Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 7 of 290
Found at i:2432443 original size:14 final size:14
Alignment explanation
Indices: 2432399--2432443 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2432389 TTAAGGTAAG
*
2432399 TAATTAAAATATTA
1 TAATTAAAATATAA
* *
2432413 TATTTTAAATATAAA
1 TAATTAAAATAT-AA
2432428 TAATTAAAATATAA
1 TAATTAAAATATAA
2432442 TA
1 TA
2432444 TGAGTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATTAAAATATAA
Found at i:2439604 original size:54 final size:54
Alignment explanation
Indices: 2439521--2439629 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
2439511 GATTTATAAG
* * *
2439521 TCAATCGATCTGACGCCTCTCTTAGATTGATACCTTGACTAATTCCCGATTCAA
1 TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
* * * *
2439575 TCAATTGATCTAATGCCTCTTTTAAATTGATACCTTGACTAATTCTCAATTCAA
1 TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
2439629 T
1 T
2439630 TGGCAAGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (54 bp):
TCAATCGATCTAACGCCTCTCTTAAATTGATACCTTGACTAATTCCCAATTCAA
Found at i:2441635 original size:21 final size:21
Alignment explanation
Indices: 2441609--2441650 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2441599 AGGCAAAATA
2441609 CAATTTGACTTCTTGTACAGG
1 CAATTTGACTTCTTGTACAGG
2441630 CAATTTGACTTCTTGTACAGG
1 CAATTTGACTTCTTGTACAGG
2441651 ACCTACATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (21 bp):
CAATTTGACTTCTTGTACAGG
Found at i:2442040 original size:26 final size:26
Alignment explanation
Indices: 2442017--2442070 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
2442007 GACAAGTACT
*
2442017 AATTTGCTATTTTTTAATAGAGTAGC
1 AATTTACTATTTTTTAATAGAGTAGC
2442043 AATTTACTATTTTTTAATAGAGTAGC
1 AATTTACTATTTTTTAATAGAGTAGC
2442069 AA
1 AA
2442071 AATGCAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (26 bp):
AATTTACTATTTTTTAATAGAGTAGC
Found at i:2443421 original size:24 final size:24
Alignment explanation
Indices: 2443393--2443442 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2443383 TTTCACATTA
* *
2443393 ATCATCCATTATTTTTAAAATAAC
1 ATCATCCATTATTTTAAAAAGAAC
2443417 ATCATCCATTATTTTAAAAAGAAC
1 ATCATCCATTATTTTAAAAAGAAC
2443441 AT
1 AT
2443443 AATGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (24 bp):
ATCATCCATTATTTTAAAAAGAAC
Found at i:2443878 original size:16 final size:15
Alignment explanation
Indices: 2443859--2443889 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2443849 TGTAATTATA
2443859 TTTTTTCCGAATTTTC
1 TTTTTTCC-AATTTTC
2443875 TTTTTTCCAATTTTC
1 TTTTTTCCAATTTTC
2443890 AAATTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.13, C:0.19, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTTCCAATTTTC
Found at i:2444942 original size:42 final size:43
Alignment explanation
Indices: 2444882--2445004 Score: 144
Period size: 42 Copynumber: 2.9 Consensus size: 43
2444872 CGCTTTACTT
*
2444882 AGTTTAA-TTTTTGAATTCGAAGTAAGGTTAATAGTATGTTTC
1 AGTTTAATTTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
* **
2444924 AGTTTACTTTTTTG-ATTCGAAGTAAGATTCTTAGTATGTTTC
1 AGTTTAATTTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
** * * *
2444966 AGTTTAATTTTCGGACTGC-AAGTAAGATTAATAATATGT
1 AGTTTAATTTTTTGAATTCGAAGTAAGATTAATAGTATGT
2445005 GTGATTAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 59 0.88
43 8 0.12
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (43 bp):
AGTTTAATTTTTTGAATTCGAAGTAAGATTAATAGTATGTTTC
Found at i:2445211 original size:42 final size:42
Alignment explanation
Indices: 2445152--2445234 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
2445142 CTTAGTTCTA
*
2445152 TTTTTGGATTCGAAGTAAGATTAATAGTATGTTTCAGTTTAC
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
* *
2445194 TTTTTGGATTCGAAGTAAGATTTAGAGTATGTTTCGGTTTA
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTA
2445235 TATTTGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.46
Consensus pattern (42 bp):
TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
Found at i:2445359 original size:96 final size:96
Alignment explanation
Indices: 2445189--2445447 Score: 267
Period size: 96 Copynumber: 2.7 Consensus size: 96
2445179 TATGTTTCAG
* * * * *
2445189 TTTACTTTTTGGATTCGAAGTAAGATTTA-GAGTATGTTTCGGTTTATATTTGATCAAATT-CCT
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGA-TATG-TTC--TTT-TGTTTGATTAAATTACCT
** * * *
2445252 CATAG--TT-CATTTCTGTATGTATTCGTTATTTAG
61 CATAGCTTTACATTTCTACATGTACTCGTTACTTAA
* * *
2445285 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAGTTATCTCGTAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
* * *
2445350 CTTTACATTTCTACATTTCCTCTTTACTTAA
66 CTTTACATTTCTACATGTACTCGTTACTTAA
* * *
2445381 TTTAATTTTTTGATTTGATGTAAGATTCATGATATTTTCTTTTGTTTGATTAAATTACCTCATAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
2445446 CT
66 CT
2445448 CTTCGTTTCC
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
92 11 0.08
93 9 0.07
95 5 0.04
96 109 0.80
97 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (96 bp):
TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
CTTTACATTTCTACATGTACTCGTTACTTAA
Found at i:2445464 original size:96 final size:96
Alignment explanation
Indices: 2445285--2445474 Score: 283
Period size: 96 Copynumber: 2.0 Consensus size: 96
2445275 CGTTATTTAG
* * *
2445285 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAGTTATCTCGTAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
*
2445350 CTTTACATTTCTACATTTCCTCTTTACTTAA
66 CTTTACATTTCCACATTTCCTCTTTACTTAA
* * *
2445381 TTTAATTTTTTGATTTGATGTAAGATTCATGATATTTTCTTTTGTTTGATTAAATTACCTCATAG
1 TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
* *
2445446 CTCTT-CGTTTCCATATTTCCTCTTTACTT
66 CT-TTACATTTCCACATTTCCTCTTTACTT
2445475 TGGTGTTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
96 82 0.98
97 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (96 bp):
TTTAATTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAG
CTTTACATTTCCACATTTCCTCTTTACTTAA
Found at i:2451680 original size:16 final size:16
Alignment explanation
Indices: 2451641--2451691 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
2451631 ATTCTTTTAG
2451641 TAATATTTAATT-TTAAT
1 TAAT-TTTAATTATT-AT
2451658 TATATTTTAATTATTAT
1 TA-ATTTTAATTATTAT
2451675 TAATTTCT-ATTATTAT
1 TAATTT-TAATTATTAT
2451691 T
1 T
2451692 TTAGGAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.42
17 14 0.45
18 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTAATTATTAT
Found at i:2451738 original size:18 final size:17
Alignment explanation
Indices: 2451714--2451761 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2451704 ACATGTTGAA
2451714 TAATTATATTTTAAT-TT
1 TAATTAT-TTTTAATATT
*
2451731 TAAATTATTTTTTACTATT
1 T-AATTA-TTTTTAATATT
2451750 TAATTATTTTTA
1 TAATTATTTTTA
2451762 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:2454645 original size:21 final size:21
Alignment explanation
Indices: 2454620--2454682 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2454610 CATATAAGAT
2454620 AAATAATATTGTGTAAATATA
1 AAATAATATTGTGTAAATATA
* *
2454641 AAATACA-A---TAT-AAGAT-
1 AAATA-ATATTGTGTAAATATA
2454657 AAATAATATTGTGTAAATATA
1 AAATAATATTGTGTAAATATA
2454678 AAATA
1 AAATA
2454683 CAAAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 2 0.06
19 2 0.06
20 4 0.13
21 11 0.35
22 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (21 bp):
AAATAATATTGTGTAAATATA
Found at i:2454652 original size:37 final size:37
Alignment explanation
Indices: 2454611--2454685 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2454601 TGACATTGAC
2454611 ATATAAGATAAATAATATTGTGTAAATATAAAATACA
1 ATATAAGATAAATAATATTGTGTAAATATAAAATACA
2454648 ATATAAGATAAATAATATTGTGTAAATATAAAATACA
1 ATATAAGATAAATAATATTGTGTAAATATAAAATACA
2454685 A
1 A
2454686 AAAATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (37 bp):
ATATAAGATAAATAATATTGTGTAAATATAAAATACA
Found at i:2457451 original size:8 final size:8
Alignment explanation
Indices: 2457440--2457513 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
2457430 TTTAAAATTT
2457440 TAAAAATA
1 TAAAAATA
*
2457448 TAAAAGTCA
1 TAAAAAT-A
2457457 -AAAAA-A
1 TAAAAATA
2457463 T-AAAAT-
1 TAAAAATA
2457469 TAAAAA-A
1 TAAAAATA
*
2457476 TAGAAATA
1 TAAAAATA
*
2457484 TTAAAATGA
1 TAAAAAT-A
2457493 TTAAAAATGA
1 -TAAAAAT-A
2457503 TAAAAATA
1 TAAAAATA
2457511 TAA
1 TAA
2457514 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:2460094 original size:21 final size:22
Alignment explanation
Indices: 2460070--2460115 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2460060 AATCACACCT
*
2460070 AAATCAAAATA-AATATGAACA
1 AAATCAAAATATAATATGAAAA
* *
2460091 AAATCCACATATAATATGAAAA
1 AAATCAAAATATAATATGAAAA
2460113 AAA
1 AAA
2460116 ATGATCTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.20
Consensus pattern (22 bp):
AAATCAAAATATAATATGAAAA
Found at i:2464436 original size:17 final size:17
Alignment explanation
Indices: 2464412--2464445 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2464402 ATTCATTGAC
2464412 CTAACCAATTC-AAAAA
1 CTAACCAATTCTAAAAA
2464428 CTAATCCAATTCTAAAAA
1 CTAA-CCAATTCTAAAAA
2464446 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:2465780 original size:23 final size:23
Alignment explanation
Indices: 2465736--2465789 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2465726 ATCAACAAAT
* **
2465736 TTAATAAAAGAATTTTTGCAGTA
1 TTAACAAAAGAATTTTAACAGTA
*
2465759 TTAACAAAATAATTTTAACAGTA
1 TTAACAAAAGAATTTTAACAGTA
*
2465782 TGAACAAA
1 TTAACAAA
2465790 TTGACCTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
TTAACAAAAGAATTTTAACAGTA
Found at i:2466185 original size:28 final size:29
Alignment explanation
Indices: 2466121--2466186 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
2466111 ATTTTTTTGT
* *
2466121 CTAATTTGACACCTGAACTTGATATTTTTT
1 CTAATTTGACACCTAAACTT-ATATTTTTA
2466151 CTAATTTGACACCTAAACTT-T-TTTTTA
1 CTAATTTGACACCTAAACTTATATTTTTA
2466178 CTCAATTTG
1 CT-AATTTG
2466187 GCACATGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.21
28 7 0.21
30 19 0.58
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (29 bp):
CTAATTTGACACCTAAACTTATATTTTTA
Found at i:2466197 original size:28 final size:26
Alignment explanation
Indices: 2466112--2466197 Score: 64
Period size: 30 Copynumber: 3.0 Consensus size: 26
2466102 TAGTATTTAA
* *
2466112 TTTTTTTGTCTAATTTGACACCTGAAC
1 TTTTTTT-TCTAATTTGACACATAAAC
*
2466139 TTGATATTTTTTCTAATTTGACACCTAAAC
1 -T--T-TTTTTTCTAATTTGACACATAAAC
* *
2466169 TTTTTTTTACTCAATTTGGCACATGAAC
1 TTTTTTTT-CT-AATTTGACACATAAAC
2466197 T
1 T
2466198 AGGCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
26 6 0.12
27 3 0.06
28 15 0.31
29 1 0.02
30 19 0.39
31 5 0.10
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (26 bp):
TTTTTTTTCTAATTTGACACATAAAC
Found at i:2466782 original size:18 final size:18
Alignment explanation
Indices: 2466753--2466808 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
2466743 GGTTAATCCC
*
2466753 TTTTTATTTTTTAT-TTT
1 TTTTTATGTTTTATCTTT
* *
2466770 TTTTTATGGTTTT-TGTTA
1 TTTTTAT-GTTTTATCTTT
*
2466788 TTTTTATGTTTCATCTTT
1 TTTTTATGTTTTATCTTT
2466806 TTT
1 TTT
2466809 GAACTGTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.79
Consensus pattern (18 bp):
TTTTTATGTTTTATCTTT
Found at i:2468543 original size:27 final size:28
Alignment explanation
Indices: 2468495--2468548 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2468485 AAAAATAGGA
* *
2468495 AAAATAATATATTTGGTAATAATAATAT
1 AAAATAATATATATGGTAATAAAAATAT
2468523 AAAATAATA-ATAT-GTACATAAAAATA
1 AAAATAATATATATGGTA-ATAAAAATA
2468549 CATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.13
27 11 0.48
28 9 0.39
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAATAATATATATGGTAATAAAAATAT
Found at i:2468852 original size:34 final size:33
Alignment explanation
Indices: 2468789--2468924 Score: 87
Period size: 36 Copynumber: 3.9 Consensus size: 33
2468779 ACACAATATG
* *
2468789 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTATATATAATA
*
2468822 GTATTTAAGAATATATACATAAGATGATATAAAATA
1 GTATTTAA-AATATATACATAAG-T-ATATATAATA
* ** * * * *
2468858 CATACATAGAATAGTATA-AGAAATATATAACTAATG
1 -GTATTTAAAATA-TATACATAAGTATAT-A-TAATA
*
2468894 GTATTAAAAAATATATACATAA-TATATATAA
1 GTATT-TAAAATATATACATAAGTATATATAA
2468925 AATACATATA
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
33 11 0.14
34 17 0.22
35 14 0.18
36 27 0.35
37 8 0.10
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTATATATAATA
Found at i:2468928 original size:11 final size:11
Alignment explanation
Indices: 2468901--2468943 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2468891 ATGGTATTAA
*
2468901 AAAATATATAC
1 AAAATATATAT
*
2468912 ATAATATATAT
1 AAAATATATAT
*
2468923 AAAATACATAT
1 AAAATATATAT
*
2468934 AATATATATA
1 AAAATATATA
2468944 CGTATTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATATATAT
Found at i:2470085 original size:17 final size:18
Alignment explanation
Indices: 2470045--2470090 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2470035 GCGTTTCTTG
2470045 ATTTTTTTTTTGAGTTAA
1 ATTTTTTTTTTGAGTTAA
* *
2470063 AATTTTTTTTTG-GTTAG
1 ATTTTTTTTTTGAGTTAA
*
2470080 GTTTTTTTTTT
1 ATTTTTTTTTT
2470091 TTGGTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (18 bp):
ATTTTTTTTTTGAGTTAA
Found at i:2470377 original size:15 final size:15
Alignment explanation
Indices: 2470357--2470393 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2470347 AAACCCCCAA
2470357 AAAAAAACCTAACCC
1 AAAAAAACCTAACCC
2470372 AAAAAAACCTAACCC
1 AAAAAAACCTAACCC
2470387 AAAAAAA
1 AAAAAAA
2470394 AAAATCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAAAAACCTAACCC
Found at i:2471526 original size:11 final size:11
Alignment explanation
Indices: 2471502--2471544 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2471492 TTCTAATACG
*
2471502 TATATATATTA
1 TATATATTTTA
*
2471513 TATGTATTTTA
1 TATATATTTTA
* *
2471524 TATATATTATG
1 TATATATTTTA
2471535 TATATATTTT
1 TATATATTTT
2471545 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:2472926 original size:7 final size:8
Alignment explanation
Indices: 2472914--2472947 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2472904 ATAATAAAGT
2472914 ATAT-AAA
1 ATATCAAA
2472921 ATAT-AAA
1 ATATCAAA
2472928 ATATCAAA
1 ATATCAAA
2472936 ATATCAAA
1 ATATCAAA
2472944 ATAT
1 ATAT
2472948 TAGAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCAAA
Found at i:2472954 original size:16 final size:15
Alignment explanation
Indices: 2472914--2472947 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2472904 ATAATAAAGT
2472914 ATATAAAATAT-AAA
1 ATATAAAATATCAAA
2472928 ATATCAAAATATCAAA
1 ATAT-AAAATATCAAA
2472944 ATAT
1 ATAT
2472948 TAGAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATAAAATATCAAA
Found at i:2473111 original size:20 final size:20
Alignment explanation
Indices: 2473054--2473113 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
2473044 AATACTACAT
2473054 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
2473073 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
2473096 AAATATGTACATAATATA
1 AAATATGTACATAATATA
2473114 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:2473207 original size:25 final size:24
Alignment explanation
Indices: 2473178--2473307 Score: 106
Period size: 23 Copynumber: 5.5 Consensus size: 24
2473168 GAAAAAAAAA
*
2473178 ATATAAATAATATAGTATTAAAGAT
1 ATATACATAATATAGTATT-AAGAT
* *
2473203 ATATACATAAAATAGTA-TAATAT
1 ATATACATAATATAGTATTAAGAT
* * *
2473226 ATATACGTAATATAGAATTTAGA-
1 ATATACATAATATAGTATTAAGAT
* * *
2473249 ATATACCTAATATATTA-AAAGAAT
1 ATATACATAATATAGTATTAAG-AT
* * *
2473273 ATATATATAATATAATATTAAGAA
1 ATATACATAATATAGTATTAAGAT
2473297 ATATA-ATAATA
1 ATATACATAATA
2473308 ACAAAAAAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.02
23 39 0.47
24 24 0.29
25 18 0.22
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATACATAATATAGTATTAAGAT
Found at i:2473227 original size:23 final size:25
Alignment explanation
Indices: 2473090--2473307 Score: 98
Period size: 25 Copynumber: 8.9 Consensus size: 25
2473080 TACGTGATAA
* *
2473090 TATTAAAAATATGTACATAATATAG
1 TATTAAAGATATATACATAATATAG
* * * *
2473115 TGTAAAAAATACATACATAATATA-
1 TATTAAAGATATATACATAATATAG
*
2473139 -ATTAAA-ATATATACATAAGATAACATG
1 TATTAAAGATATATACAT-A-AT-ATA-G
** * * *
2473166 TAGAAAAAAAAAATATAAATAATATAG
1 T--ATTAAAGATATATACATAATATAG
*
2473193 TATTAAAGATATATACATAAAATAG
1 TATTAAAGATATATACATAATATAG
* *
2473218 TA-T-AATATATATACGTAATATAG
1 TATTAAAGATATATACATAATATAG
* * *
2473241 AATT-TAGA-ATATACCTAATATA-
1 TATTAAAGATATATACATAATATAG
* * *
2473263 T-TAAAAGAATATATATATAATATAA
1 TATTAAAG-ATATATACATAATATAG
*
2473288 TATT-AAGAAATATA-ATAATA
1 TATTAAAGATATATACATAATA
2473308 ACAAAAAAAA
Statistics
Matches: 145, Mismatches: 33, Indels: 32
0.69 0.16 0.15
Matches are distributed among these distances:
21 1 0.01
22 11 0.08
23 43 0.30
24 24 0.17
25 46 0.32
26 1 0.01
27 2 0.01
28 2 0.01
29 2 0.01
30 5 0.03
31 8 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
TATTAAAGATATATACATAATATAG
Found at i:2473283 original size:24 final size:23
Alignment explanation
Indices: 2473256--2473307 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2473246 AGAATATACC
*
2473256 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
2473280 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
2473303 TAATA
1 TAATA
2473308 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:2473717 original size:16 final size:15
Alignment explanation
Indices: 2473696--2473746 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
2473686 CTCCCCCCCC
2473696 AAAAAAAACTTCTTCA
1 AAAAAAAACTTC-TCA
2473712 AAAAAAAA-TTCTCAA
1 AAAAAAAACTTCTC-A
*
2473727 AAAAAAAACTCCTCA
1 AAAAAAAACTTCTCA
2473742 AAAAA
1 AAAAA
2473747 CCCCCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.06
15 18 0.56
16 12 0.38
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAAACTTCTCA
Found at i:2475501 original size:32 final size:33
Alignment explanation
Indices: 2475460--2475532 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
2475450 CAGTTTTCCT
2475460 AAAATATTTT-CA-AGAAATC-TGCCAAACAACAG
1 AAAATATTTTACACAG-AATCAT-CCAAACAACAG
* *
2475492 AAAATATTTTACACAGATTCATCCAAACACCAG
1 AAAATATTTTACACAGAATCATCCAAACAACAG
2475525 AAAATATT
1 AAAATATT
2475533 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:2477949 original size:4 final size:4
Alignment explanation
Indices: 2477942--2477966 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2477932 TACACTTATG
2477942 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
2477967 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:2480431 original size:11 final size:11
Alignment explanation
Indices: 2480401--2480441 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
2480391 TAAACTTAGT
2480401 ACAAATTTT-A
1 ACAAATTTTGA
* *
2480411 ATATATTTTGA
1 ACAAATTTTGA
2480422 ACAAATTTTGA
1 ACAAATTTTGA
2480433 ACAAATTTT
1 ACAAATTTT
2480442 AATATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (11 bp):
ACAAATTTTGA
Found at i:2482087 original size:11 final size:11
Alignment explanation
Indices: 2482071--2482095 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2482061 TATTTCACTT
2482071 TCATATCATAA
1 TCATATCATAA
2482082 TCATATCATAA
1 TCATATCATAA
2482093 TCA
1 TCA
2482096 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:2482880 original size:27 final size:29
Alignment explanation
Indices: 2482844--2482901 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
2482834 AAAATTAAAA
*
2482844 TTCTAATTCAATTGATTTA-ATTATTTTT
1 TTCTAATTCAATTGATTTATATTAATTTT
2482872 TTCT-ATTCAATTGATTTATATTAATTTT
1 TTCTAATTCAATTGATTTATATTAATTTT
2482900 TT
1 TT
2482902 GGTCAATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (29 bp):
TTCTAATTCAATTGATTTATATTAATTTT
Found at i:2482907 original size:26 final size:27
Alignment explanation
Indices: 2482851--2482913 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
2482841 AAATTCTAAT
* *
2482851 TCAATTGATTTAATTATTTTTTTCTAT
1 TCAATTGATTTAATTATATTTTTCTAG
*
2482878 TCAATTGATTTATATTA-ATTTTT-TGG
1 TCAATTGATTTA-ATTATATTTTTCTAG
*
2482904 TCAATCGATT
1 TCAATTGATT
2482914 AAACACCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 10 0.32
27 17 0.55
28 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (27 bp):
TCAATTGATTTAATTATATTTTTCTAG
Found at i:2501497 original size:21 final size:21
Alignment explanation
Indices: 2501471--2501514 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2501461 TAGTTTTCTT
*
2501471 TTTTTTTAATTA-TTATTATAA
1 TTTTTTTAATAATTTATT-TAA
2501492 TTTTTTTAATAATTTATTTAA
1 TTTTTTTAATAATTTATTTAA
2501513 TT
1 TT
2501515 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:2506212 original size:22 final size:22
Alignment explanation
Indices: 2506164--2506212 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2506154 TCTAACTCGA
* **
2506164 ATTTTTCTACTATTTTCTTGTT
1 ATTTTCCTACTATTTTCTCATT
*
2506186 GTTTTCCTACTATTTTCTCATT
1 ATTTTCCTACTATTTTCTCATT
2506208 ATTTT
1 ATTTT
2506213 GTTATTATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.65
Consensus pattern (22 bp):
ATTTTCCTACTATTTTCTCATT
Found at i:2509236 original size:13 final size:13
Alignment explanation
Indices: 2509218--2509246 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2509208 ATACATTCTA
2509218 TAGAAAATGTTTT
1 TAGAAAATGTTTT
2509231 TAGAAAATGTTTT
1 TAGAAAATGTTTT
2509244 TAG
1 TAG
2509247 TTGAAAGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (13 bp):
TAGAAAATGTTTT
Found at i:2512604 original size:30 final size:30
Alignment explanation
Indices: 2512570--2512629 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2512560 TATTTTATTA
*
2512570 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTAGTTATTATTTTAAAGGCATTTG
* *
2512600 TTAATTTAGTTATTATTTTATAGGTATTTG
1 TTAATTTAGTTATTATTTTAAAGGCATTTG
2512630 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTAGTTATTATTTTAAAGGCATTTG
Found at i:2525098 original size:22 final size:22
Alignment explanation
Indices: 2525047--2525106 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
2525037 AAGAAATGAG
*
2525047 TAAAAAATAATATACATAATAA
1 TAAAAAATATTATACATAATAA
*
2525069 TAAGAAAATATTATA-ATAAGTAC
1 TAA-AAAATATTATACATAA-TAA
2525092 TAAAAAATATCTATA
1 TAAAAAATAT-TATA
2525107 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:2526482 original size:16 final size:16
Alignment explanation
Indices: 2526463--2526520 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2526453 TAGATTGTAA
2526463 TGGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
*** **
2526479 TGGGTTTTATTTGTAAA
1 TGGG-TTTAGGGGTATT
*
2526496 TAGGTTTAGGGGTATT
1 TGGGTTTAGGGGTATT
2526512 TGGGTTTAG
1 TGGGTTTAG
2526521 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:2526503 original size:33 final size:32
Alignment explanation
Indices: 2526457--2526518 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
2526447 ATGGGTTAGA
*
2526457 TTGTAATGGGTTTAGGGGTATTTGGGTTTTAT
1 TTGTAATAGGTTTAGGGGTATTTGGGTTTTAT
2526489 TTGTAAATAGGTTTAGGGGTATTTGGGTTT
1 TTGT-AATAGGTTTAGGGGTATTTGGGTTT
2526519 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:2527170 original size:21 final size:21
Alignment explanation
Indices: 2527137--2527180 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2527127 ATTAAATTTT
* *
2527137 AAATTATCGATTTTATTATTA
1 AAATTATCAATTTAATTATTA
* *
2527158 AAATTATTAATTTAATTGTTA
1 AAATTATCAATTTAATTATTA
2527179 AA
1 AA
2527181 TAATATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
AAATTATCAATTTAATTATTA
Found at i:2527834 original size:11 final size:11
Alignment explanation
Indices: 2527820--2527872 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
2527810 AAGAGAAAAA
*
2527820 AAGAATAAGAG
1 AAGAAGAAGAG
2527831 AAGAA-ACAGAG
1 AAGAAGA-AGAG
2527842 AAGAAGAAGAAG
1 AAGAAGAAG-AG
*
2527854 AAGAAGAGGAG
1 AAGAAGAAGAG
2527865 AAGAAGAA
1 AAGAAGAA
2527873 TTAAGAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 1 0.03
11 25 0.68
12 11 0.30
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:2527835 original size:3 final size:3
Alignment explanation
Indices: 2527802--2527872 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
2527792 CTTGGACAGT
* * *
2527802 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
*
2527843 AGA AGA AGA AGA AGA AG- AGG AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2527873 TTAAGAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 11 0.20
3 44 0.80
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:2531440 original size:24 final size:24
Alignment explanation
Indices: 2531404--2531451 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2531394 CATGTCAGGG
2531404 AAAGCGCGCCGAGCTGTACATGTT
1 AAAGCGCGCCGAGCTGTACATGTT
*
2531428 AAAGCGCGTCGAGCTGTACATGTT
1 AAAGCGCGCCGAGCTGTACATGTT
2531452 TTCTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (24 bp):
AAAGCGCGCCGAGCTGTACATGTT
Found at i:2534414 original size:23 final size:24
Alignment explanation
Indices: 2534388--2534433 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2534378 ATATACTTTA
*
2534388 AAAAATA-ATATTTTTTAAAAAAT
1 AAAAATACATAATTTTTAAAAAAT
2534411 AAAAATACTATAATTTTTAAAAA
1 AAAAATAC-ATAATTTTTAAAAA
2534434 GAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAATACATAATTTTTAAAAAAT
Found at i:2538024 original size:24 final size:24
Alignment explanation
Indices: 2537988--2538035 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2537978 CAAAGCCTCG
*
2537988 CTCTTCACGTTGGGTTTGTTCTAC
1 CTCTTCACCTTGGGTTTGTTCTAC
2538012 CTCTTCACCTTGGGTTTGTTCTAC
1 CTCTTCACCTTGGGTTTGTTCTAC
2538036 TTGTTCGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.19, T:0.46
Consensus pattern (24 bp):
CTCTTCACCTTGGGTTTGTTCTAC
Found at i:2554939 original size:24 final size:23
Alignment explanation
Indices: 2554899--2554944 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2554889 AAATAAAAAT
*
2554899 AAAAATACTAAATTTTAAATATA
1 AAAAATAATAAATTTTAAATATA
*
2554922 AAAAATAATTAATATTTAAATAT
1 AAAAATAATAAAT-TTTAAATAT
2554945 TTAATCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATAATAAATTTTAAATATA
Found at i:2565693 original size:24 final size:25
Alignment explanation
Indices: 2565654--2565701 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2565644 AATAAAAAAA
*
2565654 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAATAT-ATAAAACAAATATAT
2565680 TTAAAAATAT-TAAAACAAATAT
1 TTAAAAATATATAAAACAAATAT
2565702 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
TTAAAAATATATAAAACAAATATAT
Found at i:2565699 original size:12 final size:12
Alignment explanation
Indices: 2565684--2565742 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
2565674 ATATATTTAA
2565684 AAATATTAAAAC
1 AAATATTAAAAC
2565696 AAATATTAAAAC
1 AAATATTAAAAC
2565708 AAATA--AAAA-
1 AAATATTAAAAC
* *
2565717 TAATACTAAAAC
1 AAATATTAAAAC
* *
2565729 AATTCTTAAAAC
1 AAATATTAAAAC
2565741 AA
1 AA
2565743 TACACAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
11 4 0.10
12 27 0.69
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:2566499 original size:16 final size:16
Alignment explanation
Indices: 2566478--2566509 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2566468 ACAAAATTTT
2566478 AGGACTATTTTTTAGG
1 AGGACTATTTTTTAGG
2566494 AGGACTATTTTTTAGG
1 AGGACTATTTTTTAGG
2566510 TTAGGGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
AGGACTATTTTTTAGG
Found at i:2567133 original size:31 final size:31
Alignment explanation
Indices: 2567095--2567171 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
2567085 AAAAAAGACC
* * *
2567095 AATTTGCTCTTTGATTTAGTGTATATGGATT
1 AATTTGCTCTATGATTTAGCGTATATGAATT
2567126 AATTTGCTC-ATGATTTAGCGTATATGAATT
1 AATTTGCTCTATGATTTAGCGTATATGAATT
2567156 AATTTGCT-TATGATTT
1 AATTTGCTCTATGATTT
2567172 GAGTAGAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 33 0.79
31 9 0.21
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (31 bp):
AATTTGCTCTATGATTTAGCGTATATGAATT
Found at i:2571875 original size:15 final size:16
Alignment explanation
Indices: 2571843--2571875 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2571833 TGCTGCTGTT
*
2571843 AGTTGCCATTCAAATG
1 AGTTGCCAATCAAATG
2571859 AGTTGCCAATC-AATG
1 AGTTGCCAATCAAATG
2571874 AG
1 AG
2571876 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:2572882 original size:84 final size:84
Alignment explanation
Indices: 2572771--2572947 Score: 345
Period size: 84 Copynumber: 2.1 Consensus size: 84
2572761 CAAAATTTCC
2572771 AAAAATTGTTATTCTCTAAGCAGTGACATTGACATTGTATATGCAAATTCCCTATTAGGAAAATC
1 AAAAATTGTTATTCTCTAAGCAGTGACATTGACATTGTATATGCAAATTCCCTATTAGGAAAATC
2572836 AAGTAGGTCGATCTGATTG
66 AAGTAGGTCGATCTGATTG
2572855 AAAAATTGTTATTCTCTAAGCAGTGACATTGACATTGTATATGCAAATTCCCTATTAGGAAAATC
1 AAAAATTGTTATTCTCTAAGCAGTGACATTGACATTGTATATGCAAATTCCCTATTAGGAAAATC
2572920 AAGTAGGTCGATCTGATTG
66 AAGTAGGTCGATCTGATTG
*
2572939 AACAATTGT
1 AAAAATTGT
2572948 GGTAATATCT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (84 bp):
AAAAATTGTTATTCTCTAAGCAGTGACATTGACATTGTATATGCAAATTCCCTATTAGGAAAATC
AAGTAGGTCGATCTGATTG
Found at i:2574478 original size:30 final size:28
Alignment explanation
Indices: 2574440--2574499 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2574430 ATTAGACCTG
*
2574440 AATTTTGAAATCTGAAAAGTAGAGG-ATTA
1 AATTTTGAAA-ATG-AAAGTAGAGGTATTA
2574469 AATTCTTGAAAATGAAAGTAGAGGTATTA
1 AATT-TTGAAAATGAAAGTAGAGGTATTA
2574498 AA
1 AA
2574500 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:2575891 original size:13 final size:13
Alignment explanation
Indices: 2575875--2575904 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2575865 CAAAAAGAAC
2575875 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
*
2575888 AAAAAAGAAAAGG
1 AAAAAAAAAAAGG
2575901 AAAA
1 AAAA
2575905 TAATTACTTT
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:2579201 original size:17 final size:18
Alignment explanation
Indices: 2579179--2579212 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2579169 TACTCAATTG
2579179 ATTTTTCTTAA-ATAAAT
1 ATTTTTCTTAATATAAAT
*
2579196 ATTTTTTTTAATATAAA
1 ATTTTTCTTAATATAAA
2579213 ATCAAGGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTCTTAATATAAAT
Found at i:2580601 original size:20 final size:20
Alignment explanation
Indices: 2580578--2580629 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2580568 AAATCCAAAT
*
2580578 TAAAATACTGAAATTCAGGA
1 TAAAATACTGAAATTCAAGA
*
2580598 TAAAATCCTGAAATTCAAGA
1 TAAAATACTGAAATTCAAGA
2580618 TAAGAATACTGA
1 TAA-AATACTGA
2580630 TTTGACATAA
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:2588191 original size:34 final size:34
Alignment explanation
Indices: 2588148--2588216 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2588138 TTATATTTTT
2588148 TTTTGACTTAATTCTCAATTTATCCTTTAAAGCA
1 TTTTGACTTAATTCTCAATTTATCCTTTAAAGCA
2588182 TTTTGACTTAATTCTCAATTTATCCTTTAAAGCA
1 TTTTGACTTAATTCTCAATTTATCCTTTAAAGCA
2588216 T
1 T
2588217 ACTCATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (34 bp):
TTTTGACTTAATTCTCAATTTATCCTTTAAAGCA
Found at i:2588544 original size:15 final size:13
Alignment explanation
Indices: 2588524--2588564 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2588514 AATTATGGTC
*
2588524 TTTTTTTGTA-AA
1 TTTTTTTTTATAA
2588536 TTTTATTTTTATAA
1 TTTT-TTTTTATAA
2588550 -TTTTTTTTATAA
1 TTTTTTTTTATAA
2588562 TTT
1 TTT
2588565 GTATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 13 0.52
13 10 0.40
14 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTATAA
Found at i:2588887 original size:31 final size:30
Alignment explanation
Indices: 2588826--2588890 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2588816 TTAAAAGTAA
* *
2588826 AAAAAAAATTTATCAACATTTAGGAGACTT
1 AAAAAAAATTTATCAACATTTAAGAAACTT
* **
2588856 AAAAAAAATTTCTCCAATTTTTAAGAAACTT
1 AAAAAAAATTTAT-CAACATTTAAGAAACTT
2588887 AAAA
1 AAAA
2588891 TCTCATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAAAAAATTTATCAACATTTAAGAAACTT
Found at i:2592428 original size:58 final size:59
Alignment explanation
Indices: 2592288--2592429 Score: 144
Period size: 60 Copynumber: 2.4 Consensus size: 59
2592278 AAATATAATT
* * * *
2592288 TAGTGTTTGAACTTGATAATTTTTCTTAACTTGGTCCCTAAACCTTTTTTAATTCACATT
1 TAGT-TTTGAACTTGATAACTTTTCTTAACTTGATCCCTAAACCTTTTTTAATCCACATA
* * * * ***
2592348 TAATTTTTGAACTTAACAACTTTTCTTAATTTGATCCCTAATTTTTTTTTAA-CCACA-A
1 T-AGTTTTGAACTTGATAACTTTTCTTAACTTGATCCCTAAACCTTTTTTAATCCACATA
2592406 TAGTTTTGGAACTTGATAACTTTT
1 TAGTTTT-GAACTTGATAACTTTT
2592430 TTCCAATGTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
57 5 0.08
58 15 0.23
59 4 0.06
60 40 0.61
61 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (59 bp):
TAGTTTTGAACTTGATAACTTTTCTTAACTTGATCCCTAAACCTTTTTTAATCCACATA
Found at i:2595040 original size:3 final size:3
Alignment explanation
Indices: 2595032--2595057 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2595022 AGTGTTTTAC
2595032 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2595058 GTAGTAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2597365 original size:297 final size:300
Alignment explanation
Indices: 2596818--2597413 Score: 708
Period size: 297 Copynumber: 2.0 Consensus size: 300
2596808 CAACTTACTG
* * * * **
2596818 AGATAATAAATTGTGTATATTAAAACAAAATTATATAAATTATATTAAAATGAAGTTTTAGTTGA
1 AGATAATAAATTATGTATATTAAAACAAAAATATATAAATTATATCAAAATAAAACTTTAGTTGA
* * *
2596883 GTGATAAATCTAAGGTTTTAATAATCCAATTGGTGCGAGTTTAAATTCCACCATATGCATATTTT
66 ATAATAAATCTAAGGTTTTAAT-ATCCAATTGGCGCGAGTTTAAATTCCACCA-ATGCATATTTT
* * ** * **
2596948 TATTGGTTTTTGTTTTAATAAAAGACTAAAATATTCTCGAATAATATAACTTTTTTTTTAATTAC
129 AATTGGGTTTTGTTAAAATAAAAGACTAAAAAACCCTCGAATAATATAAC-TTTTTTTTAATTAC
* * * *
2597013 AAAAGGATATTTTCGTAATTTCTCAACCGAGTTGGTGAGCCAATTGAAGGTGACACCAACTTAGT
193 AAAAGGATATTTTCATAATTTCTCAACCGAGTTAGTGACCCAATTGAAGGTGACACCAACTCAGT
*
2597078 TAGGAGCTTAATAAAATAGTATAGAT-ATATAAACAATTAATGT
258 CAGGAGCTTAAT-AAATAGTATAGATCATATAAACAATTAATGT
* *
2597121 AGATAATAAATTATGTATATTAAAACAAAAAATGTATAAGA-TATATCAAAATAAAACTTTGGTT
1 AGATAATAAATTATGTATATTAAAAC-AAAAATATATAA-ATTATATCAAAATAAAACTTTAGTT
* *
2597185 GAATAATAAATTTAAGGTTTT-AT-T-CAATTGGCGCG-GATTTAAA-TCTTACC-ATGCATATT
64 GAATAATAAATCTAAGGTTTTAATATCCAATTGGCGCGAG-TTTAAATTC-CACCAATGCATATT
2597244 TTAATTGGGTTTTGTTAAAATAAAAAGACTAAAAAACCCTCGAATAATATAAC-TTTTTTTAATT
127 TTAATTGGGTTTTGTTAAAAT-AAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTTAATT
*** ** * * *
2597308 ATGGATTGATATTTTCATAGTTTC-CTAATCGAGTTAGTGACCCAGTTGAAGGTGACACCAACTC
191 ACAAAAGGATATTTTCATAATTTCTC-AACCGAGTTAGTGACCCAATTGAAGGTGACACCAACTC
* *
2597372 AGTCAGGGGCTTAATAAATAGTATAGATGCATATAATCAATT
255 AGTCAGGAGCTTAATAAATAGTATAGAT-CATATAAACAATT
2597414 GTGTATATTA
Statistics
Matches: 250, Mismatches: 35, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
296 14 0.06
297 74 0.30
298 37 0.15
299 31 0.12
300 19 0.08
301 1 0.00
303 27 0.11
304 46 0.18
305 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (300 bp):
AGATAATAAATTATGTATATTAAAACAAAAATATATAAATTATATCAAAATAAAACTTTAGTTGA
ATAATAAATCTAAGGTTTTAATATCCAATTGGCGCGAGTTTAAATTCCACCAATGCATATTTTAA
TTGGGTTTTGTTAAAATAAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTTAATTACAAA
AGGATATTTTCATAATTTCTCAACCGAGTTAGTGACCCAATTGAAGGTGACACCAACTCAGTCAG
GAGCTTAATAAATAGTATAGATCATATAAACAATTAATGT
Found at i:2597650 original size:285 final size:280
Alignment explanation
Indices: 2597123--2597654 Score: 585
Period size: 285 Copynumber: 1.9 Consensus size: 280
2597113 ATTAATGTAG
*
2597123 ATAATAAATTATGTATATTAAAACAAAAAATGTATAAGATATATCAAAATAAAACTTTGGTTGAA
1 ATAATAAATTATGTATATTAAAACAAAAAATGTATAAAATATATCAAAATAAAACTTTGGTTGAA
** *
2597188 TAATAAATTTAAGGTTTTATTCAATTGGCGCGGATTTAAATCTTACCATGCATATTTTAATTGGG
66 TAATAAATTTAAACTTTTATTCAATTGGCGCGGATTCAAATCTTACCATGCATATTTTAATTGGG
* * * * *** *
2597253 TTTTGTTAAAATAAAAAGACTAAAAAACCCTCGAATAATATAACTTTTTTTAATTATGGATTGAT
131 TTTTGTTAAAATAAAAAAACTAAAAAACCCTCAAACAATATAACTTTTTTTAATTATGAAAAAAC
* * *
2597318 ATTTTCATAGTTTCCTAATCGAGTTAGTGACCCAGTTGAAGGTGACACCAACTCAGTCAGGGGCT
196 ATTCTCATAATTTCCTAATCGAGTTAGTAACCCAGTTGAAGGTGACA-CAACTCAGTCAGGGGCT
2597383 TAATAAATAGTATAGATGCAT
260 TAATAAATAGTATAGATGCAT
* * * * * *
2597404 ATAATCAATTGTGTATATTAAAAC-AAAAATGTATAAAATATGTTAAAATGAAACTTTGGTTGAG
1 ATAATAAATTATGTATATTAAAACAAAAAATGTATAAAATATATCAAAATAAAACTTTGGTTGAA
** * * * *
2597468 TGGTAAATTTAAAACTTTAGTAATTCAATTGGTG-TGAGTTCAAAT-TTGACCATGTATGTTTTA
66 TAATAAATTT-AAACTTT--T-ATTCAATTGGCGCGGA-TTCAAATCTT-ACCATGCATATTTTA
* * * *
2597531 ATTTGTTTTTGTTAGAATAAAAAAAACTAAAACACCCTCAAACAATATAACTTTTTTTAATT-TC
125 ATTGGGTTTTGTTAAAAT-AAAAAAACTAAAAAACCCTCAAACAATATAACTTTTTTTAATTAT-
* * *
2597595 GAAAAAACA-TCTCTATAATTTCTTAA-CTGAGTT-GATAATCC-GATTGAGGGTGACACAACT
188 GAAAAAACATTCTC-ATAATTTCCTAATC-GAGTTAG-TAACCCAG-TTGAAGGTGACACAACT
2597655 TAATGAAGGA
Statistics
Matches: 205, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
280 43 0.21
281 27 0.13
283 5 0.02
284 57 0.28
285 73 0.36
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (280 bp):
ATAATAAATTATGTATATTAAAACAAAAAATGTATAAAATATATCAAAATAAAACTTTGGTTGAA
TAATAAATTTAAACTTTTATTCAATTGGCGCGGATTCAAATCTTACCATGCATATTTTAATTGGG
TTTTGTTAAAATAAAAAAACTAAAAAACCCTCAAACAATATAACTTTTTTTAATTATGAAAAAAC
ATTCTCATAATTTCCTAATCGAGTTAGTAACCCAGTTGAAGGTGACACAACTCAGTCAGGGGCTT
AATAAATAGTATAGATGCAT
Found at i:2597946 original size:26 final size:26
Alignment explanation
Indices: 2597894--2597947 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2597884 CAAGAAATAT
* **
2597894 TTATTATAAATTAGTTTTGCTTTTTA
1 TTATTATAAATGAGTTTTGCTCATTA
*
2597920 TTATTATAAATGAGTTTTTCTCATTA
1 TTATTATAAATGAGTTTTGCTCATTA
2597946 TT
1 TT
2597948 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:2601220 original size:6 final size:6
Alignment explanation
Indices: 2601209--2601235 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2601199 AAGATCAGAA
2601209 AGAAAG AGAAAG AGAAAG AGAAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGA
2601236 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:2605757 original size:18 final size:18
Alignment explanation
Indices: 2605734--2605770 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2605724 GTTTACTTTT
2605734 GTTTTGAAAATTGTAGAA
1 GTTTTGAAAATTGTAGAA
2605752 GTTTTGAAAATTGTAGAA
1 GTTTTGAAAATTGTAGAA
2605770 G
1 G
2605771 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:2616597 original size:17 final size:18
Alignment explanation
Indices: 2616556--2616591 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2616546 TACAGTACAC
*
2616556 AATTTTTTCTAACAAATT
1 AATTTTTTCTAAAAAATT
*
2616574 AAGTTTTTCTAAAAAATT
1 AATTTTTTCTAAAAAATT
2616592 CTTTTTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTTTTTCTAAAAAATT
Found at i:2618344 original size:7 final size:7
Alignment explanation
Indices: 2618332--2618358 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2618322 CGATTATTTG
2618332 ATTAATA
1 ATTAATA
2618339 ATTAATA
1 ATTAATA
2618346 ATTAATA
1 ATTAATA
2618353 ATTAAT
1 ATTAAT
2618359 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:2618761 original size:17 final size:16
Alignment explanation
Indices: 2618739--2618790 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2618729 ATACAACATT
2618739 AATAAATATTTAGAAAA
1 AATAAATATTTA-AAAA
*
2618756 AATAAAAAATCTT-AAAA
1 AAT-AAATAT-TTAAAAA
*
2618773 AGTAAATATTTAAAAA
1 AATAAATATTTAAAAA
2618789 AA
1 AA
2618791 AATCATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 9 0.32
18 5 0.18
19 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
AATAAATATTTAAAAA
Found at i:2619118 original size:20 final size:20
Alignment explanation
Indices: 2619095--2619156 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2619085 GTTTTTAATA
*
2619095 AATTCTTAAACATTTTTATT
1 AATTCTTAAAAATTTTTATT
2619115 AATT-TTAATAAATTTTTA-T
1 AATTCTTAA-AAATTTTTATT
*
2619134 AACTTCTTATAATTATTTTTATT
1 AA-TTCTTA-AA-AATTTTTATT
2619157 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.21
20 14 0.41
21 4 0.12
22 8 0.24
23 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTCTTAAAAATTTTTATT
Found at i:2619188 original size:44 final size:46
Alignment explanation
Indices: 2619116--2619207 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 46
2619106 ATTTTTATTA
*
2619116 ATTTTAATAAATTTTTATAACTTCTTATA-ATTATTTT-TATTTTT
1 ATTTTAATAAATTTTCATAACTTCTTATATATTATTTTGTATTTTT
* * * *
2619160 ATTTTAATAAGTTTTCCATAA-TTTTTATATGTTTTTTTGTATTTTT
1 ATTTTAATAAATTTT-CATAACTTCTTATATATTATTTTGTATTTTT
2619206 AT
1 AT
2619208 AGTAATTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 21 0.52
45 10 0.25
46 9 0.22
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.64
Consensus pattern (46 bp):
ATTTTAATAAATTTTCATAACTTCTTATATATTATTTTGTATTTTT
Found at i:2620587 original size:25 final size:23
Alignment explanation
Indices: 2620531--2620589 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
2620521 TTTACTAAAA
2620531 ATAAAAA-TTATAAAAATAAATT
1 ATAAAAATTTATAAAAATAAATT
** *
2620553 ATAATTATTTCTAAAAATAAAAATT
1 ATAAAAATTTATAAAAAT--AAATT
2620578 ATAAAAATTTAT
1 ATAAAAATTTAT
2620590 TCTACCACCA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 5 0.18
23 9 0.32
25 14 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAAATTTATAAAAATAAATT
Found at i:2622311 original size:21 final size:21
Alignment explanation
Indices: 2622286--2622326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2622276 CCACATGATT
2622286 TTAAG-TTTTGTGAGAATTTTG
1 TTAAGATTTT-TGAGAATTTTG
*
2622307 TTAAGATTTTTGATAATTTT
1 TTAAGATTTTTGAGAATTTT
2622327 TTATGAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (21 bp):
TTAAGATTTTTGAGAATTTTG
Found at i:2622373 original size:11 final size:11
Alignment explanation
Indices: 2622357--2622390 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2622347 TTTTTAATTA
2622357 AATTAAATATT
1 AATTAAATATT
*
2622368 AATTAAATAAT
1 AATTAAATATT
2622379 AATTAAGATATT
1 AATTAA-ATATT
2622391 TAAAATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AATTAAATATT
Found at i:2622654 original size:19 final size:20
Alignment explanation
Indices: 2622632--2622672 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2622622 ATAAAGAGTA
2622632 TTTATATAT-AAAAATATAT
1 TTTATATATAAAAAATATAT
2622651 TTTATATATAAAAAATATAT
1 TTTATATATAAAAAATATAT
2622671 TT
1 TT
2622673 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:2622673 original size:19 final size:18
Alignment explanation
Indices: 2622630--2622674 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
2622620 TTATAAAGAG
2622630 TATTTATATATAAAAATA
1 TATTTATATATAAAAATA
2622648 TATTTTATATATAAAAAATA
1 TA-TTTATATAT-AAAAATA
2622668 TATTTAT
1 TATTTAT
2622675 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:2622684 original size:20 final size:21
Alignment explanation
Indices: 2622630--2622686 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
2622620 TTATAAAGAG
2622630 TATTTATATATAAAAATATATT
1 TATTTATAT-TAAAAATATATT
* *
2622652 T-TATATATAAAAAATATATT
1 TATTTATATTAAAAATATATT
2622672 TATTTA-ATTAAAAAT
1 TATTTATATTAAAAAT
2622687 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:2622845 original size:25 final size:27
Alignment explanation
Indices: 2622806--2622859 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
2622796 AATTAATTTC
*
2622806 ATATTAATATATTATCATTTTAAT-TA
1 ATATTAATATATTATCATTCTAATATA
* *
2622832 ATATTACT-TATTATTATTCTAATATA
1 ATATTAATATATTATCATTCTAATATA
2622858 AT
1 AT
2622860 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:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATTAATATATTATCATTCTAATATA
Found at i:2629364 original size:29 final size:30
Alignment explanation
Indices: 2629305--2629368 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2629295 TTATTTGTTT
*
2629305 ATAAAAAAAAGGAATAAAAGAATAAAGAAC
1 ATAAAAAAAAGGAATAAAAGAATAAAAAAC
*
2629335 ATAAAGAAAAA-GAAT-AAAGTATAAAAAAC
1 ATAAA-AAAAAGGAATAAAAGAATAAAAAAC
2629364 A-AAAA
1 ATAAAA
2629369 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:2632295 original size:15 final size:15
Alignment explanation
Indices: 2632277--2632335 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
2632267 TAAATATAAT
2632277 AATAATTTATATTTA
1 AATAATTTATATTTA
* *
2632292 AATAATCTA-ATATA
1 AATAATTTATATTTA
*
2632306 ATGATAAATTATATTTA
1 A--ATAATTTATATTTA
2632323 AATAATTTGATAT
1 AATAATTT-ATAT
2632336 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:2632339 original size:31 final size:31
Alignment explanation
Indices: 2632269--2632339 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
2632259 TAAAAACTTA
* *
2632269 AATATAATAATAATTTATATTTAAATAATCT
1 AATATAATGATAAATTATATTTAAATAATCT
*
2632300 AATATAATGATAAATTATATTTAAATAATTT
1 AATATAATGATAAATTATATTTAAATAATCT
*
2632331 GATATAATG
1 AATATAATG
2632340 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:2632896 original size:36 final size:36
Alignment explanation
Indices: 2632855--2632927 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
2632845 GTATTGTTGC
* * *
2632855 TCAAGATTCGAATAAAAAATCTGCTCCAGTTGCTGT
1 TCAAGATTCGAACAAAAAACCTACTCCAGTTGCTGT
* * *
2632891 TCAAGATTTGAACAAAAGACCTACTCGAGTTGCTGT
1 TCAAGATTCGAACAAAAAACCTACTCCAGTTGCTGT
2632927 T
1 T
2632928 AAAAATGGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (36 bp):
TCAAGATTCGAACAAAAAACCTACTCCAGTTGCTGT
Found at i:2639325 original size:16 final size:16
Alignment explanation
Indices: 2639304--2639335 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2639294 ATATATTCAT
*
2639304 AAGCTAATGAAAAGGC
1 AAGCTAATCAAAAGGC
2639320 AAGCTAATCAAAAGGC
1 AAGCTAATCAAAAGGC
2639336 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:2646670 original size:25 final size:25
Alignment explanation
Indices: 2646642--2646698 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 25
2646632 GAGTAAACAC
2646642 ATTCATTGTGAAATATATTTCTCTT
1 ATTCATTGTGAAATATATTTCTCTT
2646667 ATTCATTGTGAAATATATTTCTCTT
1 ATTCATTGTGAAATATATTTCTCTT
2646692 ACTTCAT
1 A-TTCAT
2646699 CGTTTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (25 bp):
ATTCATTGTGAAATATATTTCTCTT
Found at i:2647875 original size:36 final size:36
Alignment explanation
Indices: 2647829--2647897 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
2647819 TTTTATTCAC
*
2647829 TCTTCTTGATAGCTTATACTTCGTAAACACTTATGT
1 TCTTCTTGATAGCTTATACTTCATAAACACTTATGT
2647865 TCTTCTTGATAGCTTATACTTCATAAACACTTA
1 TCTTCTTGATAGCTTATACTTCATAAACACTTA
2647898 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:2657432 original size:23 final size:25
Alignment explanation
Indices: 2657398--2657447 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
2657388 AATTAAATTT
2657398 AATTAATAAAAAA-ATAAA-ATTAA
1 AATTAATAAAAAATATAAACATTAA
2657421 AATTAACT-AAAAATATAAACATTAA
1 AATTAA-TAAAAAATATAAACATTAA
2657446 AA
1 AA
2657448 ACTAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.46
24 6 0.25
25 7 0.29
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (25 bp):
AATTAATAAAAAATATAAACATTAA
Found at i:2658063 original size:23 final size:21
Alignment explanation
Indices: 2658029--2658076 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
2658019 CAGCGACAAA
2658029 ATTAAAATAAAACAAAATAAAAT
1 ATTAAAATAAAA-AAAA-AAAAT
*
2658052 ATTAAAGA-AAAAATAAAAAAT
1 ATTAAA-ATAAAAAAAAAAAAT
2658073 ATTA
1 ATTA
2658077 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:2661221 original size:32 final size:31
Alignment explanation
Indices: 2661168--2661230 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
2661158 TTCTCATTGT
2661168 ACTTTTTAATTTTTTAAAAAATTTTAATTAA
1 ACTTTTTAATTTTTTAAAAAATTTTAATTAA
* *
2661199 ACTTTCTTAAATTTTTT-GAAAATTTTCATTAA
1 ACTTT-TT-AATTTTTTAAAAAATTTTAATTAA
2661231 TTTTACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 15 0.54
33 8 0.29
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
ACTTTTTAATTTTTTAAAAAATTTTAATTAA
Found at i:2662363 original size:20 final size:20
Alignment explanation
Indices: 2662338--2662378 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2662328 TTAACAGTAG
2662338 AAATGATAAGATTTTTTGAC
1 AAATGATAAGATTTTTTGAC
2662358 AAATGATAAGATTTTTTGAC
1 AAATGATAAGATTTTTTGAC
2662378 A
1 A
2662379 GAAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
AAATGATAAGATTTTTTGAC
Found at i:2669625 original size:20 final size:20
Alignment explanation
Indices: 2669602--2669642 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2669592 TTGTAAATAG
2669602 ATTTTAATAATAAAAATAAT
1 ATTTTAATAATAAAAATAAT
*
2669622 ATTTTAATAATAATAATAAT
1 ATTTTAATAATAAAAATAAT
2669642 A
1 A
2669643 AGAAGAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTTAATAATAAAAATAAT
Found at i:2670544 original size:18 final size:16
Alignment explanation
Indices: 2670499--2670546 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2670489 ATATTATACA
*
2670499 TATAAA-TATATTTATT
1 TATAAATTA-ATTAATT
2670515 TATAAATTAATTAATT
1 TATAAATTAATTAATT
2670531 TATTAAACTTAATTAA
1 TA-TAAA-TTAATTAA
2670547 ATGATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.50
17 6 0.21
18 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAAATTAATTAATT
Found at i:2709215 original size:29 final size:28
Alignment explanation
Indices: 2709148--2709221 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
2709138 TTTATAATTT
*
2709148 TTTTGTATTT-AGAATTTAGTCATTATA
1 TTTTGAATTTAAGAATTTAGTCATTATA
* *
2709175 TTTTTATTTTTAAGAATTTAGTCTATT-TA
1 TTTTGA-ATTTAAGAATTTAGTC-ATTATA
2709204 CTTTTGAATTTAA-AATTT
1 -TTTTGAATTTAAGAATTT
2709222 TAACTTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 4 0.11
28 8 0.21
29 18 0.47
30 8 0.21
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (28 bp):
TTTTGAATTTAAGAATTTAGTCATTATA
Found at i:2709981 original size:68 final size:68
Alignment explanation
Indices: 2709849--2709981 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 68
2709839 AGTAGAAACC
* * * * ** *
2709849 TAGAGGGACCAAAAGTGATGTTGGACCAATTTCTATAAAATGAAAAAAAAAATTGAACATGTGTC
1 TAGAGAGACAAAAAGTGATATTGGACCAATTTCAATAAAATGAAAAAAAAAATCAAACACGTGTC
2709914 AAA
66 AAA
* * *
2709917 TAGAGAGACAAAAAGTGATATTTGACCAATTTTCAAT-AAATGAAAATAAATATCAAACACGTGT
1 TAGAGAGACAAAAAGTGATATTGGACCAA-TTTCAATAAAATGAAAAAAAAAATCAAACACGTGT
2709981 C
65 C
2709982 TATCAAGGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 48 0.89
69 6 0.11
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (68 bp):
TAGAGAGACAAAAAGTGATATTGGACCAATTTCAATAAAATGAAAAAAAAAATCAAACACGTGTC
AAA
Found at i:2710587 original size:31 final size:31
Alignment explanation
Indices: 2710551--2710631 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
2710541 TTTGATTAAG
* *
2710551 GACTAAAATTTCAAATTTTGAAAAGTACAAT
1 GACTAAAATTTCAAATTTCGAAAAGTACAAC
*
2710582 GACT-AAATTTGACTAA-TTCGAAAAGTACAAC
1 GACTAAAATTT--CAAATTTCGAAAAGTACAAC
2710613 GACTAAAATTGATCAAATT
1 GACTAAAATT--TCAAATT
2710632 AAAATACAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
30 6 0.15
31 21 0.52
32 11 0.28
33 1 0.03
34 1 0.03
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (31 bp):
GACTAAAATTTCAAATTTCGAAAAGTACAAC
Found at i:2713498 original size:11 final size:11
Alignment explanation
Indices: 2713482--2713556 Score: 53
Period size: 11 Copynumber: 6.3 Consensus size: 11
2713472 CTCATTTCAA
2713482 TTATTTTTATT
1 TTATTTTTATT
2713493 TTATTTTATCATT
1 TTATTTT-T-ATT
2713506 ATATCATTTTT-TAT
1 -T-T-ATTTTTAT-T
*
2713520 ATATTTTTATT
1 TTATTTTTATT
*
2713531 TTATTTTTATA
1 TTATTTTTATT
*
2713542 TTATATTATATT
1 TTAT-TTTTATT
2713554 TTA
1 TTA
2713557 ACTAATTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
11 27 0.53
12 11 0.22
13 4 0.08
14 2 0.04
15 2 0.04
16 5 0.10
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:2713526 original size:38 final size:38
Alignment explanation
Indices: 2713483--2713556 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
2713473 TCATTTCAAT
*
2713483 TATTTTTATTTTA-TTTTATCATTATATCATTTTTTATA
1 TATTTTTATTTTATTTTTAT-ATTATATCATATTTTATA
*
2713521 TATTTTTATTTTATTTTTATATTATATTATATTTTA
1 TATTTTTATTTTATTTTTATATTATATCATATTTTA
2713557 ACTAATTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 27 0.82
39 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (38 bp):
TATTTTTATTTTATTTTTATATTATATCATATTTTATA
Found at i:2713538 original size:23 final size:23
Alignment explanation
Indices: 2713481--2713556 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
2713471 ACTCATTTCA
*
2713481 ATTAT-TTTTA-TTTTATTTTAT
1 ATTATATTTTATTTTTATATTAT
**
2713502 CATTATATCAT-TTTTTATA-TAT
1 -ATTATATTTTATTTTTATATTAT
*
2713524 -TTTTATTTTATTTTTATATTAT
1 ATTATATTTTATTTTTATATTAT
2713546 ATTATATTTTA
1 ATTATATTTTA
2713557 ACTAATTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 6 0.14
21 8 0.19
22 11 0.26
23 17 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTATATTTTATTTTTATATTAT
Found at i:2713755 original size:16 final size:15
Alignment explanation
Indices: 2713713--2713758 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2713703 ACATAAATTC
2713713 AATACTTAATTTTTT
1 AATACTTAATTTTTT
**
2713728 AATGTTTAATTTTTT
1 AATACTTAATTTTTT
*
2713743 AAATACTTGATTTTTT
1 -AATACTTAATTTTTT
2713759 TTCAGATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (15 bp):
AATACTTAATTTTTT
Found at i:2715248 original size:22 final size:21
Alignment explanation
Indices: 2715209--2715249 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2715199 CAATTCTCCT
* *
2715209 TTTATTTTAATGATTTTAAAA
1 TTTATTTTAATCAATTTAAAA
2715230 TTTATTTATAATCAATTTAA
1 TTTATTT-TAATCAATTTAA
2715250 TATCGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTATTTTAATCAATTTAAAA
Found at i:2716592 original size:17 final size:17
Alignment explanation
Indices: 2716572--2716625 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2716562 CATATTTACA
2716572 AAAATATATTGTTAAAT
1 AAAATATATTGTTAAAT
* * *
2716589 AAAA-ACTAAT-CTAAAA
1 AAAATA-TATTGTTAAAT
2716605 AAAATATATTGTTAAAT
1 AAAATATATTGTTAAAT
2716622 AAAA
1 AAAA
2716626 ACTAATCTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAATATATTGTTAAAT
Found at i:2716608 original size:16 final size:16
Alignment explanation
Indices: 2716584--2716641 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2716574 AATATATTGT
*
2716584 TAAATAAAAACTAATC
1 TAAAAAAAAACTAATC
* *
2716600 TAAAAAAAATA-TATTGT
1 TAAAAAAAA-ACTAAT-C
*
2716617 TAAATAAAAACTAATC
1 TAAAAAAAAACTAATC
2716633 TAAAAAAAA
1 TAAAAAAAA
2716642 TATATGAGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAAAAAAACTAATC
Found at i:2716610 original size:33 final size:33
Alignment explanation
Indices: 2716571--2716646 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
2716561 TCATATTTAC
2716571 AAAAATATATTGTTAAATAAAAACTAATCTAAA
1 AAAAATATATTGTTAAATAAAAACTAATCTAAA
2716604 AAAAATATATTGTTAAATAAAAACTAATCTAAA
1 AAAAATATATTGTTAAATAAAAACTAATCTAAA
2716637 AAAAATATAT
1 AAAAATATAT
2716647 GAGTGGGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (33 bp):
AAAAATATATTGTTAAATAAAAACTAATCTAAA
Found at i:2719621 original size:23 final size:23
Alignment explanation
Indices: 2719578--2719621 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2719568 ACAATTCAAT
*
2719578 ATATTTTCAAGATAAATTCATGC
1 ATATTTTCAAGATAAAGTCATGC
*
2719601 ATATTTAT-AAGATAACGTCAT
1 ATATTT-TCAAGATAAAGTCAT
2719622 CACATACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATTTTCAAGATAAAGTCATGC
Found at i:2725377 original size:21 final size:20
Alignment explanation
Indices: 2725338--2725377 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2725328 TAAATATTAA
2725338 TTTAAAAATATTATAAATAT
1 TTTAAAAATATTATAAATAT
* *
2725358 TTTACAAATAATTTTAAATA
1 TTTAAAAAT-ATTATAAATA
2725378 ATATGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAATATTATAAATAT
Found at i:2727688 original size:20 final size:20
Alignment explanation
Indices: 2727663--2727700 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2727653 GTTGGCAAAA
**
2727663 CAGTCACTCTAATTTTAATT
1 CAGTCACTAAAATTTTAATT
2727683 CAGTCACTAAAATTTTAA
1 CAGTCACTAAAATTTTAA
2727701 AAATATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (20 bp):
CAGTCACTAAAATTTTAATT
Found at i:2729263 original size:174 final size:173
Alignment explanation
Indices: 2728898--2729325 Score: 615
Period size: 174 Copynumber: 2.5 Consensus size: 173
2728888 TTCGATAATG
* * * *
2728898 ATGTTAATGGGTGATTGATTTCTTACTTTTCGATAACGTTGGTGACTAATTTGTTATTTTTTGAA
1 ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAACGTTAGTGACTAATTTGTTATTTTTTGAA
* * * *
2728963 AGTTGAGTGACTGAATTTAAAATTTGCCTCGTCCGACATGCAAGCTAATTAGCCACGTCAGCTAC
66 AGTTGAGTGACTGAATATAAAATTTGCCTCATCCAACATGCAAGCTAACTAGCCACGTCAGCTAC
* *
2729028 TTAATTGGCCACGTCACCTGTCCCGTTAAGCCTGTAACGAAAA
131 TTAATTAGCCACGTCACCTGTCCCGCTAAGCCTGTAACGAAAA
*
2729071 ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAACGTTAGTGACTAATTTGTTATTTTTTAAA
1 ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAACGTTAGTGACTAATTTGTTATTTTTTGAA
* * * *
2729136 AATTGAGTGAATGAA-ATAAAACTTTGCCTCATCCAACATGGCAAGTTAACTGGCCACGTCAGCT
66 AGTTGAGTGACTGAATATAAAA-TTTGCCTCATCCAACAT-GCAAGCTAACTAGCCACGTCAGCT
* * * * * *
2729200 AGTTAATTAGCCATGTCACCTGTCCTGCTAGGCCTGTAATGGAAA
129 ACTTAATTAGCCACGTCACCTGTCCCGCTAAGCCTGTAACGAAAA
* * *
2729245 ATGTTAATAGGTGACTGATTTGTCACTTTTCTATAACGTTAGTGACTGATTTGTTATTTTTTGAA
1 ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAACGTTAGTGACTAATTTGTTATTTTTTGAA
2729310 AGTTGAGTGACTGAAT
66 AGTTGAGTGACTGAAT
2729326 TGGAATCAGA
Statistics
Matches: 225, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
172 5 0.02
173 88 0.39
174 132 0.59
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (173 bp):
ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAACGTTAGTGACTAATTTGTTATTTTTTGAA
AGTTGAGTGACTGAATATAAAATTTGCCTCATCCAACATGCAAGCTAACTAGCCACGTCAGCTAC
TTAATTAGCCACGTCACCTGTCCCGCTAAGCCTGTAACGAAAA
Found at i:2729321 original size:30 final size:31
Alignment explanation
Indices: 2729255--2729323 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2729245 ATGTTAATAG
*
2729255 GTGACTGATTTGTCACTTTTCTATAACGTTA
1 GTGACTGATTTGTCACTTTTCTATAAAGTTA
*
2729286 GTGACTGATTTGTTA-TTTT-T-TGAAAGTTGA
1 GTGACTGATTTGTCACTTTTCTAT-AAAGTT-A
2729316 GTGACTGA
1 GTGACTGA
2729324 ATTGGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
30 13 0.38
31 14 0.41
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTCTATAAAGTTA
Found at i:2734498 original size:26 final size:26
Alignment explanation
Indices: 2734462--2734514 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2734452 TATAAGTTAA
2734462 AATAACGTAAAGAAGTCATATTTTTC
1 AATAACGTAAAGAAGTCATATTTTTC
2734488 AATAACGTAAAGAAGTCATATTTTTC
1 AATAACGTAAAGAAGTCATATTTTTC
2734514 A
1 A
2734515 TTCATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (26 bp):
AATAACGTAAAGAAGTCATATTTTTC
Found at i:2736573 original size:25 final size:25
Alignment explanation
Indices: 2736539--2736592 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
2736529 TATAAGTGTA
*
2736539 GAATGTCTTGTTAAAAGGTTGGATT
1 GAATGCCTTGTTAAAAGGTTGGATT
2736564 GAATGCCTTGTTAAAAGGTTGGATT
1 GAATGCCTTGTTAAAAGGTTGGATT
2736589 GAAT
1 GAAT
2736593 ACTTGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.37
Consensus pattern (25 bp):
GAATGCCTTGTTAAAAGGTTGGATT
Found at i:2760777 original size:7 final size:7
Alignment explanation
Indices: 2760765--2760789 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2760755 TGTTCCATTC
2760765 TCATTGA
1 TCATTGA
2760772 TCATTGA
1 TCATTGA
2760779 TCATTGA
1 TCATTGA
2760786 TCAT
1 TCAT
2760790 GTATGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (7 bp):
TCATTGA
Found at i:2761174 original size:31 final size:31
Alignment explanation
Indices: 2761133--2761202 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
2761123 CAAGTTAGTC
** *
2761133 CCTAAACTTGGCAATTTGTCCCATATTGGGA
1 CCTAAACTTGGCAATTACTCCCACATTGGGA
* *
2761164 CCTGAACTTGGCAATTACTCCCACATTGGGG
1 CCTAAACTTGGCAATTACTCCCACATTGGGA
2761195 CCTAAACT
1 CCTAAACT
2761203 CGAGGGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (31 bp):
CCTAAACTTGGCAATTACTCCCACATTGGGA
Found at i:2763076 original size:64 final size:64
Alignment explanation
Indices: 2763008--2763201 Score: 237
Period size: 64 Copynumber: 3.1 Consensus size: 64
2762998 CACCAGTATT
*
2763008 AAAAAAATTCAAATTTTTTTTGTGCTGGCTTGTCAATGGCCGGCACCAGAATACGAGTTTTTAA
1 AAAAAAATTCAAATTTTTTTTGTGCTAGCTTGTCAATGGCCGGCACCAGAATACGAGTTTTTAA
** * *
2763072 AAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAG--T---A---TTAAA
1 AAAAAAATTCAAATTTTTTTTGTGCTAGCTTGTCAATGGCCGGCACCAGAATACGAGTTTTTAA
*
2763128 AAAAAAATTCAAA-TTTTTTTATGCTAG-TCTGTCAATGGCCGGCACCAGAATACGAGTTTTTTT
1 AAAAAAATTCAAATTTTTTTTGTGCTAGCT-TGTCAATGGCCGGCACCAGAATACGAG--TTTTT
2763191 AA
63 AA
2763193 AAAAAAATT
1 AAAAAAATT
2763202 TATGCTGGCC
Statistics
Matches: 109, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
55 30 0.28
56 17 0.16
57 1 0.01
59 1 0.01
60 1 0.01
62 1 0.01
64 45 0.41
65 13 0.12
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (64 bp):
AAAAAAATTCAAATTTTTTTTGTGCTAGCTTGTCAATGGCCGGCACCAGAATACGAGTTTTTAA
Done.