Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 10 of 24
Found at i:1337690 original size:43 final size:40
Alignment explanation
Indices: 1337634--1337715 Score: 94
Period size: 43 Copynumber: 1.9 Consensus size: 40
1337624 TTGAAAACTC
*
1337634 ATTTTATTATTTAAGA-TAATAAAAAAATATTTTTATATTAAT
1 ATTTTATAATTTAA-ATTAA-AAAAAAATATTTTT-TATTAAT
*
1337676 ATTTATATAATTTAAATTTAAATAAAAATATTTTTTATTA
1 ATTT-TATAATTTAAA-TTAAAAAAAAATATTTTTTATTA
1337716 TGTAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 10 0.29
43 22 0.63
44 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (40 bp):
ATTTTATAATTTAAATTAAAAAAAAATATTTTTTATTAAT
Found at i:1339500 original size:75 final size:75
Alignment explanation
Indices: 1339369--1339508 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 75
1339359 AAAAAACCCT
* * *
1339369 TTATTTAGATTTTATATTTGTTATACACATTTTATAATTATTTATTGTGGTAACTTTAGATCTTT
1 TTATTTAGATTTTATATTTATCATACACAATTTATAATTATTTATTGTGGTAACTTTAGATCTTT
1339434 GTATTATAAA
66 GTATTATAAA
* * * *
1339444 TTATTTATATTTTATATTTATCATACTCAATTTATAATTATTTATTGAT-GTGACTTTTGATCTT
1 TTATTTAGATTTTATATTTATCATACACAATTTATAATTATTTATTG-TGGTAACTTTAGATCTT
1339508 T
65 T
1339509 ATCATTCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 56 0.98
76 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (75 bp):
TTATTTAGATTTTATATTTATCATACACAATTTATAATTATTTATTGTGGTAACTTTAGATCTTT
GTATTATAAA
Found at i:1339683 original size:31 final size:33
Alignment explanation
Indices: 1339648--1339728 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
1339638 TATAACAGAT
1339648 AAAAAATAAATATTAATTT-T-TTTATCTATAC
1 AAAAAATAAATATTAATTTATCTTTATCTATAC
* *
1339679 AAAAAATAAAAAATTATTTTATCTTTATCTATAC
1 AAAAAAT-AAATATTAATTTATCTTTATCTATAC
* *
1339713 AAGAGATAAATGATTA
1 AAAAAATAAAT-ATTA
1339729 GCTGCAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 7 0.17
32 10 0.24
33 4 0.10
34 20 0.49
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (33 bp):
AAAAAATAAATATTAATTTATCTTTATCTATAC
Found at i:1340145 original size:2 final size:2
Alignment explanation
Indices: 1340140--1340176 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1340130 TATAATTTGA
1340140 AT AT 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 AT AT A
1340177 AGTAGGTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1340276 original size:15 final size:16
Alignment explanation
Indices: 1340256--1340290 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1340246 ATAGTAAATG
1340256 ATAGATTAAA-TTTAA
1 ATAGATTAAACTTTAA
1340271 ATAGATTAAACTTTTAA
1 ATAGATTAAAC-TTTAA
1340288 ATA
1 ATA
1340291 TGTTATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (16 bp):
ATAGATTAAACTTTAA
Found at i:1340621 original size:27 final size:27
Alignment explanation
Indices: 1340582--1340637 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1340572 ACAAATATTT
1340582 TTTTTTATGAAAATACTGGATTTCTAC
1 TTTTTTATGAAAATACTGGATTTCTAC
* *
1340609 TTTTTTATTAAAATACTGTATTTCTAC
1 TTTTTTATGAAAATACTGGATTTCTAC
1340636 TT
1 TT
1340638 CTAGTAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.54
Consensus pattern (27 bp):
TTTTTTATGAAAATACTGGATTTCTAC
Found at i:1342732 original size:21 final size:19
Alignment explanation
Indices: 1342707--1342761 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 19
1342697 TAAAATTTAT
1342707 TATATTTTTATTTTATAATG
1 TATA-TTTTATTTTATAATG
1342727 ATATATTTTA-TTTAT-ATG
1 -TATATTTTATTTTATAATG
*
1342745 T-TATTTTATTATATAAT
1 TATATTTTATTTTATAAT
1342762 AATAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.23
17 5 0.16
18 5 0.16
19 5 0.16
20 5 0.16
21 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TATATTTTATTTTATAATG
Found at i:1342756 original size:15 final size:15
Alignment explanation
Indices: 1342702--1342758 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
1342692 ATAATTAAAA
*
1342702 TTTATTATATTTTTAT
1 TTTATTATA-TGTTAT
1342718 TTTA-TA-ATGATATAT
1 TTTATTATATG-T-TAT
1342733 TTTATTTATATGTTAT
1 TTTA-TTATATGTTAT
1342749 TTTATTATAT
1 TTTATTATAT
1342759 AATAATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 15 0.43
16 11 0.31
17 3 0.09
18 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTATTATATGTTAT
Found at i:1342979 original size:13 final size:13
Alignment explanation
Indices: 1342961--1343029 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 13
1342951 ATTTTAAAGG
1342961 TAATATAAAAATA
1 TAATATAAAAATA
1342974 TAATATTAAATAATA
1 TAATA-TAAA-AATA
*
1342989 T-AT-T--TAATA
1 TAATATAAAAATA
1342998 -AATATAAAAAT-
1 TAATATAAAAATA
1343009 T-ATATAATAAATA
1 TAATATAA-AAATA
1343022 TAATATAA
1 TAATATAA
1343030 TATTTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 19
0.68 0.03 0.29
Matches are distributed among these distances:
9 6 0.14
10 1 0.02
11 6 0.14
12 8 0.18
13 6 0.14
14 12 0.27
15 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATATAAAAATA
Found at i:1342997 original size:47 final size:49
Alignment explanation
Indices: 1342933--1343027 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 49
1342923 ACTCTATTAA
* * **
1342933 AAATAGATATATATAATAATTTTAAAGGTAATATAA-AAATATAATATT
1 AAATAGATATATATAATAAATATAAAAATAATATAATAAATATAATATT
* *
1342981 AAATA-ATATATTTAATAAATATAAAAATTATATAATAAATATAATAT
1 AAATAGATATATATAATAAATATAAAAATAATATAATAAATATAATAT
1343028 AATATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 24 0.60
48 16 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (49 bp):
AAATAGATATATATAATAAATATAAAAATAATATAATAAATATAATATT
Found at i:1343018 original size:20 final size:22
Alignment explanation
Indices: 1342933--1343032 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 22
1342923 ACTCTATTAA
* *
1342933 AAATAGATATATATAATAATTTT
1 AAATA-ATATATATAATAAATAT
*
1342956 AAAGGTAATATA-AAAATATAATATT
1 AAA--TAATATATATAATA-AATA-T
*
1342981 AAATAATATATTTAATAAATAT
1 AAATAATATATATAATAAATAT
1343003 AAA-AAT-TATATAATAAATAT
1 AAATAATATATATAATAAATAT
1343023 AATATAATAT
1 AA-ATAATAT
1343033 TTTTAAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
20 15 0.24
21 4 0.06
22 7 0.11
23 20 0.32
24 11 0.17
25 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
AAATAATATATATAATAAATAT
Found at i:1343022 original size:9 final size:9
Alignment explanation
Indices: 1342962--1343063 Score: 57
Period size: 9 Copynumber: 10.9 Consensus size: 9
1342952 TTTTAAAGGT
1342962 AATATAA-A
1 AATATAATA
1342970 AATATAATA
1 AATATAATA
1342979 TTAA-ATAATA
1 --AATATAATA
* *
1342989 TATTTAATA
1 AATATAATA
*
1342998 AATATAAAA
1 AATATAATA
1343007 ATTATATAATA
1 A--ATATAATA
1343018 AATATAATA
1 AATATAATA
**
1343027 TAATATTTTTA
1 -AATA-TAATA
* *
1343038 AATTTAATT
1 AATATAATA
1343047 AATATAATTA
1 AATATAA-TA
1343057 AA-ATAAT
1 AATATAAT
1343064 TAATTTCTTA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
8 9 0.13
9 33 0.46
10 16 0.23
11 13 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATAATA
Found at i:1343127 original size:19 final size:17
Alignment explanation
Indices: 1343080--1343129 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
1343070 CTTATATATT
1343080 TTTTATTTATATTTAAAA
1 TTTTA-TTATATTTAAAA
**
1343098 TTTTAAAATATTTAATAA
1 TTTTATTATATTTAA-AA
1343116 GTTTTATTATATTT
1 -TTTTATTATATTT
1343130 TTATTCACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.31
18 7 0.27
19 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATTATATTTAAAA
Found at i:1343341 original size:3 final size:3
Alignment explanation
Indices: 1343333--1343361 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1343323 AAACAGCCAT
1343333 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1343362 CCAACCAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1346349 original size:2 final size:2
Alignment explanation
Indices: 1346342--1346372 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1346332 TCTCTGTAAC
1346342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1346373 GTGGTGGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1346563 original size:30 final size:30
Alignment explanation
Indices: 1346529--1346667 Score: 99
Period size: 30 Copynumber: 4.5 Consensus size: 30
1346519 TAAACTCGAA
*
1346529 TATATTTTTA-TATTTTTTACATATTATAAT
1 TATATTTATATTATTTTTTA-ATATTATAAT
**
1346559 TATATTTA-ATATAAATTTTAATA-TATTAA-
1 TATATTTATAT-TATTTTTTAATATTA-TAAT
*
1346588 TATAATTATATTATTTTTATATTATATTATATAT
1 TATATTTATATTATTTTT-TA--ATATTATA-AT
* *
1346622 TTTATTT-TGATTATTTTTTAATATTATATT
1 TATATTTAT-ATTATTTTTTAATATTATAAT
1346652 TATATTATATAATTAT
1 TATATT-TAT-ATTAT
1346668 ATTATATTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
29 15 0.18
30 23 0.27
31 16 0.19
32 11 0.13
33 6 0.07
34 14 0.16
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
TATATTTATATTATTTTTTAATATTATAAT
Found at i:1346600 original size:5 final size:5
Alignment explanation
Indices: 1346549--1346675 Score: 61
Period size: 5 Copynumber: 25.0 Consensus size: 5
1346539 TATTTTTTAC
* * *
1346549 ATATT ATAATT ATATT -TAATAT AAATT TTAAT ATATT A-A-T ATAATT
1 ATATT AT-ATT ATATT AT-AT-T ATATT ATATT ATATT ATATT AT-ATT
* * * *
1346595 ATATT ATTTTT ATATT ATATT ATA-T ATTTT ATTTT GATTATT -TTTT
1 ATATT A-TATT ATATT ATATT ATATT ATATT ATATT -A-TATT ATATT
1346641 AATATT ATATTT ATATT ATA-T A-ATT ATATT ATATT
1 -ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT
1346676 TAAATTTATC
Statistics
Matches: 94, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
3 3 0.03
4 12 0.13
5 52 0.55
6 24 0.26
7 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:1346609 original size:19 final size:19
Alignment explanation
Indices: 1346542--1346677 Score: 58
Period size: 19 Copynumber: 7.3 Consensus size: 19
1346532 ATTTTTATAT
*
1346542 TTTTTACAT-ATTATAATTA
1 TTTTTATATAATTAT-ATTA
* * *
1346561 TATTTAATATAAATTTTAATA
1 T-TTTTATAT-AATTATATTA
* *
1346582 TATTAATATAATTATATTA
1 TTTTTATATAATTATATTA
1346601 TTTTTATATTATATTATA-TA
1 TTTTTATA-TA-ATTATATTA
*
1346621 -TTTTAT-T--TT-GATTA
1 TTTTTATATAATTATATTA
1346635 TTTTT-TA-ATATTATATT-
1 TTTTTATATA-ATTATATTA
*
1346652 TATATTATATAATTATATTA
1 T-TTTTATATAATTATATTA
*
1346672 TATTTA
1 TTTTTA
1346678 AATTTATCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
13 1 0.01
14 5 0.06
15 4 0.05
17 4 0.05
18 6 0.07
19 34 0.39
20 19 0.22
21 10 0.11
22 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTTATATAATTATATTA
Found at i:1346677 original size:24 final size:24
Alignment explanation
Indices: 1346580--1346677 Score: 103
Period size: 24 Copynumber: 4.1 Consensus size: 24
1346570 TAAATTTTAA
*
1346580 TATATTAATATAATTATATTATTTT
1 TATATT-ATATAATTATATTATATT
* *
1346605 TATATTATATTA-TATATTTTATT
1 TATATTATATAATTATATTATATT
**
1346628 T-TGATTAT-TTTTTAATATTATATT
1 TAT-ATTATATAATT-ATATTATATT
1346652 TATATTATATAATTATATTATATT
1 TATATTATATAATTATATTATATT
1346676 TA
1 TA
1346678 AATTTATCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.05
23 16 0.26
24 32 0.52
25 10 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (24 bp):
TATATTATATAATTATATTATATT
Found at i:1349164 original size:55 final size:56
Alignment explanation
Indices: 1349051--1349165 Score: 126
Period size: 55 Copynumber: 2.1 Consensus size: 56
1349041 CAAATGAGTT
* * * ** * *
1349051 AAAAAAGGAAAAAGGAAAGTTAACTTTTCAGGGTTGGAGCAATCCCTAAAGTAAAA
1 AAAAAAAGAAAAAGAAAAGTTAACTTTTCAAGGTTAAAACAATCCCCAAAGTAAAA
* *
1349107 AAAAAAAGAAAAA-AAAAGTTAACTTTTCAAGGTTAAAACAA-CCTCCAAGGTAGAA
1 AAAAAAAGAAAAAGAAAAGTTAACTTTTCAAGGTTAAAACAATCC-CCAAAGTAAAA
1349162 AAAA
1 AAAA
1349166 GAATATTTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
54 2 0.04
55 35 0.71
56 12 0.24
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (56 bp):
AAAAAAAGAAAAAGAAAAGTTAACTTTTCAAGGTTAAAACAATCCCCAAAGTAAAA
Found at i:1349313 original size:15 final size:15
Alignment explanation
Indices: 1349294--1349333 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1349284 TATTCCCCGA
1349294 CAAGATGATTC-TTGG
1 CAAGATG-TTCTTTGG
*
1349309 TAAGATGTTCTTTGG
1 CAAGATGTTCTTTGG
1349324 CAAGATGTTC
1 CAAGATGTTC
1349334 CTTTCGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (15 bp):
CAAGATGTTCTTTGG
Found at i:1349610 original size:22 final size:22
Alignment explanation
Indices: 1349582--1349626 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1349572 AAATATCCCT
1349582 TTGACTAAATATTTTGGCGAGA
1 TTGACTAAATATTTTGGCGAGA
* *
1349604 TTGACTAGATCTTTTGGCGAGA
1 TTGACTAAATATTTTGGCGAGA
1349626 T
1 T
1349627 CCCTTTCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (22 bp):
TTGACTAAATATTTTGGCGAGA
Found at i:1350195 original size:44 final size:44
Alignment explanation
Indices: 1350093--1350212 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 44
1350083 AGCATTTCGA
* * * * *
1350093 ATCTTCAAGCATCATCTAGCTAAAGGCCTCTTCAAGCTTAACAC
1 ATCTTCAAGCATCATCTAGCCAAAAGCCTCTTCAAACTCAAAAC
* *
1350137 ATGTTTAAGCATCATCTAGCCAAAAGCCTCTTCAAACTCAAAAC
1 ATCTTCAAGCATCATCTAGCCAAAAGCCTCTTCAAACTCAAAAC
* * *
1350181 ATCTTCAGGAATCAT-TCAGCCAAAAGGCTCTT
1 ATCTTCAAGCATCATCT-AGCCAAAAGCCTCTT
1350213 TAGGAATCAT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 62 0.98
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.27
Consensus pattern (44 bp):
ATCTTCAAGCATCATCTAGCCAAAAGCCTCTTCAAACTCAAAAC
Found at i:1350241 original size:27 final size:27
Alignment explanation
Indices: 1350182--1350241 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1350172 ACTCAAAACA
* *
1350182 TCTTCAGGAATCATTCAGCCAAAAGGC
1 TCTTTAGGAATCATTCAGCCAAAAGCC
* * *
1350209 TCTTTAGGAATCATTTAGTCACAAGCC
1 TCTTTAGGAATCATTCAGCCAAAAGCC
*
1350236 TTTTTA
1 TCTTTA
1350242 AGCTTAATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (27 bp):
TCTTTAGGAATCATTCAGCCAAAAGCC
Found at i:1350470 original size:71 final size:71
Alignment explanation
Indices: 1350303--1350491 Score: 170
Period size: 71 Copynumber: 2.6 Consensus size: 71
1350293 GTTAAAAGAC
* * * * * * * *
1350303 TTTTCAAGCATCATCTAGCTAGAAAAGCTCT-TTAGGCATTAGCTAAC-CAAAGGCCTCTTTAGG
1 TTTTCAAGCATCATATAGCTA-AAAGGCT-TGTTAGGCATCATCTAGCTGAAA-GTCTTTTTAGG
*
1350366 CTCAACATA
63 CTCAACACA
** * *
1350375 TTTTCAAGCATTTTCTAGCTAAAAGGCTCT-TTAGGTATCATCTAGCTGAAAGTCTTTTTAGGCT
1 TTTTCAAGCATCATATAGCTAAAAGGCT-TGTTAGGCATCATCTAGCTGAAAGTCTTTTTAGGCT
*
1350439 TAACACA
65 CAACACA
*
1350446 TTTTCAAGCATCATATAG-TCAAAAGGCTTGTTATGCATCATCTAGC
1 TTTTCAAGCATCATATAGCT-AAAAGGCTTGTTAGGCATCATCTAGC
1350492 CAAAAACCTC
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
70 2 0.02
71 73 0.75
72 22 0.23
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (71 bp):
TTTTCAAGCATCATATAGCTAAAAGGCTTGTTAGGCATCATCTAGCTGAAAGTCTTTTTAGGCTC
AACACA
Found at i:1350764 original size:51 final size:51
Alignment explanation
Indices: 1350721--1350846 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
1350711 CGAGGCTCGT
* *
1350721 GTATTGTTTTGCCTTTTCAAGCTTTAACGCATCTCG-TCCCACGAGGCTTAA
1 GTATTGCTTTGCCTTTTCAAGCTTTAACCCATCTCGCT-CCACGAGGCTTAA
* * * * *
1350772 GTATTACTTTACCTTTTCAAGCCTTAACCCATCTCGCTCTACAAGGCTTAA
1 GTATTGCTTTGCCTTTTCAAGCTTTAACCCATCTCGCTCCACGAGGCTTAA
1350823 GTATTGCTTTGCCTTTTCAAGCTT
1 GTATTGCTTTGCCTTTTCAAGCTT
1350847 AGAGACTTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 63 0.98
52 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (51 bp):
GTATTGCTTTGCCTTTTCAAGCTTTAACCCATCTCGCTCCACGAGGCTTAA
Found at i:1354820 original size:17 final size:18
Alignment explanation
Indices: 1354800--1354842 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1354790 TTATTTTTAA
*
1354800 TATTTTTTAA-AAATATT
1 TATTTATTAATAAATATT
1354817 TA-TTATTAATAAATATT
1 TATTTATTAATAAATATT
*
1354834 AATTTATTA
1 TATTTATTA
1354843 GTAACAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTATTAATAAATATT
Found at i:1360395 original size:13 final size:13
Alignment explanation
Indices: 1360367--1360421 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1360357 AAAAGAAAAA
**
1360367 AAATTTAAATAAT
1 AAATTTAAATTTT
1360380 AAATTTAAATTTT
1 AAATTTAAATTTT
*
1360393 AAATTT-GA-TTT
1 AAATTTAAATTTT
1360404 AAA--TAAATTTT
1 AAATTTAAATTTT
1360415 AAATTTA
1 AAATTTA
1360422 CTAATCCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 1 0.03
10 1 0.03
11 12 0.35
12 1 0.03
13 19 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:1360572 original size:6 final size:6
Alignment explanation
Indices: 1360547--1360616 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
1360537 AAGAGAAAAA
* *
1360547 AAATTT AAAATTT AAGTTT AAATTT ATATTT AAATTT -AATTT -AA-TT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
1360593 AAATTTT AAATTT ATTATTT AAAT
1 AAA-TTT AAATTT A-AATTT AAAT
1360617 ATATTAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 26 0.49
7 16 0.30
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:1360623 original size:22 final size:24
Alignment explanation
Indices: 1360554--1360624 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 24
1360544 AAAAAATTTA
*
1360554 AAATTTAAGTTTAAATT-TATAT-TT
1 AAATTTAA-TTT-AATTAAATATATT
1360578 AAATTTAATTTAATTAAAT-T-TT
1 AAATTTAATTTAATTAAATATATT
*
1360600 AAATTT-A-TTATTTAAATATATT
1 AAATTTAATTTAATTAAATATATT
1360622 AAA
1 AAA
1360625 ATATTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.21
21 2 0.05
22 18 0.43
23 5 0.12
24 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
AAATTTAATTTAATTAAATATATT
Found at i:1361536 original size:12 final size:13
Alignment explanation
Indices: 1361519--1361550 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1361509 ACTATCAGTA
1361519 ATAATTTAA-AAT
1 ATAATTTAATAAT
1361531 ATAATTTAATAAT
1 ATAATTTAATAAT
1361544 A-AATTTA
1 ATAATTTA
1361551 TGATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTAATAAT
Found at i:1369692 original size:16 final size:17
Alignment explanation
Indices: 1369673--1369726 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
1369663 AAAAAAAGTC
*
1369673 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCAAAA
1369689 AAAATG-AAAAG-AAAA
1 AAAATGCAAAAGCAAAA
1369704 AAAAGTGCAAAAGCAAAA
1 AAAA-TGCAAAAGCAAAA
1369722 TAAAA
1 -AAAA
1369727 AAAGGGAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.22
16 11 0.34
17 6 0.19
18 4 0.12
19 4 0.12
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAATGCAAAAGCAAAA
Found at i:1369743 original size:39 final size:38
Alignment explanation
Indices: 1369663--1369743 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
1369653 TCAAAATGAC
* *
1369663 AAAAAAAGTCAAAAGCAAAAGCACAAAAAATGAAAAGA
1 AAAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAACA
*
1369701 AAAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGGAACAACA
1 AAAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GGAA-AACA
1369740 AAAA
1 AAAA
1369744 TAAAAAACGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 6 0.16
38 13 0.35
39 18 0.49
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (38 bp):
AAAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAACA
Found at i:1371775 original size:51 final size:52
Alignment explanation
Indices: 1371660--1371779 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 52
1371650 GAGATAATAA
*
1371660 CGGGGTTAGAGTATCCCCGATTATGGAAAAACAGTGTTCTAAAAAATAAAAT
1 CGGGGTTAGAGTATCCCCGATTATGGAAAAACAGTGTTCTAAAAAATAAAAC
* ** * *
1371712 CGAGGTTAGAGTATCCCCGATTAT-GAAAAATTGATGTT-TTAGAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGGAAAAACAG-TGTTCTAAAAAATAAAAC
*
1371763 CGGGGTTGGAGTATCCC
1 CGGGGTTAGAGTATCCC
1371780 TTCGAAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
51 32 0.54
52 27 0.46
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (52 bp):
CGGGGTTAGAGTATCCCCGATTATGGAAAAACAGTGTTCTAAAAAATAAAAC
Found at i:1371924 original size:79 final size:79
Alignment explanation
Indices: 1371715--1372060 Score: 568
Period size: 79 Copynumber: 4.4 Consensus size: 79
1371705 ATAAAATCGA
*
1371715 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
1371780 TTCGAAAATAACGG
66 CTCGAAAATAACGG
* *
1371794 GGTTGGA-TATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTCGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
1371858 CTCGGAAATAACGG
66 CTCGAAAATAACGG
* *
1371872 GATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
1371937 CTCGGAAATAACGG
66 CTCGAAAATAACGG
* * * *
1371951 GGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAGATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1372016 CTCGAAAATAACGG
66 CTCGAAAATAACGG
*
1372030 GGTTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA
1372061 GAAACTTAAC
Statistics
Matches: 249, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 73 0.29
79 176 0.71
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGAAAATAACGG
Found at i:1373279 original size:26 final size:24
Alignment explanation
Indices: 1373250--1373445 Score: 106
Period size: 27 Copynumber: 7.0 Consensus size: 24
1373240 TTTTCGAATT
1373250 TGCCTTCTTTTTTTTCCAT-CATTCCA
1 TGCCTTCTTTTTTTTCCATGC---CCA
*
1373276 TGCCTTCATTTGTTATTCCATGCCCA
1 TGCCTTC-TTT-TTTTTCCATGCCCA
1373302 TGCCTTCATTTTTTTATTCCATGCCCATTATCCCA
1 TGCCTTC--TTTTTT-TTCCATG--------CCCA
**
1373337 TGCCTTCAATTTTTTATTCCATGCCCA
1 TGCCTTCTTTTTTT---TCCATGCCCA
1373364 TGCCTTCATTTTTTTATTCCATGCCCA
1 TGCCTTC--TTTTTT-TTCCATGCCCA
1373391 TGCCTTCATTTTTTTATTCCATGCCCA
1 TGCCTTC--TTTTTT-TTCCATGCCCA
1373418 TGCCTTCATTTTTTTATTCCATGCCCA
1 TGCCTTC--TTTTTT-TTCCATGCCCA
1373445 T
1 T
1373446 CATCCCGTGT
Statistics
Matches: 144, Mismatches: 7, Indels: 37
0.77 0.04 0.20
Matches are distributed among these distances:
26 19 0.13
27 89 0.62
28 8 0.06
29 5 0.03
30 1 0.01
32 1 0.01
33 4 0.03
35 17 0.12
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.47
Consensus pattern (24 bp):
TGCCTTCTTTTTTTTCCATGCCCA
Found at i:1373337 original size:35 final size:35
Alignment explanation
Indices: 1373298--1373364 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
1373288 TTATTCCATG
*
1373298 CCCATGCCTTCATTTTTTTATTCCATGCCCATTAT
1 CCCATGCCTTCAATTTTTTATTCCATGCCCATTAT
1373333 CCCATGCCTTCAATTTTTTATTCCATGCCCAT
1 CCCATGCCTTCAATTTTTTATTCCATGCCCAT
1373365 GCCTTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.43
Consensus pattern (35 bp):
CCCATGCCTTCAATTTTTTATTCCATGCCCATTAT
Found at i:1373459 original size:27 final size:27
Alignment explanation
Indices: 1373273--1373445 Score: 249
Period size: 27 Copynumber: 6.1 Consensus size: 27
1373263 TTCCATCATT
*
1373273 CCATGCCTTCA-TTTGTTATTCCATGC
1 CCATGCCTTCATTTTTTTATTCCATGC
1373299 CCATGCCTTCATTTTTTTATTCCATGCCCATTATC
1 CCATGCCTTCATTTTTTTATTCCATG--------C
*
1373334 CCATGCCTTCAATTTTTTATTCCATGC
1 CCATGCCTTCATTTTTTTATTCCATGC
1373361 CCATGCCTTCATTTTTTTATTCCATGC
1 CCATGCCTTCATTTTTTTATTCCATGC
1373388 CCATGCCTTCATTTTTTTATTCCATGC
1 CCATGCCTTCATTTTTTTATTCCATGC
1373415 CCATGCCTTCATTTTTTTATTCCATGC
1 CCATGCCTTCATTTTTTTATTCCATGC
1373442 CCAT
1 CCAT
1373446 CATCCCGTGT
Statistics
Matches: 135, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
26 11 0.08
27 98 0.73
35 26 0.19
ACGTcount: A:0.16, C:0.31, G:0.08, T:0.46
Consensus pattern (27 bp):
CCATGCCTTCATTTTTTTATTCCATGC
Found at i:1373459 original size:54 final size:54
Alignment explanation
Indices: 1373347--1373459 Score: 174
Period size: 54 Copynumber: 2.1 Consensus size: 54
1373337 TGCCTTCAAT
* * *
1373347 TTTTTATTCCATGCCCATGCCTTCATTTTTTTATTCCATGCCCATGCCTTCATT
1 TTTTTATTCCATGCCCATGCCTTCATTTTTTTATTCCATGCCCATGCATCCATG
*
1373401 TTTTTATTCCATGCCCATGCCTTCATTTTTTTATTCCATGCCCAT-CATCCCGTG
1 TTTTTATTCCATGCCCATGCCTTCATTTTTTTATTCCATGCCCATGCAT-CCATG
1373455 TTTTT
1 TTTTT
1373460 TTTATTTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.04
54 52 0.96
ACGTcount: A:0.14, C:0.29, G:0.08, T:0.49
Consensus pattern (54 bp):
TTTTTATTCCATGCCCATGCCTTCATTTTTTTATTCCATGCCCATGCATCCATG
Found at i:1374137 original size:28 final size:28
Alignment explanation
Indices: 1374097--1375861 Score: 1026
Period size: 28 Copynumber: 59.9 Consensus size: 28
1374087 TGGCATTTCT
* * *
1374097 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
1374125 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * * * *
1374153 TTTTAAAGTCTACAACTCCGTGGCATCA
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
1374181 TTTT-AAGTCCACAACTCCGTGGTACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
1374208 -TTTAAAGTCCACAACTCCA-TGGCACCC
1 TTTTAAAGCCCACAAGT-CAGTGGCACCC
* * * * *
1374235 TTTTAAAGTCCACAACTCCGTGGCATCA
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
1374263 TTTT-AAGTCCACAACTCCGTGGTACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
1374290 -TTTAAAGTCCACAA-TCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* * *
1374316 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** * *
1374344 TTTT-AAGTTCACAACTTCA-TGGCATCC
1 TTTTAAAGCCCACAA-GTCAGTGGCACCC
* * * *
1374371 TTTTTAAGCCCACAAGTCAGTAGTAGCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
1374399 TTTTAAAGCCCACACAAGTCGGTGGCAACC
1 TTTTAAAG-CC-CACAAGTCAGTGGCACCC
*
1374429 TATTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 T-TTT-AAAG-CC-CACAAGTCAGTGGC-ACCC
* * *
1374462 ATTTCAAAGCCCACAAATCAGTGGTACCC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1374491 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1374519 TTTTAAAGCCCACAAGTCGGTGGCAACCC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
* *
1374548 ATTTCAAAGCCCACAAATCAGTGGCA-CC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
1374576 TTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
*
1374605 TTTTAAAGCCCACAAGTCGGTGGCAACCC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
* *
1374634 ATTTCAAAGCCCACAAGTTAGTGGCACCC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1374663 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1374691 TTTTAAAGCCCACAAATCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
1374719 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1374747 TTTTCAAAGCCCACACGAGTCGGTGGCAACCC
1 TTTT-AAAGCCCACA--AGTCAGTGGC-ACCC
* *
1374779 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
*
1374808 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** ***
1374836 TTCCAAAGCCCACAAGTCAGTGGCGGTC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
* *
1374864 TTTTCAAAGCCCACACGAGTC-GATTGCAACCT
1 TTTT-AAAGCCCACA--AGTCAG-TGGC-ACCC
*
1374896 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * * *
1374925 TTTCAAAGCCCACGAGTCGGTGGCAACAC
1 TTTTAAAGCCCACAAGTCAGTGGC-ACCC
*
1374954 TTTTCAAAGCCCACAAGTCAGTTGCACCC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* * * *
1374983 TTTCAAAGCCCACAAATCGGTGGCAACACA
1 TTTTAAAGCCCACAAGTCAGTGGC-AC-CC
* ** *
1375013 TTTCAAAGCCCACACAAGTTGGTGGCAACC
1 TTTTAAAG-CC-CACAAGTCAGTGGCACCC
* *
1375043 TATTTCAAAGCCCACATAAGTCGGTGGCAACTCA
1 T-TTT-AAAGCCCAC--AAGTCAGTGGC-AC-CC
* *
1375077 TTTTAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTTAAAG-CC-CACAAGTCAGTGGC-AC-CC
* ** * *
1375109 TTTCAAAGCTCACACAAGTTGGTGGCAACT
1 TTTTAAAGC-C-CACAAGTCAGTGGCACCC
** *
1375139 TATTTCAAAGCCCACACAAGTTGGTGGCAATCCA
1 T-TTT-AAAG-CC-CACAAGTCAGTGGC-A-CCC
** * *
1375173 TTTTAAAGCCCACACAAGTTGGTGGCAAGTCA
1 TTTTAAAG-CC-CACAAGTCAGTGGC-A-CCC
* * *
1375205 TTTGAAAGCCCACACAAGTTAGTGGCAACTCA
1 TTTTAAAG-CC-CACAAGTCAGTGGC-AC-CC
* ** *
1375237 TTTCAAAGCCCACACAAGTTGGTGACAACCC
1 TTTTAAAG-CC-CACAAGTCAGTGGC-ACCC
** * * *
1375268 ATTTTAAAGCCCATACAAGTTGGTGGTAAGTCA
1 -TTTTAAAGCCC--ACAAGTCAGTGG-CA-CCC
* *
1375301 TTTGAAAGCCCACACAAGTCAGTGGCAACTCA
1 TTTTAAAG-CC-CACAAGTCAGTGGC-AC-CC
* **
1375333 TTTCAAAGCCCATACAAGTTGGTGGCAACCC
1 TTTTAAAGCCC--ACAAGTCAGTGGC-ACCC
* * * *
1375364 ATTTCAAAGCCCATATAAGTCGGTGGCAACC
1 -TTTTAAAGCCC--ACAAGTCAGTGGCACCC
*
1375395 TATTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 T-TTT-AAAG-CC-CACAAGTCAGTGGC-ACCC
* *
1375428 ATTTCAAAGCCCACAAGTCAGTGG--CGC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1375455 TATTCAAAGCCCACAAGTCAGTGGCACCC
1 T-TTTAAAGCCCACAAGTCAGTGGCACCC
* * * *
1375484 TTTCAAAGCCTACAAATCAGTGGCATCC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** * *
1375512 TTTCCAAGCCCACAAGTTAGTGGCA-AC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** * *
1375539 TTTTCAAAGCCCACGCGTCGGTGGCAACTCA
1 TTTT-AAAGCCCACAAGTCAGTGGC-AC-CC
* ** *
1375570 TTTCAAAGCCCACACAAGTTGGTGGTAACCC
1 TTTTAAAG-CC-CACAAGTCAGTGG-CACCC
* *
1375601 ATTTCAAAGCCCACACAAGTCAGTGGCAACC
1 -TTTTAAAG-CC-CACAAGTCAGTGGCACCC
* * *
1375632 TACTTCAAAGCCCACACAAGT-TGTGGCAACC
1 T--TTTAAAG-CC-CACAAGTCAGTGGCACCC
*
1375663 TATTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 T-TTT-AAAG-CC-CACAAGTCAGTGGC-ACCC
* * *
1375696 ATTTCAAAGCCCACAAGTCGGTGGCA-TC
1 -TTTTAAAGCCCACAAGTCAGTGGCACCC
*
1375724 TTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* *
1375753 TTTTAAAGCCCACAAGTCAGTGGCATCA
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** * *
1375781 TTTCCAAGCCCACAAGTTAGTGGCA-AC
1 TTTTAAAGCCCACAAGTCAGTGGCACCC
** *
1375808 TTTTCAAAGCCCACGCGTCAGTGGCA-AC
1 TTTT-AAAGCCCACAAGTCAGTGGCACCC
* *
1375836 TTTTCAAAGCCCACGAGTTAGTGGCA
1 TTTT-AAAGCCCACAAGTCAGTGGCA
1375862 TCTGAAAGCT
Statistics
Matches: 1455, Mismatches: 191, Indels: 182
0.80 0.10 0.10
Matches are distributed among these distances:
26 18 0.01
27 143 0.10
28 542 0.37
29 80 0.05
30 153 0.11
31 82 0.06
32 394 0.27
33 31 0.02
34 12 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTTAAAGCCCACAAGTCAGTGGCACCC
Found at i:1374233 original size:82 final size:82
Alignment explanation
Indices: 1374064--1374761 Score: 464
Period size: 86 Copynumber: 8.2 Consensus size: 82
1374054 TGTACTATGA
* * * *
1374064 CCTTTTCAAAGTCCACGACTCAGTGGCATTTCTTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
1 CCTTTT-AAAGTCCACAACTCCGTGGCA--TCATTTT-AAGTCCACAACTCCGTGGTACCC-TTT
1374129 AAAGTCCACAACTCCGTGGCAC
61 AAAGTCCACAACTCCGTGGCAC
*
1374151 CCTTTTAAAGTCTACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTACCCTTTAAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTACCCTTTAAAGT
*
1374216 CCACAACTCCATGGCAC
66 CCACAACTCCGTGGCAC
1374233 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTACCCTTTAAAGT
1 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTACCCTTTAAAGT
1374298 CCACAA-TCCGTGGCAC
66 CCACAACTCCGTGGCAC
* * * * * * * *
1374314 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCACAACTTCATGGCATCCTTTTTAAG
1 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTA-CCCTTTAAAG
* * * * * *
1374379 CCCACAAGTCAGTAGTAG
65 TCCACAACTCCGTGGCAC
* * * * * * * * *
1374397 CCTTTTAAAGCCCACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 CCTTTTAAAG-TC-CACAACTCCGTGGC-ATC-ATTT-TAAG-TC-CACAACTCCGTGG-TACCC
* * * *
1374462 ATTTCAAAGCCCACAAATCAGTGGTAC
58 -TTT-AAAGTCCACAACTCCGTGGCAC
* * * * * * * * * *
1374489 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCGGTGGCAACCCATTTCA
1 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTT-AAGTCCACAACTCCGTGG-TACCC-TTT-A
* * *
1374554 AAGCCCACAAATCAGTGGCA-
62 AAGTCCACAACTCCGTGGCAC
* * * * * * * * *
1374574 CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCGGTGGCAACCCATTTC
1 CCTTTT-AAAGTCCACAACTCCGTGGCATCATTTT-AAGTCCACAACTCCGTGG-TACCC-TTT-
* * **
1374639 AAAGCCCACAAGTTAGTGGCAC
61 AAAGTCCACAACTCCGTGGCAC
* * * * * * * * * *
1374661 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAATCAGTGGCACCCTTTCAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCATCATTTT-AAGTCCACAACTCCGTGGTACCCTTT-AAA
* * *
1374726 GCCCACAAGTCAGTGGCAC
64 GTCCACAACTCCGTGGCAC
* *
1374745 TCTTTTCAAAGCCCACA
1 CCTTTT-AAAGTCCACA
1374762 CGAGTCGGTG
Statistics
Matches: 542, Mismatches: 53, Indels: 34
0.86 0.08 0.05
Matches are distributed among these distances:
81 57 0.11
82 108 0.20
83 38 0.07
84 36 0.07
85 31 0.06
86 187 0.35
87 16 0.03
88 9 0.02
89 3 0.01
90 24 0.04
91 6 0.01
92 27 0.05
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (82 bp):
CCTTTTAAAGTCCACAACTCCGTGGCATCATTTTAAGTCCACAACTCCGTGGTACCCTTTAAAGT
CCACAACTCCGTGGCAC
Found at i:1374442 original size:32 final size:32
Alignment explanation
Indices: 1374381--1375849 Score: 1150
Period size: 32 Copynumber: 49.0 Consensus size: 32
1374371 TTTTTAAGCC
* * *
1374381 CACAAGTCAGTAGTAGCCT-TTT-AAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374411 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374443 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374475 CA-AA-TCAGTGG-TACC-CTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374501 CACAAGTCAGTGGCACCCT-TTT-AAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374529 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
1374561 CA-AA-TCAGTGGC-ACCT-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374587 CACAAGTCAGTGGCACCCT-TTT-AAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374615 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374645 CACAAGTTAGTGGC-ACC-CTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374673 CACAAGTCAGTGGCACCCT-TTT-AAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374703 CA-AA-TCAGTGGC-ACC-CTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
1374729 CACAAGTCAGTGGC-ACTCT-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAAC-CTATTTCAAAGCCCA
* *
1374760 CACGAGTCGGTGGCAACCCT-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAA-CCTATTTCAAAGCCCA
* *
1374790 CACAAGTTAGTGGCATCC--TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374818 CACAAGTCAGTGGC-ACC-CTTCCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
***
1374846 CACAAGTCAGTGGCGGTCT-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* * *
1374877 CACGAGTC-GATTGCAACCTTTTTCAAAG-CC-
1 CACAAGTCAG-TGGCAACCTATTTCAAAGCCCA
*
1374907 CACAAGTCAGTGGCATCC--TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1374935 CACGAGTCGGTGGCAACACT-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAAC-CTATTTCAAAGCCCA
* *
1374965 CACAAGTCAGTTGC-ACC-CTTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1374995 CA-AA-TCGGTGGCAACAC-ATTTCAAAGCCCA
1 CACAAGTCAGTGGCAAC-CTATTTCAAAGCCCA
**
1375025 CACAAGTTGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* * *
1375057 CATAAGTCGGTGGCAA-CTCATTTTAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
* *
1375089 CACAAGTCGGTGGCAA-CTCATTTCAAAGCTCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
** *
1375121 CACAAGTTGGTGGCAACTTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
** *
1375153 CACAAGTTGGTGGCAATCC-ATTTTAAAGCCCA
1 CACAAGTCAGTGGCAA-CCTATTTCAAAGCCCA
** * *
1375185 CACAAGTTGGTGGCAA-GTCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
*
1375217 CACAAGTTAGTGGCAA-CTCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
** * * *
1375249 CACAAGTTGGTGACAACCCATTTTAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* ** * * *
1375281 TACAAGTTGGTGGTAA-GTCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
1375313 CACAAGTCAGTGGCAA-CTCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
* ** *
1375345 TACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* * *
1375377 TATAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375409 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375439 CACAAGTCAGTGGC--GCTA-TTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375466 CACAAGTCAGTGGC-ACC-CTTTCAAAGCCTA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375496 CA-AA-TCAGTGGCATCC--TTTCCAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375522 CACAAGTTAGTGGCAA-CT-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375552 CGC--GTCGGTGGCAA-CTCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCT-ATTTCAAAGCCCA
** * *
1375582 CACAAGTTGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375614 CACAAGTCAGTGGCAACCTACTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375646 CACAAGT-TGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375677 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
* *
1375707 CACAAGTCGGTGGC-ATCT-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
1375735 CACAAGTCAGTGGC-ACTCT-TTT-AAAG-CC-
1 CACAAGTCAGTGGCAAC-CTATTTCAAAGCCCA
* *
1375763 CACAAGTCAGTGGC-ATC-ATTTCCAAG-CC-
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375791 CACAAGTTAGTGGCAA-CT-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
*
1375821 CGC--GTCAGTGGCAA-CT-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
1375849 C
1 C
1375850 GAGTTAGTGG
Statistics
Matches: 1226, Mismatches: 135, Indels: 158
0.81 0.09 0.10
Matches are distributed among these distances:
26 8 0.01
27 50 0.04
28 356 0.29
29 80 0.07
30 167 0.14
31 76 0.06
32 483 0.39
33 6 0.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (32 bp):
CACAAGTCAGTGGCAACCTATTTCAAAGCCCA
Found at i:1376645 original size:13 final size:13
Alignment explanation
Indices: 1376627--1376652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1376617 CAATTTTTTG
1376627 TGTATCGATACAT
1 TGTATCGATACAT
1376640 TGTATCGATACAT
1 TGTATCGATACAT
1376653 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1377320 original size:40 final size:39
Alignment explanation
Indices: 1377274--1377357 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
1377264 TTTTATTTCT
*
1377274 CCCTTAAACAAAATAATTTTAACAAATTTATACATTCTCC
1 CCCTT-AACAAAATAATTTTAACAAATTTACACATTCTCC
* ** * *
1377314 CCCTTAATAAGGTAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAACAAAATAATTTTAACAAATTTACACATTCTCC
1377353 CCCTT
1 CCCTT
1377358 TTTGAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 33 0.87
40 5 0.13
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (39 bp):
CCCTTAACAAAATAATTTTAACAAATTTACACATTCTCC
Found at i:1379213 original size:13 final size:13
Alignment explanation
Indices: 1379195--1379233 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1379185 ATAATCCTCC
*
1379195 TGTATCGATACAG
1 TGTATCGATACAA
1379208 TGTATCGATACAA
1 TGTATCGATACAA
1379221 TGTATCGATACAA
1 TGTATCGATACAA
1379234 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1381324 original size:15 final size:15
Alignment explanation
Indices: 1381304--1381334 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1381294 ATTTCGTTTG
*
1381304 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1381319 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1381334 G
1 G
1381335 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1383167 original size:21 final size:21
Alignment explanation
Indices: 1383138--1383182 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1383128 AAGTTTTCAT
*
1383138 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1383158 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1383180 TTT
1 TTT
1383183 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1385422 original size:13 final size:13
Alignment explanation
Indices: 1385404--1385429 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1385394 CAATTTTTTA
1385404 TGTATCGATACAT
1 TGTATCGATACAT
1385417 TGTATCGATACAT
1 TGTATCGATACAT
1385430 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1385846 original size:28 final size:28
Alignment explanation
Indices: 1385812--1386034 Score: 205
Period size: 28 Copynumber: 7.7 Consensus size: 28
1385802 GATCCTAACA
* *
1385812 GCATCCTTCCAAAGCCTACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * *
1385840 GTATCCTTTCAAAGCTCATAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * * *
1385868 GCATCCTTTCAATGTCCACAAGTTAGTT
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* *
1385896 GCACCCTTTCAAAGCCCACAAGTTAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
*
1385924 GC-GCCATTTCAAAGCCCACAAGTCAGTG
1 GCATCC-TTTCAAAGCCCACAAGTCAGTG
* *
1385952 GCACTCTTTTCAAAGCCCACAAGCCAGTG
1 GCA-TCCTTTCAAAGCCCACAAGTCAGTG
* * *
1385981 GTAACTCTTTTCAAAGCCCACACGAGTCGGTG
1 G-CA-TCCTTTCAAAGCCCACA--AGTCAGTG
*
1386013 GCAACTCTTTTCAAAGCCCACA
1 GC-A-TCCTTTCAAAGCCCACA
1386035 CAAGCTAGTG
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.01
28 93 0.57
29 22 0.13
30 20 0.12
32 26 0.16
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (28 bp):
GCATCCTTTCAAAGCCCACAAGTCAGTG
Found at i:1386493 original size:8 final size:8
Alignment explanation
Indices: 1386480--1386508 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1386470 CTTATTTTTA
1386480 AAAAAAAT
1 AAAAAAAT
1386488 -AAAAAAT
1 AAAAAAAT
1386495 AAAAAAAT
1 AAAAAAAT
1386503 AAAAAA
1 AAAAAA
1386509 GGTGAGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1386498 original size:15 final size:15
Alignment explanation
Indices: 1386480--1386508 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1386470 CTTATTTTTA
1386480 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
1386495 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
1386509 GGTGAGTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:1394599 original size:24 final size:24
Alignment explanation
Indices: 1394553--1394602 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1394543 TTTGGTAAGA
*
1394553 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
1394577 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
1394601 TT
1 TT
1394603 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:1397198 original size:24 final size:24
Alignment explanation
Indices: 1397152--1397201 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1397142 TTTGGTAAGA
*
1397152 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
1397176 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
1397200 TT
1 TT
1397202 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:1402725 original size:2 final size:2
Alignment explanation
Indices: 1402718--1402755 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1402708 ATACCTCATA
1402718 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
1402756 CATTTTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1405102 original size:20 final size:20
Alignment explanation
Indices: 1405077--1405119 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1405067 ATATTTAGTA
1405077 ATCAAATTTAAATTGTTTTG
1 ATCAAATTTAAATTGTTTTG
1405097 ATCAAATTTAAATTGTTTTG
1 ATCAAATTTAAATTGTTTTG
1405117 ATC
1 ATC
1405120 CTTACTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
ATCAAATTTAAATTGTTTTG
Found at i:1405321 original size:35 final size:35
Alignment explanation
Indices: 1405275--1405378 Score: 127
Period size: 35 Copynumber: 3.0 Consensus size: 35
1405265 TTTTAACGTC
* *
1405275 TTTTTCATATCATTTATTAGTTTTTGACTTTATTG
1 TTTTTCATATCATTTATTAGTCTTTGACTTTATCG
* * *
1405310 TTTTTTATATCATTTATTAGTGTTTGACTTTGTCG
1 TTTTTCATATCATTTATTAGTCTTTGACTTTATCG
* ** *
1405345 CTTTTCAGGTCATTTATTAGTCTTTGTCTTTATC
1 TTTTTCATATCATTTATTAGTCTTTGACTTTATC
1405379 CCCCTTTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (35 bp):
TTTTTCATATCATTTATTAGTCTTTGACTTTATCG
Found at i:1406223 original size:10 final size:10
Alignment explanation
Indices: 1406208--1406240 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1406198 CTGCTCCATT
1406208 TATATATAAA
1 TATATATAAA
1406218 TATATAT--A
1 TATATATAAA
1406226 TATATATAAA
1 TATATATAAA
1406236 TATAT
1 TATAT
1406241 CCAGCGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATAAA
Found at i:1407689 original size:15 final size:15
Alignment explanation
Indices: 1407669--1407720 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1407659 ATACAATATT
*
1407669 TTTTATTAATTTTTA
1 TTTTATTAATTTTCA
1407684 TTTTATTTAATTTTCA
1 TTTTA-TTAATTTTCA
* *
1407700 TCTTTAATACTTTTCA
1 T-TTTATTAATTTTCA
1407716 TTTTA
1 TTTTA
1407721 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 9 0.28
16 19 0.59
17 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTAATTTTCA
Found at i:1408471 original size:14 final size:13
Alignment explanation
Indices: 1408452--1408486 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
1408442 TTATGAGAGG
1408452 AAAAAATAATAAAT
1 AAAAAATAA-AAAT
1408466 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1408479 AATAAAAT
1 AA-AAAAT
1408487 TGTGATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1412636 original size:25 final size:24
Alignment explanation
Indices: 1412587--1412637 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1412577 TTTATGAATA
*
1412587 AATAAATAAATAATTTAATCGTCT
1 AATAAATAAATAATTTAATCATCT
1412611 AATAAA-AAATAATTACTAATCATCT
1 AATAAATAAATAATT--TAATCATCT
1412636 AA
1 AA
1412638 ATATTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 6 0.25
25 10 0.42
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAATAAATAATTTAATCATCT
Found at i:1415761 original size:19 final size:19
Alignment explanation
Indices: 1415732--1415787 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
1415722 GGATTAAATT
1415732 TAATAATTTATATTTTTATA
1 TAAT-ATTTATATTTTTATA
1415752 TAATATTTATATATTTTTTATA
1 TAATA-TT-TATA-TTTTTATA
*
1415774 TAATA-ATATATTTT
1 TAATATTTATATTTT
1415788 AATTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.12
19 5 0.16
20 6 0.19
21 4 0.12
22 13 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATATTTATATTTTTATA
Found at i:1415772 original size:22 final size:20
Alignment explanation
Indices: 1415732--1415780 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
1415722 GGATTAAATT
1415732 TAATAATTTATATTTTTATA
1 TAATAATTTATATTTTTATA
*
1415752 TAATATTTATATATTTTTTATA
1 TAATAATT-TATA-TTTTTATA
1415774 TAATAAT
1 TAATAAT
1415781 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 4 0.16
22 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATAATTTATATTTTTATA
Found at i:1422261 original size:3 final size:3
Alignment explanation
Indices: 1422250--1422305 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
1422240 GAATTTCTTC
1422250 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1422296 TAA TAA -AA TA
1 TAA TAA TAA TA
1422306 GCAATAATGG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1426063 original size:102 final size:102
Alignment explanation
Indices: 1425953--1426142 Score: 242
Period size: 102 Copynumber: 1.9 Consensus size: 102
1425943 CCTATTTTTC
* *
1425953 TAGATTTTCTATTTCTTTCAGTC-CCTAAAGATTTTTAAAGTCCTTTCCATAACTTTTAATAGTC
1 TAGATTTTCTATATCTTTCAGTCTCC-AAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTC
*
1426017 TTAGTGTTTGT-TTT-TATCTTTCTTCTTTCTATATCTT
65 TCAGTGTTTGTATTTCT-TCTTTCTTCTTTCTATATCTT
** * * * *
1426054 TAGATTTTTCTATATCTTTTTGTCTCCAGAGATTTTTAAAATCCTTTTCATATCTTTTATTAGTC
1 TAGA-TTTTCTATATCTTTCAGTCTCCAAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTC
*
1426119 TCAGTTTTTGTATTTCTTCTTTCT
65 TCAGTGTTTGTATTTCTTCTTTCT
1426143 ATTTCTTTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
101 4 0.05
102 58 0.77
103 12 0.16
104 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (102 bp):
TAGATTTTCTATATCTTTCAGTCTCCAAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTCT
CAGTGTTTGTATTTCTTCTTTCTTCTTTCTATATCTT
Found at i:1429542 original size:2 final size:2
Alignment explanation
Indices: 1429529--1429568 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1429519 ATACCTCGTA
*
1429529 AT AT AT AC 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
1429569 CATTTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1430820 original size:9 final size:10
Alignment explanation
Indices: 1430790--1430831 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1430780 TAACTAAATT
*
1430790 AAATAAATAA
1 AAATATATAA
1430800 AAATTATATAA
1 AAA-TATATAA
1430811 AAAT-TATAA
1 AAATATATAA
1430820 AAATATATAA
1 AAATATATAA
1430830 AA
1 AA
1430832 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.31
10 11 0.38
11 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATATATAA
Found at i:1432433 original size:103 final size:102
Alignment explanation
Indices: 1432245--1432435 Score: 240
Period size: 103 Copynumber: 1.9 Consensus size: 102
1432235 TCTATTTTTC
* * * * *
1432245 TAGATTTTCTATTTGTTTCTGTCTCTAAAGATTTTTAAAGTCCTTTCCATAACTTTTAATAGTGT
1 TAGATTTTCTATATCTTTCTGTCTCCAAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTCT
* *
1432310 TAGTGTTTGTCTTTTATCTTTCTTCTTTCTATATCTT
66 CAGTGTTTGTATTTTATCTTTCTTCTTTCTATATCTT
* * * * *
1432347 TAGATTTTTCTATATCTTTTTGTCTCCAGAGATTTTTAAAATCCTTTTCATATCTTTTATTAGTC
1 TAGA-TTTTCTATATCTTTCTGTCTCCAAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTC
*
1432412 TCAGTTTTTGTATTTCT-TCTTTCT
65 TCAGTGTTTGTATTT-TATCTTTCT
1432436 ATTTCTTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
102 4 0.05
103 69 0.93
104 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (102 bp):
TAGATTTTCTATATCTTTCTGTCTCCAAAGATTTTTAAAATCCTTTCCATAACTTTTAATAGTCT
CAGTGTTTGTATTTTATCTTTCTTCTTTCTATATCTT
Found at i:1434709 original size:18 final size:18
Alignment explanation
Indices: 1434671--1434706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1434661 TAAATTTTTT
*
1434671 TATATATTTAATAGATAA
1 TATATATTTAATAAATAA
1434689 TATATATTTATATAAATA
1 TATATATTTA-ATAAATA
1434707 TATGTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATATATTTAATAAATAA
Found at i:1434937 original size:21 final size:21
Alignment explanation
Indices: 1434911--1434962 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1434901 AAAAGTATTT
1434911 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
1434932 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
1434953 TTGGATGAAA
1 TTGGATGAAA
1434963 AAATATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:1435104 original size:9 final size:9
Alignment explanation
Indices: 1435090--1435115 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1435080 ATTTTCATTC
1435090 CACCTATTG
1 CACCTATTG
1435099 CACCTATTG
1 CACCTATTG
1435108 CACCTATT
1 CACCTATT
1435116 CCATTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (9 bp):
CACCTATTG
Found at i:1438383 original size:21 final size:21
Alignment explanation
Indices: 1438342--1438383 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1438332 ATGTATTAGC
* *
1438342 TGGATGAAAGAATGCATTTTT
1 TGGATGAAAAAATGCACTTTT
1438363 TGGAT-AAAAAATGCAACTTTT
1 TGGATGAAAAAATGC-ACTTTT
1438384 AATAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (21 bp):
TGGATGAAAAAATGCACTTTT
Found at i:1446515 original size:70 final size:71
Alignment explanation
Indices: 1446414--1446554 Score: 223
Period size: 70 Copynumber: 2.0 Consensus size: 71
1446404 TATTATGCAG
*
1446414 TCAAGTCAAATTAGGTTTGGTATTTGTAGTTATTTTCTAA-CTAGATTAAGTCTATCCAATTATA
1 TCAAGTCAAATTAGGTTTGGTATTTGTAGTTATTTTCTAATC-AGATTAAGCCTATCCAATTATA
*
1446478 TTTTAGT
65 ATTTAGT
* *
1446485 TCAAGTC-AATTAGGTTTGGTATTTGTAGTTATTTTCTAATCAGATTAAGCCTCTCCAATTGTAA
1 TCAAGTCAAATTAGGTTTGGTATTTGTAGTTATTTTCTAATCAGATTAAGCCTATCCAATTATAA
1446549 TTTAGT
66 TTTAGT
1446555 CAAAGGTTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 57 0.88
71 8 0.12
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (71 bp):
TCAAGTCAAATTAGGTTTGGTATTTGTAGTTATTTTCTAATCAGATTAAGCCTATCCAATTATAA
TTTAGT
Found at i:1447995 original size:2 final size:2
Alignment explanation
Indices: 1447988--1448020 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1447978 ATACCTCATA
1447988 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
1448021 CATCATGCTA
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:1454366 original size:27 final size:25
Alignment explanation
Indices: 1454333--1454396 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1454323 TAAATAAATT
1454333 ATTTAAAAATAAAATAAAAATAAAAAA
1 ATTTAAAAATAAAA-AAAAA-AAAAAA
** *
1454360 ATTTAAATCTAAAAATAAAAAAAAA
1 ATTTAAAAATAAAAAAAAAAAAAAA
*
1454385 ATATAAAAATAA
1 ATTTAAAAATAA
1454397 CATATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 15 0.48
26 4 0.13
27 12 0.39
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
ATTTAAAAATAAAAAAAAAAAAAAA
Found at i:1454707 original size:17 final size:17
Alignment explanation
Indices: 1454668--1454701 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1454658 TTGAATGAAT
*
1454668 TATTGATATATGTTTAA
1 TATTAATATATGTTTAA
1454685 TATTAATATAT-TTTAA
1 TATTAATATATGTTTAA
1454701 T
1 T
1454702 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TATTAATATATGTTTAA
Found at i:1454726 original size:22 final size:23
Alignment explanation
Indices: 1454700--1454762 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1454690 ATATATTTTA
*
1454700 ATTTTTAAATTTTG-TTATATAT
1 ATTTTTAAATTATGTTTATATAT
*
1454722 ATTTTAAAAATTATGTTTATATAT
1 ATTTT-TAAATTATGTTTATATAT
* *
1454746 ATATTTAGATATATGTT
1 ATTTTTAAAT-TATGTT
1454763 AAATATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 5 0.15
23 10 0.30
24 18 0.55
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
ATTTTTAAATTATGTTTATATAT
Found at i:1454741 original size:24 final size:24
Alignment explanation
Indices: 1454706--1454778 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 24
1454696 TTTAATTTTT
*
1454706 AAATTTTGTTATATATAT-TTTAA
1 AAATTATGTTATATATATATTTAA
*
1454729 AAATTATGTTTATATATATATTTAG
1 AAATTATG-TTATATATATATTTAA
* * * *
1454754 ATA-TATGTTAAATATAAATATAA
1 AAATTATGTTATATATATATTTAA
1454777 AA
1 AA
1454779 GACCAACAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 20 0.50
24 14 0.35
25 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
AAATTATGTTATATATATATTTAA
Found at i:1456102 original size:28 final size:27
Alignment explanation
Indices: 1456047--1456117 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1456037 ATCACCCATT
*
1456047 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGATTATTTTG
1456074 TGTTTGTCAAAAATGGTGATT-TCCTTTG
1 TGTTTGTCAAAAATGGTGATTAT--TTTG
* *
1456102 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
1456118 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGATTATTTTG
Found at i:1458722 original size:21 final size:22
Alignment explanation
Indices: 1458693--1458738 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1458683 TGTTCAGACA
** *
1458693 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1458715 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1458736 AGT
1 AGT
1458739 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1460656 original size:27 final size:28
Alignment explanation
Indices: 1460622--1460692 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
1460612 GCCACCCATT
1460622 TATTTGTCAAAAATGGTGG-TTATTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
* *
1460649 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TATTTGTCAAAAATGGTGGTTTATTTTG
*
1460677 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
1460693 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTGGTTTATTTTG
Found at i:1460676 original size:28 final size:27
Alignment explanation
Indices: 1460622--1460713 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 27
1460612 GCCACCCATT
1460622 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
* *
1460649 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TATTTGTCAAAAATGGTGG-TTATTTTG
* * * *
1460677 TATTTGTCAAATATGGAGGCT-TGTT-
1 TATTTGTCAAAAATGGTGGTTATTTTG
1460702 TATTTGTCAAAA
1 TATTTGTCAAAA
1460714 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.34
28 23 0.41
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:1471283 original size:19 final size:18
Alignment explanation
Indices: 1471258--1471325 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1471248 AATTCCACAA
1471258 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1471276 TGTTGTATCGATA-A-AA-
1 T-TTGTATCGATACATAAG
1471292 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1471308 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
1471326 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
15 2 0.05
17 2 0.05
18 2 0.05
19 26 0.60
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1471301 original size:32 final size:32
Alignment explanation
Indices: 1471260--1471320 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1471250 TTCCACAATT
*
1471260 TGTATCGATACATAAGTGTTGTATCGATAAAA
1 TGTATCGATACATAAGTATTGTATCGATAAAA
1471292 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
1471321 CATAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATAAAA
Found at i:1471383 original size:13 final size:13
Alignment explanation
Indices: 1471365--1471390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1471355 CATTTTTCTG
1471365 TATATCGATACAT
1 TATATCGATACAT
1471378 TATATCGATACAT
1 TATATCGATACAT
1471391 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:1473813 original size:50 final size:51
Alignment explanation
Indices: 1473753--1473869 Score: 140
Period size: 50 Copynumber: 2.4 Consensus size: 51
1473743 CAATCCTCCG
*
1473753 TAATCGGGGATA-TCCCAAGTCCGATTTTATTT-TCAAAACA-CTAATTTTCTA
1 TAATCGGGGATACT-CCAACTCCGATTTTATTTCT-AAAACATC-AATTTTCTA
1473804 TAATC-GGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTA
*
1473851 TCATCGGGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
1473870 CCCGTTAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
47 4 0.07
48 14 0.23
49 3 0.05
50 31 0.52
51 8 0.13
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTA
Found at i:1473920 original size:28 final size:27
Alignment explanation
Indices: 1473851--1473927 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
1473841 CATCAATTTT
1473851 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
1473878 TCATCGGGGATACTCTAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
1473904 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
1473928 CGGCTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.09
27 24 0.55
28 16 0.36
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:1473978 original size:79 final size:79
Alignment explanation
Indices: 1473880--1474058 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 79
1473870 CCCGTTAATC
* * *
1473880 ATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGCTTTATTTC-AAAA
* *
1473945 T-ATTAA-TTTCTCATA
64 TCATCAATTTTC-CACA
* * *
1473960 ATCGGGG-TACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCTGGTTTTATTTCCAAATC
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCAAAATC
*
1474024 ATCGATTTTCCACA
66 ATCAATTTTCCACA
1474038 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1474059 ATTTTATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 4 0.05
78 26 0.30
79 50 0.57
80 7 0.08
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCAAAATC
ATCAATTTTCCACA
Found at i:1474112 original size:52 final size:50
Alignment explanation
Indices: 1473990--1474160 Score: 191
Period size: 52 Copynumber: 3.3 Consensus size: 50
1473980 TTATCTCCGA
* * * *
1473990 GGGGATACTCCAACCCTGGTTTTATTTCCAAATCA-TCGATTTTCCACAATC
1 GGGGATACTCCAACCC-GATTTTATTTCCAAAACACT-AATTTTCCATAATC
* *
1474041 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACACTAATTTTCC-ATAATC
* * * *
1474093 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCATGATT
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAACACTAATTTTCCATAATC
1474145 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1474161 CGTTATTTCC
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
51 38 0.37
52 51 0.50
53 14 0.14
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACTAATTTTCCATAATC
Found at i:1476377 original size:17 final size:17
Alignment explanation
Indices: 1476340--1476377 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1476330 ATATTTATAT
*
1476340 ATAAAATTAATTGTTAT
1 ATAAAATTAATTGTTAA
*
1476357 ATAAAATTAATTTTTAA
1 ATAAAATTAATTGTTAA
1476374 ATAA
1 ATAA
1476378 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATAAAATTAATTGTTAA
Found at i:1477107 original size:17 final size:18
Alignment explanation
Indices: 1477073--1477108 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1477063 TTGATTAAGC
*
1477073 TTTTTATTTTTTATATAT
1 TTTTTATGTTTTATATAT
1477091 TTTTTATGTTTTA-ATAT
1 TTTTTATGTTTTATATAT
1477108 T
1 T
1477109 AAATTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTATGTTTTATATAT
Found at i:1477761 original size:22 final size:22
Alignment explanation
Indices: 1477736--1477778 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1477726 AAAGTTCATA
*
1477736 ATATAATTTAATTTTTTATAAG
1 ATATAATTTAATTTTTGATAAG
*
1477758 ATATAATTTACTTTTTGATAA
1 ATATAATTTAATTTTTGATAA
1477779 ATTACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
ATATAATTTAATTTTTGATAAG
Found at i:1478014 original size:15 final size:16
Alignment explanation
Indices: 1477980--1478015 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1477970 TGAGTTCGAC
1477980 TTTTTTCAAATTCAAG
1 TTTTTTCAAATTCAAG
*
1477996 TTTTTTCAACTTCAA-
1 TTTTTTCAAATTCAAG
1478011 TTTTT
1 TTTTT
1478016 GTTGGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTTTCAAATTCAAG
Found at i:1478474 original size:19 final size:19
Alignment explanation
Indices: 1478450--1478490 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1478440 TTTAGAGTAA
1478450 TATTTGATAAATTAAATAC
1 TATTTGATAAATTAAATAC
* * *
1478469 TATTTGATTACTTAGATAC
1 TATTTGATAAATTAAATAC
1478488 TAT
1 TAT
1478491 ACTTAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (19 bp):
TATTTGATAAATTAAATAC
Found at i:1479089 original size:102 final size:103
Alignment explanation
Indices: 1478903--1479102 Score: 262
Period size: 102 Copynumber: 2.0 Consensus size: 103
1478893 AGTCTTTGCC
* *
1478903 TTTATCTTTCTTCTTTCTATTTCTTTAGATTTTTCTATTTATTTCTGACTCTGGAGAGTTTTAAA
1 TTTATCTTTCTTCTTTCTATTTCTTTAGATTTTTCTATTTACTTCTGACTCTAGAGAGTTTTAAA
* * *
1478968 ATCTTTTTCATATATTTTATTAGTCTTGGTCTTTATCT
66 ACCTTTTTCATATATTTTATAAGTCTTAGTCTTTATCT
* * * *
1479006 TTTATCTTTCTTTTTTTCTATTTCTTTAGGTTTTTGC-ATTT-CTT-TGTCTCTAGAGATTTTTA
1 TTTATCTTTC-TTCTTTCTATTTCTTTAGATTTTT-CTATTTACTTCTGACTCTAGAGAGTTTTA
* *
1479068 AAACCTTTTTCATCTCTTTTATAAGTCTTAGTCTT
64 AAACCTTTTTCATATATTTTATAAGTCTTAGTCTT
1479103 AGCTTTGTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
102 45 0.54
103 12 0.14
104 26 0.31
105 1 0.01
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.59
Consensus pattern (103 bp):
TTTATCTTTCTTCTTTCTATTTCTTTAGATTTTTCTATTTACTTCTGACTCTAGAGAGTTTTAAA
ACCTTTTTCATATATTTTATAAGTCTTAGTCTTTATCT
Found at i:1479612 original size:20 final size:19
Alignment explanation
Indices: 1479587--1479642 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1479577 TTCTTTTTAA
*
1479587 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
1479607 TATATTTATATATAAAAT-
1 TATATTTATATATAAAATC
*
1479625 TA-ATTTGTTATATAAAAT
1 TATATTT-ATATATAAAAT
1479643 TAATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.12
18 12 0.36
19 6 0.18
20 11 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:1480576 original size:22 final size:22
Alignment explanation
Indices: 1480551--1480593 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1480541 AAAGTTCATA
*
1480551 ATATAATTTAATTTTTTATAAG
1 ATATAATTTAATTTTTGATAAG
*
1480573 ATATAATTTACTTTTTGATAA
1 ATATAATTTAATTTTTGATAA
1480594 ATTACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
ATATAATTTAATTTTTGATAAG
Found at i:1481789 original size:98 final size:96
Alignment explanation
Indices: 1481671--1481900 Score: 227
Period size: 101 Copynumber: 2.3 Consensus size: 96
1481661 TTTCTAAGGT
* *
1481671 CTTTTTCATATCA-TTCATTAGTCTTTA-C-C-TTTATCTTTCTTCTTTCCATTTCTTTAGATTT
1 CTTTTTCATAT-ATTTTATTAGTC-TTAGCTCTTTTATCTATCTTCTTTCCATTTCTTTAGATTT
*
1481732 TTTTATTTCTTTCTGACTCTCTGGAGAGTTTTAAAAT
64 TTTTATTTC-TT-TG--TCTCTGGAGAGTTTTAAAAC
* * * *
1481769 TTTTTTCATATATTTTATTAGTCTTAGTCTTTGTCTTTTATCTATCTTTTTTCTATTTCTTTAGG
1 CTTTTTCATATATTTTATTAGTCTTAG-C----TCTTTTATCTATCTTCTTTCCATTTCTTTAGA
1481834 TTTTTTTATTTCTTTGTCTCTGGAGAGTTTTAAAAC
61 TTTTTTTATTTCTTTGTCTCTGGAGAGTTTTAAAAC
* * * *
1481870 CTTTTTCATCTCTTTTATAAGCCTTAG-TCTT
1 CTTTTTCATATATTTTATTAGTCTTAGCTCTT
1481901 AGCCTTTGCC
Statistics
Matches: 111, Mismatches: 12, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
95 4 0.04
97 4 0.04
98 19 0.17
99 1 0.01
101 41 0.37
103 2 0.02
104 3 0.03
105 37 0.33
ACGTcount: A:0.17, C:0.16, G:0.08, T:0.58
Consensus pattern (96 bp):
CTTTTTCATATATTTTATTAGTCTTAGCTCTTTTATCTATCTTCTTTCCATTTCTTTAGATTTTT
TTATTTCTTTGTCTCTGGAGAGTTTTAAAAC
Found at i:1481878 original size:101 final size:104
Alignment explanation
Indices: 1481700--1481900 Score: 282
Period size: 101 Copynumber: 2.0 Consensus size: 104
1481690 AGTCTTTACC
*
1481700 TTTATCTTTCTTCTTTCCATTTCTTTAGATTTTTTTATTTCTTTCTGACTCTCTGGAGAGTTTTA
1 TTTATCTATCTTCTTTCCATTTCTTTAGATTTTTTTATTTCTTTCTGA-TCTCTGGAGAGTTTTA
** * *
1481765 AAATTTTTTTCATATATTTTATTAGTCTTAGTCTTTGTCT
65 AAACCTTTTTCATATATTTTATAAGCCTTAGTCTTTGTCT
* * *
1481805 TTTATCTATCTTTTTTCTATTTCTTTAGGTTTTTTTATTTC-TT-TG-TCTCTGGAGAGTTTTAA
1 TTTATCTATCTTCTTTCCATTTCTTTAGATTTTTTTATTTCTTTCTGATCTCTGGAGAGTTTTAA
* *
1481867 AACCTTTTTCATCTCTTTTATAAGCCTTAGTCTT
66 AACCTTTTTCATATATTTTATAAGCCTTAGTCTT
1481901 AGCCTTTGCC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 45 0.52
103 2 0.02
104 2 0.02
105 37 0.43
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (104 bp):
TTTATCTATCTTCTTTCCATTTCTTTAGATTTTTTTATTTCTTTCTGATCTCTGGAGAGTTTTAA
AACCTTTTTCATATATTTTATAAGCCTTAGTCTTTGTCT
Found at i:1484135 original size:20 final size:20
Alignment explanation
Indices: 1484112--1484149 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1484102 ATTTTTTATA
1484112 TAAATATATTTA-ATATTTTT
1 TAAAT-TATTTATATATTTTT
*
1484132 TAAATTTTTTATATATTT
1 TAAATTATTTATATATTT
1484150 AATGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTATTTATATATTTTT
Found at i:1485282 original size:83 final size:83
Alignment explanation
Indices: 1485138--1485302 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 83
1485128 ACAAGTTTGA
*
1485138 GGTGTGATTATGCGTGAAAAATTTTCATTATTAATATTGTTACACAATAGAAACCATGTATTTTT
1 GGTGAGATTATGCGTGAAAAATTTTCATTATTAATATTGTTACACAATAGAAACCATGTATTTTT
1485203 TAAAGCCATTAAATTCAT
66 TAAAGCCATTAAATTCAT
*
1485221 GGTGAGATTATGCGTGAAAATTTTTCATTATTAATATTGTTACACAATAGAAACCATGTATTTTT
1 GGTGAGATTATGCGTGAAAAATTTTCATTATTAATATTGTTACACAATAGAAACCATGTATTTTT
*
1485286 TAAAGTCATTAAATTCA
66 TAAAGCCATTAAATTCA
1485303 GCCATGTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (83 bp):
GGTGAGATTATGCGTGAAAAATTTTCATTATTAATATTGTTACACAATAGAAACCATGTATTTTT
TAAAGCCATTAAATTCAT
Found at i:1487424 original size:23 final size:23
Alignment explanation
Indices: 1487367--1487426 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1487357 ACACGTATAT
1487367 ATAAAAATATAA-ATGAAATAAA
1 ATAAAAATATAATATGAAATAAA
*
1487389 AT-AAATTATTAATATGTAAA-AAA
1 ATAAAAATA-TAATATG-AAATAAA
1487412 ATAAAAATATAATAT
1 ATAAAAATATAATAT
1487427 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.16
22 5 0.16
23 14 0.44
24 8 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAAAAATATAATATGAAATAAA
Found at i:1487487 original size:22 final size:22
Alignment explanation
Indices: 1487461--1487508 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1487451 ATACATAAAT
* *
1487461 TTTTTTCTCTTTTTCTTTTTTTC
1 TTTTTTCT-TTATTCTTTCTTTC
*
1487484 TTTTTTTTTTATTCTTTCTTTC
1 TTTTTTCTTTATTCTTTCTTTC
1487506 TTT
1 TTT
1487509 CTTTTTTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTTCTTTATTCTTTCTTTC
Found at i:1487489 original size:8 final size:8
Alignment explanation
Indices: 1487460--1487515 Score: 67
Period size: 8 Copynumber: 6.8 Consensus size: 8
1487450 AATACATAAA
1487460 TTTTTTTC
1 TTTTTTTC
*
1487468 TCTTTTTC
1 TTTTTTTC
1487476 TTTTTTTC
1 TTTTTTTC
*
1487484 TTTTTTTT
1 TTTTTTTC
1487492 TTATTCTTTC
1 TT-TT-TTTC
*
1487502 TTTCTTTC
1 TTTTTTTC
1487510 TTTTTT
1 TTTTTT
1487516 CAGCCTTTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 32 0.80
9 3 0.08
10 5 0.12
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1487513 original size:22 final size:22
Alignment explanation
Indices: 1487473--1487515 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1487463 TTTTCTCTTT
* *
1487473 TTCTTTTTTTCTTTTTTTTTTA
1 TTCTTTCTTTCTTTCTTTTTTA
1487495 TTCTTTCTTTCTTTCTTTTTT
1 TTCTTTCTTTCTTTCTTTTTT
1487516 CAGCCTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTCTTTCTTTCTTTCTTTTTTA
Found at i:1488106 original size:13 final size:13
Alignment explanation
Indices: 1488088--1488114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1488078 ACATTATGCT
1488088 TTGTATCGATACA
1 TTGTATCGATACA
1488101 TTGTATCGATACA
1 TTGTATCGATACA
1488114 T
1 T
1488115 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1488111 original size:33 final size:32
Alignment explanation
Indices: 1488069--1488132 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1488059 CATACCCAGA
* *
1488069 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
1488102 TGTATCGATACATGATCATTGTATCGATACA
1 TGTATCGATACATGATCATTGTATCGATACA
1488133 GGGACAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:1488123 original size:19 final size:18
Alignment explanation
Indices: 1488098--1488153 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 18
1488088 TTGTATCGAT
1488098 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
*
1488116 ATCATTGTATCGATACAGGG
1 A-CATTGTATCGATACA-TG
1488136 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
1488154 AAAACTAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 16 0.48
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1488220 original size:13 final size:13
Alignment explanation
Indices: 1488202--1488260 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 13
1488192 TACATGGACT
1488202 TTGTATCGATACA
1 TTGTATCGATACA
1488215 TTGTATCGATACATGGA
1 TTGTATCGATAC----A
*
1488232 CTTTATATCGATACA
1 --TTGTATCGATACA
1488247 TTGTATCGATACA
1 TTGTATCGATACA
1488260 T
1 T
1488261 GGACTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 25 0.66
15 1 0.03
17 1 0.03
19 11 0.29
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1488226 original size:32 final size:32
Alignment explanation
Indices: 1488183--1488292 Score: 193
Period size: 32 Copynumber: 3.4 Consensus size: 32
1488173 CTACCACTGT
* *
1488183 TTGTATTGATACATGGACTTTGTATCGATACA
1 TTGTATCGATACATGGACTTTATATCGATACA
1488215 TTGTATCGATACATGGACTTTATATCGATACA
1 TTGTATCGATACATGGACTTTATATCGATACA
1488247 TTGTATCGATACATGGACTTTATATCGATACA
1 TTGTATCGATACATGGACTTTATATCGATACA
*
1488279 TTGCATCGATACAT
1 TTGTATCGATACAT
1488293 TGCTTCTAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATGGACTTTATATCGATACA
Found at i:1488242 original size:19 final size:19
Alignment explanation
Indices: 1488218--1488279 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
1488208 CGATACATTG
1488218 TATCGATACATGGACTTTA
1 TATCGATACATGGACTTTA
*
1488237 TATCGATAC----A--TTG
1 TATCGATACATGGACTTTA
1488250 TATCGATACATGGACTTTA
1 TATCGATACATGGACTTTA
1488269 TATCGATACAT
1 TATCGATACAT
1488280 TGCATCGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 11 0.31
15 1 0.03
17 1 0.03
19 22 0.63
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (19 bp):
TATCGATACATGGACTTTA
Found at i:1488288 original size:13 final size:13
Alignment explanation
Indices: 1488270--1488295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1488260 TGGACTTTAT
1488270 ATCGATACATTGC
1 ATCGATACATTGC
1488283 ATCGATACATTGC
1 ATCGATACATTGC
1488296 TTCTAACGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
ATCGATACATTGC
Found at i:1496390 original size:13 final size:13
Alignment explanation
Indices: 1496372--1496398 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1496362 ATATTATGCT
1496372 TTGTATCGATACA
1 TTGTATCGATACA
1496385 TTGTATCGATACA
1 TTGTATCGATACA
1496398 T
1 T
1496399 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1496407 original size:19 final size:19
Alignment explanation
Indices: 1496383--1496458 Score: 109
Period size: 19 Copynumber: 3.9 Consensus size: 19
1496373 TGTATCGATA
1496383 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
1496402 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
* *
1496421 CATTATATCGATATATGGA-
1 CATTGTATCGATACAT-GAT
1496440 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
1496459 AATTGGTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 36 0.71
20 15 0.29
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:1496413 original size:32 final size:33
Alignment explanation
Indices: 1496353--1496417 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1496343 CATACCCAGA
* * *
1496353 TGTATCGATATATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
1496386 TGTATCGATACATGAT-CATTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
1496418 GATCATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGATGCATTGTATCGATACAT
Found at i:1497532 original size:21 final size:20
Alignment explanation
Indices: 1497484--1497532 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1497474 AGATACATAA
* *
1497484 TTTTTTTCTTTCTTTTCTTT
1 TTTTTTTCTTTATGTTCTTT
*
1497504 TTCATTTTCTTTATGTTCTTT
1 TT-TTTTTCTTTATGTTCTTT
1497525 CTTTTTTT
1 -TTTTTTT
1497533 TCAACCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTTATGTTCTTT
Found at i:1497713 original size:24 final size:25
Alignment explanation
Indices: 1497655--1497713 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
1497645 GAATTGAGAT
* *
1497655 ATAATAT-AAACTCAACATATATAA
1 ATAATATAAAACACAACATAGATAA
* *
1497679 AAAAAATTAAAACACAACATAGA-AA
1 ATAATA-TAAAACACAACATAGATAA
1497704 ATAATATAAA
1 ATAATATAAA
1497714 TATAGTACGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
24 8 0.30
25 7 0.26
26 12 0.44
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (25 bp):
ATAATATAAAACACAACATAGATAA
Found at i:1497942 original size:21 final size:19
Alignment explanation
Indices: 1497888--1497942 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
1497878 ATACACATAC
1497888 ATATAAAAATATAA-ATTA
1 ATATAAAAATATAATATTA
1497906 A-AT-AAAATA-AATTATTAA
1 ATATAAAAATATAA-TATT-A
1497924 TATATAAAAATATAATATT
1 -ATATAAAAATATAATATT
1497943 TTAAATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 5 0.17
18 2 0.07
19 1 0.03
20 2 0.07
21 10 0.33
22 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATAAAAATATAATATTA
Found at i:1497960 original size:22 final size:24
Alignment explanation
Indices: 1497909--1497962 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
1497899 TAAATTAAAT
*
1497909 AAAATAA-ATTATTAATATATAAA
1 AAAATAATATTATTAATATACAAA
*
1497932 AATATAATATT-TTAA-ATACAAA
1 AAAATAATATTATTAATATACAAA
1497954 AAAATAATA
1 AAAATAATA
1497963 CAAATACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.52
23 10 0.37
24 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATAATATTATTAATATACAAA
Found at i:1498001 original size:4 final size:4
Alignment explanation
Indices: 1497992--1498073 Score: 67
Period size: 4 Copynumber: 19.8 Consensus size: 4
1497982 TTATTCTCTT
* *
1497992 TTTC TTTC TTTC CTT- TTTC TTCTC TTCTC TTTTC TCTC TTTC TTTCC
1 TTTC TTTC TTTC TTTC TTTC TT-TC TT-TC -TTTC TTTC TTTC TTT-C
** * *
1498039 GCTC TTTC TTTT TTTC TTCC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1498074 GTCAGCTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
3 2 0.03
4 47 0.76
5 11 0.18
6 2 0.03
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:1498157 original size:44 final size:44
Alignment explanation
Indices: 1498105--1498188 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
1498095 TATATATTAA
*
1498105 CAATTCCTCTCTTATATATGTAGTTCAAATTAGATATATAACGT
1 CAATTCCTCACTTATATATGTAGTTCAAATTAGATATATAACGT
*
1498149 CAATTCCTCACTTATATATGTAGTTTAAATTAGATATATA
1 CAATTCCTCACTTATATATGTAGTTCAAATTAGATATATA
1498189 GTAGATAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (44 bp):
CAATTCCTCACTTATATATGTAGTTCAAATTAGATATATAACGT
Done.