCTTCTTGATAGCTTATACTTCGTAAACACTTATGT
1 TCTTCTTGATAGCTTATACTTCATAAACACTTATGT
2649424 TCTTCTTGATAGCTTATACTTCATAAACACTTA
1 TCTTCTTGATAGCTTATACTTCATAAACACTTA
2649457 CGTTAGAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (36 bp):
TCTTCTTGATAGCTTATACTTCATAAACACTTATGT
Found at i:2652990 original size:46 final size:44
Alignment explanation
Indices: 2652931--2653045 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2652921 ACAGGACAGA
* *
2652931 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2652977 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2653021 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2653046 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2653026 original size:44 final size:45
Alignment explanation
Indices: 2652931--2653064 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2652921 ACAGGACAGA
* *
2652931 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2652977 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2653021 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2653065 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2659143 original size:46 final size:44
Alignment explanation
Indices: 2659084--2659198 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2659074 ACAGGACAGA
* *
2659084 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2659130 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2659174 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2659199 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2659179 original size:44 final size:45
Alignment explanation
Indices: 2659084--2659217 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2659074 ACAGGACAGA
* *
2659084 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2659130 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2659174 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2659218 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2662077 original size:21 final size:21
Alignment explanation
Indices: 2662038--2662077 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2662028 AATTTTCTCT
*
2662038 ATTTTTAAATATATTTTTATA
1 ATTTTTAAATATATATTTATA
* *
2662059 ATTTTTAATTATCTATTTA
1 ATTTTTAAATATATATTTA
2662078 ATATAAACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAATATATATTTATA
Found at i:2667479 original size:2 final size:2
Alignment explanation
Indices: 2667472--2667505 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2667462 TCTCTTGATA
2667472 AT AT AT 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 AT AT AT
2667506 GAATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2667929 original size:18 final size:18
Alignment explanation
Indices: 2667874--2667923 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2667864 CTCTTTTTAA
**
2667874 AAAATTAATAATTAAATT
1 AAAATTAATAAAAAAATT
*
2667892 -TAATTAATAAAAAAATT
1 AAAATTAATAAAAAAATT
2667909 AAAATTAACTAAAAA
1 AAAATTAA-TAAAAA
2667924 TATAAACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTAATAAAAAAATT
Found at i:2668568 original size:23 final size:21
Alignment explanation
Indices: 2668534--2668581 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
2668524 CAGCGACAAA
2668534 ATTAAAATAAAACAAAATAAAAT
1 ATTAAAATAAAA-AAAA-AAAAT
*
2668557 ATTAAAGA-AAAAATAAAAAAT
1 ATTAAA-ATAAAAAAAAAAAAT
2668578 ATTA
1 ATTA
2668582 TTATTCCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 10 0.43
24 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
ATTAAAATAAAAAAAAAAAAT
Found at i:2678599 original size:18 final size:18
Alignment explanation
Indices: 2678576--2678613 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2678566 TTTAATTGTT
*
2678576 TTATTATTAT-ATAGTATA
1 TTATTATAATAATA-TATA
2678594 TTATTATAATAATATATA
1 TTATTATAATAATATATA
2678612 TT
1 TT
2678614 CTTAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTATTATAATAATATATA
Done.