Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 5 of 325
Found at i:1122689 original size:15 final size:15
Alignment explanation
Indices: 1122669--1122724 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
1122659 AAGTAGCGGG
1122669 ATTAAATAATATTTA
1 ATTAAATAATATTTA
1122684 ATTAAATAATATTT-
1 ATTAAATAATATTTA
1122698 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
1122713 ATTAAATAATAT
1 ATTAAATAATAT
1122725 ACATGTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:1122929 original size:24 final size:24
Alignment explanation
Indices: 1122901--1122968 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
1122891 ACTTAAATGG
1122901 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
1122925 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
1122949 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
1122969 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:1127810 original size:28 final size:27
Alignment explanation
Indices: 1127758--1127810 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
1127748 GGTCTCTCTA
*
1127758 ATATATTTAAATTTTAGATTTATTTGC
1 ATATATTTAAATTTTAGATTCATTTGC
*
1127785 ATATACTTTAATTTTTA-ATATCATTT
1 ATATA-TTTAAATTTTAGAT-TCATTT
1127811 AGTCTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (27 bp):
ATATATTTAAATTTTAGATTCATTTGC
Found at i:1127993 original size:12 final size:12
Alignment explanation
Indices: 1127976--1128020 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
1127966 CATTAATATC
*
1127976 TATATATATCAA
1 TATATATATCCA
1127988 TATATATATCCA
1 TATATATATCCA
1128000 TATATATATCCA
1 TATATATATCCA
1128012 TATATATAT
1 TATATATAT
1128021 ATTATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATATCCA
Found at i:1128138 original size:22 final size:22
Alignment explanation
Indices: 1128054--1128138 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 22
1128044 TTAGGATTTA
1128054 TATAGTATTTAAGTGTTTAAGGGTT
1 TATAGT-TTTAAGT-TTT-AGGGTT
* * * * *
1128079 TGTTG-TCTATAGTTTAAGGTTT
1 TATAGTTTTA-AGTTTTAGGGTT
*
1128101 TATAGTTTT-AGATTTAGGGTT
1 TATAGTTTTAAGTTTTAGGGTT
1128122 TATAGTTTTAAGTTTTA
1 TATAGTTTTAAGTTTTA
1128139 TAATTTAGGG
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
21 18 0.40
22 14 0.31
23 7 0.16
24 3 0.07
25 3 0.07
ACGTcount: A:0.25, C:0.01, G:0.21, T:0.53
Consensus pattern (22 bp):
TATAGTTTTAAGTTTTAGGGTT
Found at i:1128669 original size:40 final size:40
Alignment explanation
Indices: 1128583--1128672 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
1128573 TCTTTAATCT
* * * *
1128583 TTTAGCGGCGCTTACGTAAAAACGCCGCTATAGGTCGGTC
1 TTTAGCGGCGCTTACCTAAAAACGCCACTATAGCTCGATC
*
1128623 TATAGCGGCGCTT-CTCTAAAAACGCCACTA-ATGCTCGATC
1 TTTAGCGGCGCTTAC-CTAAAAACGCCACTATA-GCTCGATC
1128663 TTTAGCGGCG
1 TTTAGCGGCG
1128673 TTTTTTGAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
TTTAGCGGCGCTTACCTAAAAACGCCACTATAGCTCGATC
Found at i:1128847 original size:11 final size:11
Alignment explanation
Indices: 1128833--1128858 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1128823 CATTTTCTAT
1128833 TAAAACGCCGC
1 TAAAACGCCGC
1128844 TAAAACGCCGC
1 TAAAACGCCGC
1128855 TAAA
1 TAAA
1128859 GGAATGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.31, G:0.15, T:0.12
Consensus pattern (11 bp):
TAAAACGCCGC
Found at i:1131397 original size:28 final size:28
Alignment explanation
Indices: 1131357--1131426 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1131347 ATGAAAATTT
* *
1131357 CACTAAGCATGCGAGTTTGGTTAAT-GAG
1 CACTAAGTATGCGAGTTTGATT-ATCGAG
*
1131385 CACTAAGTGTGCGAGTTTGATTATCGAG
1 CACTAAGTATGCGAGTTTGATTATCGAG
1131413 CACTAAGTATGCGA
1 CACTAAGTATGCGA
1131427 AAGAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
CACTAAGTATGCGAGTTTGATTATCGAG
Found at i:1131721 original size:3 final size:3
Alignment explanation
Indices: 1131700--1131747 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
1131690 GTTGAAAAGT
1131700 ATA A-A ATA A-A ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1131744 ATA A
1 ATA A
1131748 AATGATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1134658 original size:5 final size:5
Alignment explanation
Indices: 1134648--1134675 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1134638 TTATGTATTC
1134648 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1134676 CACACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1137867 original size:3 final size:3
Alignment explanation
Indices: 1137859--1137907 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1137849 ACTTACAAGA
1137859 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1137907 A
1 A
1137908 TTACTGCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1146785 original size:22 final size:22
Alignment explanation
Indices: 1146759--1146804 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1146749 ATTTATACCA
1146759 TGACTTAAATATCAATACCTTT
1 TGACTTAAATATCAATACCTTT
1146781 TGACTTAAATATCAATACCTTT
1 TGACTTAAATATCAATACCTTT
1146803 TG
1 TG
1146805 CTTGGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (22 bp):
TGACTTAAATATCAATACCTTT
Found at i:1147688 original size:15 final size:15
Alignment explanation
Indices: 1147668--1147719 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1147658 AAATTAATAA
1147668 TTTAATTTAAACATT
1 TTTAATTTAAACATT
*
1147683 TTTAATATAAA-ATT
1 TTTAATTTAAACATT
* *
1147697 TTTAATTAAAACCTT
1 TTTAATTTAAACATT
*
1147712 TTAAATTT
1 TTTAATTT
1147720 TATAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATTTAAACATT
Found at i:1147713 original size:14 final size:14
Alignment explanation
Indices: 1147668--1147715 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1147658 AAATTAATAA
*
1147668 TTTAATTTAAACATT
1 TTTAATTAAAAC-TT
1147683 TTTAATATAAAA-TT
1 TTTAAT-TAAAACTT
*
1147697 TTTAATTAAAACCT
1 TTTAATTAAAACTT
1147711 TTTAA
1 TTTAA
1147716 ATTTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 5 0.17
14 14 0.48
15 6 0.21
16 4 0.14
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAAAACTT
Found at i:1148632 original size:24 final size:24
Alignment explanation
Indices: 1148583--1148650 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
1148573 GTTTAAAATT
*
1148583 AAATTAAAATATAAAAATTC-AAA
1 AAATAAAAATATAAAAATTCAAAA
* *
1148606 AAATAAAAATATTAATAATTCATAA
1 AAATAAAAATA-TAAAAATTCAAAA
1148631 AAATAAAAATTTATAAAAAT
1 AAATAAAAA--TATAAAAAT
1148651 GCACCTGTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 10 0.27
24 8 0.22
25 11 0.30
26 6 0.16
27 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAAAATATAAAAATTCAAAA
Found at i:1148646 original size:16 final size:18
Alignment explanation
Indices: 1148608--1148650 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
1148598 AATTCAAAAA
1148608 ATAAAAATATTAATAATTC
1 ATAAAAATA-TAATAATTC
*
1148627 ATAAAAATA-AA-AATTT
1 ATAAAAATATAATAATTC
1148643 ATAAAAAT
1 ATAAAAAT
1148651 GCACCTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 12 0.52
17 2 0.09
19 9 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATATAATAATTC
Found at i:1149995 original size:29 final size:28
Alignment explanation
Indices: 1149934--1150032 Score: 139
Period size: 28 Copynumber: 3.5 Consensus size: 28
1149924 ACAGTAAGTC
*
1149934 CGCACACTTAGTGCT-TAATATTCAAACT
1 CGCACACTTAGTGCTATCA-ATTCAAACT
1149962 CGCACACTTAGTGCTATGCAATTCAAACT
1 CGCACACTTAGTGCTAT-CAATTCAAACT
1149991 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTAT-CAATTCAAACT
*
1150019 CGTACACTTAGTGC
1 CGCACACTTAGTGC
1150033 CAATCTCATT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
28 33 0.50
29 32 0.48
30 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATCAATTCAAACT
Found at i:1157752 original size:29 final size:29
Alignment explanation
Indices: 1157691--1157789 Score: 168
Period size: 28 Copynumber: 3.5 Consensus size: 29
1157681 ACAGTAAGTC
1157691 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
1157719 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
1157748 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
1157776 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1157790 CAATCTCATT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 34 0.49
29 34 0.49
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:1165499 original size:29 final size:28
Alignment explanation
Indices: 1165438--1165536 Score: 148
Period size: 28 Copynumber: 3.5 Consensus size: 28
1165428 ACAGTAAGTC
*
1165438 CGCACACTTAGTGCT-TAATATTCAAACT
1 CGCACACTTAGTGCTATCA-ATTCAAACT
1165466 CGCACACTTAGTGCTATGCAATTCAAACT
1 CGCACACTTAGTGCTAT-CAATTCAAACT
1165495 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTAT-CAATTCAAACT
1165523 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1165537 CAATCTCATT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 34 0.51
29 32 0.48
30 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATCAATTCAAACT
Found at i:1167142 original size:21 final size:20
Alignment explanation
Indices: 1167104--1167142 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1167094 AATCTTTTAG
*
1167104 AATTTTTTTTAAAAATTATT
1 AATTTTTTATAAAAATTATT
*
1167124 AATTTGTTTATAATAATTA
1 AATTT-TTTATAAAAATTA
1167143 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTTTATAAAAATTATT
Found at i:1169213 original size:19 final size:19
Alignment explanation
Indices: 1169189--1169228 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1169179 TTAGTTTAAC
1169189 TCCAAAGAAGAAATAAAGT
1 TCCAAAGAAGAAATAAAGT
1169208 TCCAAAGAAGAAATAAAGT
1 TCCAAAGAAGAAATAAAGT
1169227 TC
1 TC
1169229 ACTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (19 bp):
TCCAAAGAAGAAATAAAGT
Found at i:1171258 original size:2 final size:2
Alignment explanation
Indices: 1171251--1171279 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1171241 ATAGAAACAA
1171251 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 A
1171280 CTCCTCTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1175873 original size:31 final size:31
Alignment explanation
Indices: 1175838--1176853 Score: 326
Period size: 31 Copynumber: 34.1 Consensus size: 31
1175828 GTTCAGTACA
* *
1175838 GTCTTATTTTGAAAATACGCATTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* *
1175869 GTCTTGTTCTG--AATACGCACTTTGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * *
1175898 G-----TTCTAAAAATACACACATT-GATGTT
1 GTCTTATTCTGAAAATACGCAC-TTCGGTGTT
* *
1175924 GTCTTGTTCT--AAATACGCACTTCAGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* *
1175953 GTCTTGTTCTGAAAATACACACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * *
1175984 GTCCTATTTTGAAAATACGAACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * **** * * * *
1176015 GTCCTATTTTGGTGTTGTCCTGTTCTGAATATGCGCT-TC
1 GTCTTATTCT-G-AAAATAC-G--C--ACT-T-CGGTGTT
* * * * * *
1176054 GCTGTTGTTCTAAAAATACACTCTTCGATGTT
1 G-TCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176086 GTCTTGTTCCG--AATACACACTTCAGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * *
1176115 GTCTTGTTCTGGAAATACACACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * ** * *
1176146 GTCCTATTTTGAAAATACAAACTTCAGTGCT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* *
1176177 GTCTTGTTCTG---ATACACACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * **
1176205 G-----TTCTAAAAATACACACTTCAATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * * *
1176231 GTCCTCTTTTAAAAATACGCACTTCGATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176262 GTCTTGTTCTG--AATACGTATTTCAGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176291 GTCTTGTTCTAAAAATACACACTTCAGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * *
1176322 GTC---TT-TGTAAATACGCATTTCGGTGCT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* *
1176349 GTCCTGTTCTG--AATACGCACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176378 G-----TTCTAAAAATACACACTTTGATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * * * *
1176404 GTCCTCTTCTAAAAATACACACTTCGATGTC
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* **
1176435 GTCTTGTTCTG--AATACGCACTTCAATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * **
1176464 GTCTTGTTCTGAAAATACACACTTTAGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * * *
1176495 GTCCTATGT-TGAAAATACGCATTTTGATGCT
1 GTCTTAT-TCTGAAAATACGCACTTCGGTGTT
*
1176526 GT-TCTGTTCTG--AATACGCACTTC-G-G-T
1 GTCT-TATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176552 G-C-TATTCTAAAAATACACACTTTGATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176581 GTCCTCTTCTGAAAATATGCACTTCGATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* ** *
1176612 GTCTTGTTCTG--AATACGCACTTCAATATT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * *
1176641 GTCTTGTTCTGAAAATACACGCTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176672 GTCCTATTTTGAAAATACGCATTTTGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * *
1176703 GTCTTGTT-TCAAAAATACGCATTTCGATG--
1 GTCTTATTCT-GAAAATACGCACTTCGGTGTT
* * * * *
1176732 CTC-TATTTTGAAAATATGCACTTCGATATT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* * * **
1176762 GTCCTT-CTCT--AAATACACATTTCAATGTT
1 GT-CTTATTCTGAAAATACGCACTTCGGTGTT
* * * * * *
1176791 TTCCTGTTCTGAAAATACACACTTTGATGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
* *
1176822 GTCTTGTTCTG--AATACGAACTTCGGTGTT
1 GTCTTATTCTGAAAATACGCACTTCGGTGTT
1176851 GTC
1 GTC
1176854 CTCCTTTGAC
Statistics
Matches: 743, Mismatches: 173, Indels: 140
0.70 0.16 0.13
Matches are distributed among these distances:
23 4 0.01
24 13 0.02
26 58 0.08
27 22 0.03
28 40 0.05
29 208 0.28
30 6 0.01
31 366 0.49
32 6 0.01
33 3 0.00
34 1 0.00
35 1 0.00
38 4 0.01
39 3 0.00
40 8 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (31 bp):
GTCTTATTCTGAAAATACGCACTTCGGTGTT
Found at i:1175886 original size:29 final size:29
Alignment explanation
Indices: 1175850--1176017 Score: 137
Period size: 29 Copynumber: 5.8 Consensus size: 29
1175840 CTTATTTTGA
*
1175850 AAATACGCATTTCGGTGTTGTCTTGTTCT
1 AAATACGCACTTCGGTGTTGTCTTGTTCT
* * * **
1175879 GAATACGCACTTTGGTGTTG--TT-CTAA
1 AAATACGCACTTCGGTGTTGTCTTGTTCT
* *
1175905 AAATACACACATT-GATGTTGTCTTGTTCT
1 AAATACGCAC-TTCGGTGTTGTCTTGTTCT
*
1175934 AAATACGCACTTCAGTGTTGTCTTGTTCT
1 AAATACGCACTTCGGTGTTGTCTTGTTCT
* * **
1175963 GAAAATACACACTTCGGTGTTGTCCTATTTTGA
1 --AAATACGCACTTCGGTGTTGT-CT-TGTTCT
*
1175996 AAATACGAACTTCGGTGTTGTC
1 AAATACGCACTTCGGTGTTGTC
1176018 CTATTTTGGT
Statistics
Matches: 108, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
26 15 0.14
27 4 0.04
28 4 0.04
29 41 0.38
30 1 0.01
31 38 0.35
32 2 0.02
33 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (29 bp):
AAATACGCACTTCGGTGTTGTCTTGTTCT
Found at i:1176133 original size:162 final size:162
Alignment explanation
Indices: 1175858--1176179 Score: 502
Period size: 162 Copynumber: 2.0 Consensus size: 162
1175848 GAAAATACGC
* * *
1175858 ATTTCGGTGTTGTCTTGTTCTGAATACGCACTTTGGTGTTGTTCTAAAAATACACACATTGATGT
1 ATTTCGGTGTTGTCCTGTTCTGAATACGCACTTCGCTGTTGTTCTAAAAATACACACATTGATGT
* *
1175923 TGTCTTGTTCTAAATACGCACTTCAGTGTTGTCTTGTTCTGAAAATACACACTTCGGTGTTGTCC
66 TGTCTTGTTCCAAATACACACTTCAGTGTTGTCTTGTTCTGAAAATACACACTTCGGTGTTGTCC
* * *
1175988 TATTTTGAAAATACGAACTTCGGTGTTGTCCT
131 TATTTTGAAAATACAAACTTCAGTGCTGTCCT
* * * *
1176020 ATTTTGGTGTTGTCCTGTTCTGAATATGCGCTTCGCTGTTGTTCTAAAAATACACTC-TTCGATG
1 ATTTCGGTGTTGTCCTGTTCTGAATACGCACTTCGCTGTTGTTCTAAAAATACACACATT-GATG
* *
1176084 TTGTCTTGTTCCGAATACACACTTCAGTGTTGTCTTGTTCTGGAAATACACACTTCGGTGTTGTC
65 TTGTCTTGTTCCAAATACACACTTCAGTGTTGTCTTGTTCTGAAAATACACACTTCGGTGTTGTC
1176149 CTATTTTGAAAATACAAACTTCAGTGCTGTC
130 CTATTTTGAAAATACAAACTTCAGTGCTGTC
1176180 TTGTTCTGAT
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 2 0.01
162 143 0.99
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (162 bp):
ATTTCGGTGTTGTCCTGTTCTGAATACGCACTTCGCTGTTGTTCTAAAAATACACACATTGATGT
TGTCTTGTTCCAAATACACACTTCAGTGTTGTCTTGTTCTGAAAATACACACTTCGGTGTTGTCC
TATTTTGAAAATACAAACTTCAGTGCTGTCCT
Found at i:1176146 original size:60 final size:60
Alignment explanation
Indices: 1176058--1176720 Score: 357
Period size: 60 Copynumber: 11.2 Consensus size: 60
1176048 CGCTTCGCTG
* * **
1176058 TTGTTCTAAAAATACACTCTTCGATGTTGTCTTGTTCCGAATACACACTTCAGTGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
** * * * *
1176118 TTGTTCTGGAAATACACACTTCGGTGTTGTCCTATTTTGAAAATACAAACTTCAGTGCTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGT-CT-TGTTCAAAATACACACTTCAGTGTTGTC
* * * *
1176180 TTGTTCT---GATACACACTTCGGTGTTG--TT-CTAAAAATACACACTTCAATGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
* * * * * ** ** *
1176234 CTCTTTTAAAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGTATTTCAGTGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
* * * * *
1176294 TTGTTCTAAAAATACACACTTCAGTGTTGTCTT-TGT--AAATACGCATTTCGGTGCTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGT-TCAAAATACACACTTCAGTGTTGTC
* * * * * *
1176352 CTGTTCT--GAATACGCACTTCGGTGTTG--TT-CTAAAAATACACACTT-TGATGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAG-TGTTGTC
* * * * ** * *
1176407 CTCTTCTAAAAATACACACTTCGATGTCGTCTTGTTCTGAATACGCACTTCAATGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
* ** * * ** *
1176467 TTGTTCTGAAAATACACACTTTAGTGTTGTCCTATGTTGAAAATACGCA-TTTTGATGCTGT-
1 TTGTTCTAAAAATACACACTTCGGTGTTGT-CT-TGTTCAAAATACACACTTCAG-TGTTGTC
* * * * * * *
1176528 TCTGTTCT--GAATACGCACTTCGGTG--CTATT-CTAAAAATACACACTT-TGATGTTGTC
1 T-TGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAG-TGTTGTC
* * * ** * ** * * *
1176584 CTCTTCTGAAAATATGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAATATTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
* * * * * * **
1176644 TTGTTCTGAAAATACACGCTTCGGTGTTGTCCTATTTTGAAAATACGCATTTTGGTGTTGTC
1 TTGTTCTAAAAATACACACTTCGGTGTTGT-CT-TGTTCAAAATACACACTTCAGTGTTGTC
1176706 TTGTT-TCAAAAATAC
1 TTGTTCT-AAAAATAC
1176721 GCATTTCGAT
Statistics
Matches: 454, Mismatches: 116, Indels: 64
0.72 0.18 0.10
Matches are distributed among these distances:
53 1 0.00
54 28 0.06
55 46 0.10
56 21 0.05
57 47 0.10
58 25 0.06
59 26 0.06
60 167 0.37
61 10 0.02
62 83 0.18
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (60 bp):
TTGTTCTAAAAATACACACTTCGGTGTTGTCTTGTTCAAAATACACACTTCAGTGTTGTC
Found at i:1176315 original size:145 final size:145
Alignment explanation
Indices: 1176050--1176326 Score: 344
Period size: 145 Copynumber: 1.9 Consensus size: 145
1176040 TGAATATGCG
* * ***
1176050 CTTCGCTGTTGTTCTAAAAATACACTCTTCGATGTTGTCTTGTTCCGAATACACACTTCAGTGTT
1 CTTCGCTGTTGTTCTAAAAATACACACTTCAATGTTGTCTTGTTAAAAATACACACTTCAGTGTT
* * *
1176115 GTCTTGTTCTGGAAATACACACTTCGGTGTTGTCCTATTTTGAAAATACAAACTTCAGTGCTGTC
66 GTCTTGTTCTGGAAATACACACTTCAGTGTTGTCCTATTCTAAAAATACAAACTTCAGTGCTGTC
1176180 TTGTTCTGATACACA
131 TTGTTCTGATACACA
* * *
1176195 CTTCGGTGTTGTTCTAAAAATACACACTTCAATGTTGTCCTCTTTTAAAAATACGCACTTC-GAT
1 CTTCGCTGTTGTTCTAAAAATACACACTTCAATGTTGT-CT-TGTTAAAAATACACACTTCAG-T
** * * * * *
1176259 GTTGTCTTGTTCT-G-AATACGTATTTCAGTGTTGTCTTGTTCTAAAAATACACACTTCAGTGTT
63 GTTGTCTTGTTCTGGAAATACACACTTCAGTGTTGTCCTATTCTAAAAATACAAACTTCAGTGCT
1176322 GTCTT
128 GTCTT
1176327 TGTAAATACG
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
145 79 0.71
146 4 0.04
147 28 0.25
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (145 bp):
CTTCGCTGTTGTTCTAAAAATACACACTTCAATGTTGTCTTGTTAAAAATACACACTTCAGTGTT
GTCTTGTTCTGGAAATACACACTTCAGTGTTGTCCTATTCTAAAAATACAAACTTCAGTGCTGTC
TTGTTCTGATACACA
Found at i:1176322 original size:91 final size:91
Alignment explanation
Indices: 1176066--1176710 Score: 663
Period size: 91 Copynumber: 7.3 Consensus size: 91
1176056 TGTTGTTCTA
* * * * **
1176066 AAAATACACTCTTCGATGTTGTCTTGTTCCGAATACACACTTCAGTGTTGTCTTGTTCTGGAAAT
1 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
*
1176131 ACACACTTCGGTGTTGTCCTATTTTG
66 ACACACTTCAGTGTTGTCCTATTTTG
** * *
1176157 AAAATACAAACTTC-AGTGCTGTCTTGTTCTG-ATACACACTTC-G-G-TG--TTGTTCTAAAAA
1 AAAATACGCACTTCGA-TGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAA
* * *
1176215 TACACACTTCAATGTTGTCCTCTTTTA
65 TACACACTTCAGTGTTGTCCTATTTTG
* *
1176242 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGTATTTCAGTGTTGTCTTGTTCTAAAAAT
1 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
1176307 ACACACTTCAGTGTTGT-C---TTTG
66 ACACACTTCAGTGTTGTCCTATTTTG
* * * * *
1176329 TAAATACGCATTTCGGTGCTGTCCTGTTCTGAATACGCACTTC-G-G-TG--TTGTTCTAAAAAT
1 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
* * * *
1176389 ACACACTT-TGATGTTGTCCTCTTCTA
66 ACACACTTCAG-TGTTGTCCTATTTTG
* * * *
1176415 AAAATACACACTTCGATGTCGTCTTGTTCTGAATACGCACTTCAATGTTGTCTTGTTCTGAAAAT
1 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
* *
1176480 ACACACTTTAGTGTTGTCCTATGTTG
66 ACACACTTCAGTGTTGTCCTATTTTG
* * * *
1176506 AAAATACGCATTTTGATGCTGT-TCTGTTCTGAATACGCACTTC-G-G-TG-C-TATTCTAAAAA
1 AAAATACGCACTTCGATGTTGTCT-TGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAA
* * *
1176565 TACACACTT-TGATGTTGTCCTCTTCTG
65 TACACACTTCAG-TGTTGTCCTATTTTG
* * * *
1176592 AAAATATGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAATATTGTCTTGTTCTGAAAAT
1 AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
* *
1176657 ACACGCTTCGGTGTTGTCCTATTTTG
66 ACACACTTCAGTGTTGTCCTATTTTG
* * *
1176683 AAAATACGCATTTTGGTGTTGTCTTGTT
1 AAAATACGCACTTCGATGTTGTCTTGTT
1176711 TCAAAAATAC
Statistics
Matches: 456, Mismatches: 70, Indels: 56
0.78 0.12 0.10
Matches are distributed among these distances:
81 1 0.00
82 27 0.06
83 1 0.00
84 2 0.00
85 61 0.13
86 115 0.25
87 44 0.10
88 5 0.01
89 8 0.02
90 15 0.03
91 175 0.38
92 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (91 bp):
AAAATACGCACTTCGATGTTGTCTTGTTCTGAATACGCACTTCAGTGTTGTCTTGTTCTAAAAAT
ACACACTTCAGTGTTGTCCTATTTTG
Found at i:1176351 original size:27 final size:29
Alignment explanation
Indices: 1176243--1176554 Score: 118
Period size: 29 Copynumber: 10.7 Consensus size: 29
1176233 CCTCTTTTAA
* * *
1176243 AAATACGCACTTCGATGTTGTCTTGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
* * * * * *
1176272 GAATACGTATTTCAGTGTTGTCTTGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
* * * *
1176301 AAAAATACACACTTCAGTGTTGT-CT-TTGT
1 --AAATACGCACTTCGGTGCTGTCCTGTTCT
*
1176330 AAATACGCATTTCGGTGCTGTCCTGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
*
1176359 GAATACGCACTTC-G-G-TGT--TGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
* * * * *
1176383 AAAAATACACACTTTGATGTTGTCCTCTTCT
1 --AAATACGCACTTCGGTGCTGTCCTGTTCT
* * *
1176414 AAAAATACACACTTCGATG-TCGTCTTGTTCT
1 --AAATACGCACTTCGGTGCT-GTCCTGTTCT
* ** * *
1176445 GAATACGCACTTCAATGTTGTCTTGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
* ** * **
1176474 GAAAATACACACTTTAGTGTTGTCCTATGTTGA
1 --AAATACGCACTTCGGTGCTGTCC--TGTTCT
* * * *
1176507 AAATACGCATTTTGATGCTGTTCTGTTCT
1 AAATACGCACTTCGGTGCTGTCCTGTTCT
*
1176536 GAATACGCACTTCGGTGCT
1 AAATACGCACTTCGGTGCT
1176555 ATTCTAAAAA
Statistics
Matches: 218, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
24 6 0.03
26 13 0.06
27 18 0.08
28 4 0.02
29 87 0.40
30 3 0.01
31 83 0.38
33 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (29 bp):
AAATACGCACTTCGGTGCTGTCCTGTTCT
Found at i:1176837 original size:60 final size:60
Alignment explanation
Indices: 1176068--1176855 Score: 335
Period size: 60 Copynumber: 13.4 Consensus size: 60
1176058 TTGTTCTAAA
* * * * * *
1176068 AATACACTCTTCGATGTTGTCTTGTTCCG--AATACACAC-TTCAGTGTTGTCTTGTTCTGG
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGA-TGTTGTCTTGTTCT-G
* * ** * *
1176127 AAATACACACTTCGGTGTTGTCCTATTTTGAAAATACAAAC-TTCAGTGCTGTCTTGTTCTG
1 -AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGA-TGTTGTCTTGTTCTG
* * * ** * ***
1176188 -ATACACACTTCG--G-TGT--TGTTCTAAAAATACACACTTCAATGTTGTCCTCTTTTAAA
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGT-CT-TGTTCTG
* * * * * *
1176244 AATACGCACTTCGATGTTGTCTTGTTCTG--AATACGTA-TTTCAGTGTTGTCTTGTTCTAAA
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGA-TGTTGTCTTGTTCT--G
* * * *
1176304 AATACACACTTC-AGTGTTGT-C--TT-TGTAAATACGCA-TTTCGGTGCTGTCCTGTTCTG
1 AATACACACTTCGA-TGTTGTCCTATTCTGAAAATACGCACTTT-GATGTTGTCTTGTTCTG
* * * * * * *
1176360 AATACGCACTTCG--G-TGT--TGTTCTAAAAATACACACTTTGATGTTGTCCTCTTCTAAA
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCT--G
* * * **
1176417 AATACACACTTCGATGTCGTCTTGTTCTG--AATACGCACTTCAATGTTGTCTTGTTCTG
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCTG
* * *
1176475 AAAATACACACTT-TAGTGTTGTCCTATGT-TGAAAATACGCATTTTGATGCTGT-TCTGTTCTG
1 --AATACACACTTCGA-TGTTGTCCTAT-TCTGAAAATACGCACTTTGATGTTGTCT-TGTTCTG
* * * * *
1176537 AATACGCACTTCG--G-TG--CTATTCTAAAAATACACACTTTGATGTTGTCCTCTTCTG
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCTG
** * * ** *
1176592 AAAATATGCACTTCGATGTTGTCTTGTTCTG--AATACGCACTTCAATATTGTCTTGTTCTG
1 --AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCTG
* * * * * **
1176652 AAAATACACGCTTCGGTGTTGTCCTATTTTGAAAATACGCATTTTGGTGTTGTCTTGTTTCAAA
1 --AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTG-TTC-TG
* * * * * * * * *
1176716 AATACGCATTTCGATG--CT-CTATTTTGAAAATATGCACTTCGATATTGTCCTT-CTCTA
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGT-CTTGTTCTG
* * * * *
1176773 AATACACATTTCAATGTTTTCCTGTTCTGAAAATACACACTTTGATGTTGTCTTGTTCTG
1 AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCTG
*
1176833 AATACGA-ACTTCGGTGTTGTCCT
1 AATAC-ACACTTCGATGTTGTCCT
1176856 CCTTTGACAT
Statistics
Matches: 551, Mismatches: 120, Indels: 114
0.70 0.15 0.15
Matches are distributed among these distances:
53 3 0.01
54 23 0.04
55 56 0.10
56 22 0.04
57 55 0.10
58 28 0.05
59 51 0.09
60 209 0.38
61 4 0.01
62 97 0.18
63 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (60 bp):
AATACACACTTCGATGTTGTCCTATTCTGAAAATACGCACTTTGATGTTGTCTTGTTCTG
Found at i:1180284 original size:22 final size:22
Alignment explanation
Indices: 1180259--1180302 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1180249 TTTATTTTTA
1180259 AAAATATT-TAAAATATTAATAT
1 AAAATATTAT-AAATATTAATAT
*
1180281 AAAATATTATAAATTTTAATAT
1 AAAATATTATAAATATTAATAT
1180303 TATAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATTATAAATATTAATAT
Found at i:1180425 original size:13 final size:14
Alignment explanation
Indices: 1180396--1180448 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
1180386 AATATTTAAT
1180396 ATTTTAAT--TAT-
1 ATTTTAATAATATA
1180407 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
1180420 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
1180435 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1180449 TCTTCACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 8 0.24
13 12 0.35
14 1 0.03
15 8 0.24
16 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1180433 original size:16 final size:16
Alignment explanation
Indices: 1180411--1180447 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1180401 AATTATATTT
1180411 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
1180428 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
1180443 TAATA
1 TAATA
1180448 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:1186601 original size:19 final size:20
Alignment explanation
Indices: 1186577--1186614 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1186567 ATAACATGAC
1186577 TTAAAAGTTATTTA-AAAAA
1 TTAAAAGTTATTTAGAAAAA
1186596 TTAAAAGTTATTTAGAAAA
1 TTAAAAGTTATTTAGAAAA
1186615 GTTTTAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TTAAAAGTTATTTAGAAAAA
Found at i:1187743 original size:23 final size:22
Alignment explanation
Indices: 1187700--1187757 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1187690 AAAAGGTATC
* *
1187700 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1187721 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1187744 TGCATATCATATCT
1 TACAAATCATATCT
1187758 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1187771 original size:22 final size:19
Alignment explanation
Indices: 1187727--1187774 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1187717 AGATTACAAA
1187727 ATCATATCTTCTAAGATTG
1 ATCATATCTTCTAAGATTG
1187746 --CATATCATATCTAAGATTG
1 ATCATATC-T-TCTAAGATTG
1187765 TATCATATCT
1 -ATCATATCT
1187775 AAGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 10 0.42
21 1 0.04
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATCATATCTTCTAAGATTG
Found at i:1187815 original size:36 final size:36
Alignment explanation
Indices: 1187739--1187816 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
1187729 CATATCTTCT
*
1187739 AAGATTGCATATCATATCTAAGATTGTATCATATCT
1 AAGATTGCATATCATATCTAAGATTGTATCATATCG
1187775 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATTG--TATCATATCG
1187811 AAGATT
1 AAGATT
1187817 ATATTTCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 32 0.82
37 1 0.03
38 6 0.15
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTGTATCATATCG
Found at i:1187816 original size:17 final size:19
Alignment explanation
Indices: 1187736--1187808 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
1187726 AATCATATCT
1187736 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1187755 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
1187772 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1187791 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
1187809 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.33
19 35 0.67
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1188517 original size:61 final size:61
Alignment explanation
Indices: 1188421--1188538 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
1188411 CTGCACGGCC
* * *
1188421 ATGTGTCAGGCCGTGTGTGACACACGGTATGGGCTATTTGGGTCATGTGGACCACACGGAT
1 ATGTGTCAGGCCGTGTGGGACACACGGTATAGGCTATTTGGGCCATGTGGACCACACGGAT
* * * *
1188482 ATGTGTGAGGCCGTGTGGGTCATACGGGT-TAGGCTATTTGGGCCATGTGGGCCACAC
1 ATGTGTCAGGCCGTGTGGGACACAC-GGTATAGGCTATTTGGGCCATGTGGACCACAC
1188539 AAGCATGCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 46 0.94
62 3 0.06
ACGTcount: A:0.18, C:0.19, G:0.36, T:0.26
Consensus pattern (61 bp):
ATGTGTCAGGCCGTGTGGGACACACGGTATAGGCTATTTGGGCCATGTGGACCACACGGAT
Found at i:1189418 original size:5 final size:5
Alignment explanation
Indices: 1189408--1189435 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1189398 TTTTGTGTTC
1189408 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1189436 TCTCAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1193859 original size:5 final size:5
Alignment explanation
Indices: 1193849--1193881 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1193839 TTGTGTGTTC
1193849 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1193882 TCTCACTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1197965 original size:20 final size:20
Alignment explanation
Indices: 1197940--1197989 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1197930 ATATATATGC
*
1197940 TTTTATTTTTG-CATTTTTTA
1 TTTTATTTTTGTCA-TTATTA
* *
1197960 TTTTATTATCGTCATTATTA
1 TTTTATTTTTGTCATTATTA
1197980 TTTTATTTTT
1 TTTTATTTTT
1197990 ATTTTTGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTATTTTTGTCATTATTA
Found at i:1201683 original size:13 final size:14
Alignment explanation
Indices: 1201667--1201708 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1201657 TTTCAATTTT
1201667 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
1201680 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
1201695 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1201709 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1201693 original size:16 final size:16
Alignment explanation
Indices: 1201671--1201707 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1201661 AATTTTATTT
1201671 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
1201688 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
1201703 TAATA
1 TAATA
1201708 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:1201760 original size:15 final size:15
Alignment explanation
Indices: 1201740--1201796 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1201730 ATTCAAGATT
1201740 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1201755 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
1201774 AATATATTAATAATA
1 AATATTTTAATAATA
*
1201789 TATATTTT
1 AATATTTT
1201797 GTAATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1201792 original size:19 final size:20
Alignment explanation
Indices: 1201747--1201792 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1201737 ATTAATATTT
1201747 TAATA-ATAAATATTTATTAA
1 TAATATATAAATA-TTATTAA
1201767 -AAT-TATAAATA-TATTAA
1 TAATATATAAATATTATTAA
1201784 TAATATATA
1 TAATATATA
1201793 TTTTGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
19 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATATAAATATTATTAA
Found at i:1202844 original size:39 final size:38
Alignment explanation
Indices: 1202783--1202883 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 38
1202773 TAAATCAAGC
* * *
1202783 TTAATATTATT--ATATTGATAATAAAATTTATTTTTATTT
1 TTAATATTATTAAATATTAAT-ATAAAA--TATTATAATTT
1202822 TT-ATAATTATTAAAATATTAATATAAAATATTATAATTT
1 TTAAT-ATTATT-AAATATTAATATAAAATATTATAATTT
*
1202861 TTAATATTATTAATTATTAATAT
1 TTAATATTATTAAATATTAATAT
1202884 TTAATCATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
38 13 0.25
39 25 0.47
40 2 0.04
41 6 0.11
42 7 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (38 bp):
TTAATATTATTAAATATTAATATAAAATATTATAATTT
Found at i:1202877 original size:46 final size:47
Alignment explanation
Indices: 1202812--1202903 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 47
1202802 AATAAAATTT
* *
1202812 ATTTTTATTTTTATAATTATTAAAATATTAAT-ATA-AA-ATATTATA
1 ATTTTTAATATTATAATTATTAAAAT-TTAATCATATAATATATTATA
*
1202857 ATTTTTAATATTATTAATTATTAATATTTAATCATATAATATATTAT
1 ATTTTTAATATTA-TAATTATTAAAATTTAATCATATAATATATTAT
1202904 TAATATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 16 0.40
46 15 0.38
47 2 0.05
48 7 0.17
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (47 bp):
ATTTTTAATATTATAATTATTAAAATTTAATCATATAATATATTATA
Found at i:1202902 original size:26 final size:25
Alignment explanation
Indices: 1202827--1202909 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 25
1202817 TATTTTTATA
*
1202827 ATTATTAAAATATTAATATA-AA-AT
1 ATTATTAATAT-TTAATATATAATAT
* *
1202851 ATTA-TAATTTTTAATAT-TATTA-
1 ATTATTAATATTTAATATATAATAT
1202873 ATTATTAATATTTAATCATATAATAT
1 ATTATTAATATTTAAT-ATATAATAT
1202899 ATTATTAATAT
1 ATTATTAATAT
1202910 AATTGATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
22 12 0.25
23 15 0.31
24 6 0.12
25 4 0.08
26 11 0.23
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTATTAATATTTAATATATAATAT
Found at i:1202911 original size:16 final size:16
Alignment explanation
Indices: 1202837--1202912 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
1202827 ATTATTAAAA
*
1202837 TATTAATATAAAATAT
1 TATTAATATAATATAT
**
1202853 TA-TAAT-TTTTAATAT
1 TATTAATATAAT-ATAT
1202868 TATTAATTATTAATAT-T
1 TATTAA-TA-TAATATAT
* *
1202885 TAATCATATAATATAT
1 TATTAATATAATATAT
1202901 TATTAATATAAT
1 TATTAATATAAT
1202913 TGATATAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.02
15 16 0.36
16 18 0.40
17 6 0.13
18 2 0.04
19 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTAATATAATATAT
Found at i:1202977 original size:14 final size:15
Alignment explanation
Indices: 1202958--1202999 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1202948 TTTCAATTTA
1202958 TTTTAATAATA-AAT
1 TTTTAATAATATAAT
*
1202972 TTTTAAAAATAATAAT
1 TTTTAATAAT-ATAAT
*
1202988 TTTAAATAATAT
1 TTTTAATAATAT
1203000 TCTTCACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAATAATATAAT
Found at i:1204330 original size:16 final size:17
Alignment explanation
Indices: 1204306--1204338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1204296 ATAATTTTAG
1204306 TTTTATT-AATTTAAAT
1 TTTTATTAAATTTAAAT
*
1204322 TTTTTTTAAATTTAAAT
1 TTTTATTAAATTTAAAT
1204339 ACTTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTAAATTTAAAT
Found at i:1206502 original size:12 final size:12
Alignment explanation
Indices: 1206487--1206531 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1206477 CAATAGTGAA
1206487 AATAATAAATAT
1 AATAATAAATAT
1206499 AATAATAAATAT
1 AATAATAAATAT
* *
1206511 AATGATATATAT
1 AATAATAAATAT
1206523 -ATAA-AAATA
1 AATAATAAATA
1206532 ATACTACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 4 0.14
11 3 0.10
12 22 0.76
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:1206949 original size:2 final size:2
Alignment explanation
Indices: 1206937--1206971 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1206927 GAGTATAATC
*
1206937 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1206972 TAAAAGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1209628 original size:74 final size:75
Alignment explanation
Indices: 1209480--1209645 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 75
1209470 GAAAAGTGTG
** *
1209480 AAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATA
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
* **
1209540 CTGAGCTGTG
66 CCGAGCTGAA
1209550 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TCCCAT
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-CCAT
*
1209613 ACCGAGTTGAA
65 ACCGAGCTGAA
1209624 AAATGTAGGTATGGTATT-TCAA
1 AAATGTAGGTATGGTATTATCAA
1209646 TGAGGAAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 14 0.17
73 9 0.11
74 46 0.55
75 14 0.17
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
CCGAGCTGAA
Found at i:1209643 original size:35 final size:35
Alignment explanation
Indices: 1209480--1209643 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
1209470 GAAAAGTGTG
* **
1209480 AAATGTAGGTATGGTATCAT-CCATACTGAGTTGTG
1 AAATGTAGGTATGGTAT-TTCCCATACTGAGTTGAA
* **
1209515 AAATGTAGGTATGGTATTAT-CCATACTGAGCTGTG
1 AAATGTAGGTATGGTATT-TCCCATACTGAGTTGAA
1209550 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 AAATGTAGGTATGGTATT-TC----CCATACTGAGTTGAA
* *
1209589 AAATGTAGGTATGGCATTTCCCATACCGAGTTGAA
1 AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
1209624 AAATGTAGGTATGGTATTTC
1 AAATGTAGGTATGGTATTTC
1209644 AATGAGGAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
34 11 0.10
35 73 0.64
38 2 0.02
39 17 0.15
40 11 0.10
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (35 bp):
AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
Found at i:1217112 original size:74 final size:75
Alignment explanation
Indices: 1216964--1217129 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 75
1216954 GAAAAGTGTG
** *
1216964 AAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATA
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
* **
1217024 CTGAGCTGTG
66 CCGAGCTGAA
1217034 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TCCCAT
1 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-CCAT
*
1217097 ACCGAGTTGAA
65 ACCGAGCTGAA
1217108 AAATGTAGGTATGGTATT-TCAA
1 AAATGTAGGTATGGTATTATCAA
1217130 TGAGGAAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 14 0.17
73 9 0.11
74 46 0.55
75 14 0.17
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
AAATGTAGGTATGGTATTATCAAATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATA
CCGAGCTGAA
Found at i:1217127 original size:35 final size:35
Alignment explanation
Indices: 1216964--1217127 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
1216954 GAAAAGTGTG
* **
1216964 AAATGTAGGTATGGTATCAT-CCATACTGAGTTGTG
1 AAATGTAGGTATGGTAT-TTCCCATACTGAGTTGAA
* **
1216999 AAATGTAGGTATGGTATTAT-CCATACTGAGCTGTG
1 AAATGTAGGTATGGTATT-TCCCATACTGAGTTGAA
1217034 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 AAATGTAGGTATGGTATT-TC----CCATACTGAGTTGAA
* *
1217073 AAATGTAGGTATGGCATTTCCCATACCGAGTTGAA
1 AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
1217108 AAATGTAGGTATGGTATTTC
1 AAATGTAGGTATGGTATTTC
1217128 AATGAGGAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
34 11 0.10
35 73 0.64
38 2 0.02
39 17 0.15
40 11 0.10
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (35 bp):
AAATGTAGGTATGGTATTTCCCATACTGAGTTGAA
Found at i:1218835 original size:86 final size:87
Alignment explanation
Indices: 1218690--1219055 Score: 494
Period size: 86 Copynumber: 4.3 Consensus size: 87
1218680 TAATTTTTAG
* * * * *
1218690 CCTGTTACCCTACTGCTTAGGGGATTAAGG--CTTGTCATCTTTGATTTGTTTCC-CTACTGCTT
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTT-TCGTCTTCGATCTG-CTCCACTACTGCTT
** * * *
1218752 AGGG-TTTTAGATCTGTAAACTCAA
64 AGGGAGATAAGATCTG-CAATTCAA
1218776 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTT-GTCTTCGATCTGCTCCACTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTTCGTCTTCGATCTGCTCCACTACTGCTTAG
*
1218840 GGAGATAAGATCTGCAATTTAA
66 GGAGATAAGATCTGCAATTCAA
1218862 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTT-TTTCGTCTTCGATCTGCTCCACTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTTCGTCTTCGATCTGCTCCACTACTGCTTAG
1218926 GGAGATAAGATCTGCAATTCAA
66 GGAGATAAGATCTGCAATTCAA
*
1218948 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTC-TTCGTCTTCGATCTGCTCCACGACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTTCGTCTTCGATCTGCTCCACTACTGCTTAG
* ***
1219012 GGAGATAAGATCTACAATTTGG
66 GGAGATAAGATCTGCAATTCAA
* *
1219034 TCTGTTTCCCTACTGCTTAGGG
1 CCTGTTACCCTACTGCTTAGGG
1219056 CGATAATATC
Statistics
Matches: 255, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
85 6 0.02
86 237 0.93
87 9 0.04
88 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (87 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTTCGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGCAATTCAA
Found at i:1218839 original size:44 final size:44
Alignment explanation
Indices: 1218785--1219013 Score: 169
Period size: 44 Copynumber: 5.3 Consensus size: 44
1218775 ACCTGTTACC
1218785 CTACTGCTTAGGGGTTTAAGGTTCTTTGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTTGTCTTCGATCTGCTCCA
* * ** * *
1218829 CTACTGCTTAGGGAG-ATAA-GATC--TG-CAATTTAACCTGTTACC-
1 CTACTGCTTAGGG-GTTTAAGGTTCTTTGTC--TTCGATCTGCT-CCA
1218871 CTACTGCTTAGGGGTTTAAGGTT-TTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTT-GTCTTCGATCTGCTCCA
* * * * *
1218915 CTACTGCTTAGGGAG-ATAA-GATC--TG-CAATTCAACCTGTTACC-
1 CTACTGCTTAGGG-GTTTAAGGTTCTTTGTC--TTCGATCTGCT-CCA
*
1218957 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTTGTCTTCGATCTGCTCCA
*
1219001 CGACTGCTTAGGG
1 CTACTGCTTAGGG
1219014 AGATAAGATC
Statistics
Matches: 139, Mismatches: 24, Indels: 44
0.67 0.12 0.21
Matches are distributed among these distances:
40 2 0.01
41 5 0.04
42 48 0.35
43 18 0.13
44 60 0.43
45 4 0.03
46 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (44 bp):
CTACTGCTTAGGGGTTTAAGGTTCTTTGTCTTCGATCTGCTCCA
Found at i:1218883 original size:42 final size:42
Alignment explanation
Indices: 1218829--1218969 Score: 135
Period size: 42 Copynumber: 3.3 Consensus size: 42
1218819 ATCTGCTCCA
1218829 CTACTGCTTAGGGAGATAAGATCTGCAATTTAACCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTAACCTGTTACC
* * * * * * * *
1218871 CTACTGCTTAGGG-GTTTAAGGTTTTTC-GTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGAG-ATAA-GATCTGCAAT-TT-AACCTGTTACC
*
1218914 ACTACTGCTTAGGGAGATAAGATCTGCAATTCAACCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAATTTAACCTGTTACC
1218957 CTACTGCTTAGGG
1 CTACTGCTTAGGG
1218970 GTTTAAGGTT
Statistics
Matches: 74, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
41 1 0.01
42 35 0.47
43 15 0.20
44 22 0.30
45 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (42 bp):
CTACTGCTTAGGGAGATAAGATCTGCAATTTAACCTGTTACC
Found at i:1219093 original size:172 final size:170
Alignment explanation
Indices: 1218685--1219100 Score: 462
Period size: 172 Copynumber: 2.4 Consensus size: 170
1218675 ATGTTTAATT
* * * * * *
1218685 TTTAGCCTGTTACCCTACTGCTTAGGGG-ATTAAG-GCTTGTCATCTTTGATTTGTTTCCCTACT
1 TTTAACCTGTTACCCTACTGCTTAGGGGTA-TAAGATC-TATAAACTTCGA-TTG-TTCCCTACT
** * *
1218748 GCTTAGGGTTTTAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTTG
62 GCTTAGGGGATAAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCG
* *
1218813 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAA
127 TCTTCGATCTGCTCCACGACTGCTTAGGGAGATAAGATCTACAA
* * * * *** *
1218857 TTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTTTCGTCTTCGATCTGCTCCACTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGTATAAGATCTATAAACTTCGAT-TGTTCC-CTACTGC
* *
1218922 TTAGGGAGATAAGATCTG-CAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGT
64 TTAGGG-GATAAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGT
1218986 CTTCGATCTGCTCCACGACTGCTTAGGGAGATAAGATCTACAA
128 CTTCGATCTGCTCCACGACTGCTTAGGGAGATAAGATCTACAA
*** * * *
1219029 TTTGGTCTGTTTCCCTACTGCTTAGGGCG-ATAATATCTATAAACTTCAGCTTGTTACCCTACTG
1 TTTAACCTGTTACCCTACTGCTTAGGG-GTATAAGATCTATAAACTTC-GATTGTT-CCCTACTG
1219093 CTTAGGGG
63 CTTAGGGG
1219101 GTTAAAGCTT
Statistics
Matches: 206, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
171 5 0.02
172 188 0.91
173 13 0.06
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (170 bp):
TTTAACCTGTTACCCTACTGCTTAGGGGTATAAGATCTATAAACTTCGATTGTTCCCTACTGCTT
AGGGGATAAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTT
CGATCTGCTCCACGACTGCTTAGGGAGATAAGATCTACAA
Found at i:1219295 original size:43 final size:44
Alignment explanation
Indices: 1219211--1219329 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 44
1219201 GATTTTCAGC
* *
1219211 CTGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAATTTGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGAT
* * *
1219255 -TGTTACCCTACTGGTTAGGGGGTTAAAGCTCAT-T-ATTTTGGAT
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAATTTGGAT
* * *
1219298 CTGTTTCCCTACTGCTTAGGGTGATAAGATCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT
1219330 AAGAATTTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
42 1 0.02
43 34 0.55
44 26 0.42
45 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGAT
Found at i:1227187 original size:9 final size:9
Alignment explanation
Indices: 1227169--1227200 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1227159 TGCAATGCTG
1227169 ATGC-ATGA
1 ATGCAATGA
1227177 ATGCAATGA
1 ATGCAATGA
1227186 ATGCAATGA
1 ATGCAATGA
1227195 ATGCAA
1 ATGCAA
1227201 AGAAAATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (9 bp):
ATGCAATGA
Found at i:1231306 original size:12 final size:12
Alignment explanation
Indices: 1231291--1231349 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
1231281 CAATAGTGAA
1231291 AATAATAAATAT
1 AATAATAAATAT
1231303 AATAATAAATAT
1 AATAATAAATAT
* *
1231315 AATGATATATAT
1 AATAATAAATAT
1231327 -ATAA-AAA-AT
1 AATAATAAATAT
* *
1231336 AATACTACATAT
1 AATAATAAATAT
1231348 AA
1 AA
1231350 AGAGTATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 5 0.13
11 5 0.13
12 26 0.68
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:1231337 original size:30 final size:33
Alignment explanation
Indices: 1231303--1231363 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
1231293 TAATAAATAT
*
1231303 AATAATA-A-ATATAATGA-TATATATATAAAA
1 AATAATACACATATAAAGAGTATATATATAAAA
1231333 AATAATACTACATATAAAGAGTATATATATA
1 AATAATAC-ACATATAAAGAGTATATATATA
1231364 TATATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
32 1 0.04
33 8 0.31
34 10 0.38
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (33 bp):
AATAATACACATATAAAGAGTATATATATAAAA
Found at i:1231756 original size:2 final size:2
Alignment explanation
Indices: 1231744--1231784 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1231734 GAGTATAATC
*
1231744 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1231785 TAAAAGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1233379 original size:24 final size:23
Alignment explanation
Indices: 1233332--1233379 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1233322 TATTATATTT
* *
1233332 TTTAATAATATTAATTATTTATA
1 TTTAATAATAATAATTATTAATA
*
1233355 TTTAATCATAATACATTATTAATA
1 TTTAATAATAATA-ATTATTAATA
1233379 T
1 T
1233380 AATTGATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATAATAATAATTATTAATA
Found at i:1235691 original size:46 final size:44
Alignment explanation
Indices: 1235632--1235746 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1235622 ACAGGACAGA
* *
1235632 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1235678 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1235722 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1235747 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:1235727 original size:44 final size:45
Alignment explanation
Indices: 1235632--1235765 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1235622 ACAGGACAGA
* *
1235632 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1235678 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1235722 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1235766 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1236927 original size:46 final size:44
Alignment explanation
Indices: 1236853--1236967 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1236843 ACAGGACAGA
* *
1236853 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1236899 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1236943 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1236968 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:1236948 original size:44 final size:45
Alignment explanation
Indices: 1236853--1236986 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1236843 ACAGGACAGA
* *
1236853 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1236899 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1236943 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1236987 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1246036 original size:130 final size:126
Alignment explanation
Indices: 1245796--1246283 Score: 599
Period size: 130 Copynumber: 3.8 Consensus size: 126
1245786 AGCCGAGTGA
* * * * *
1245796 AATTTTGAAGGGATATTTGATTATTTTAAAC-AAT-CGAGGAATTGCTACCCAACACGTTAGGGC
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGA--AATTGCAACCCAACACGTTAGGGC
* * * * * * * ** * *
1245859 ACGATCCCACAAATTGCCAAATACCGAATATCGCCTTTGTTTTAGGGATTTTAAAAGACACGAGC
64 ACGATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGA-A-GAG-
1245924 G
126 G
* * * *
1245925 AAATTTCAAAGTGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
1 -AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* *
1245990 CGATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTT--ATGAA-TGG
65 CGATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAGAGG
1246049 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
*
1246114 GATTCCGCGAATTGCTAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAATGAATGG
66 GATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAG-AA-G-A-GG
* *
1246179 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCAT
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
* * *
1246244 GATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
66 GATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTT
1246284 TGAAGAATTT
Statistics
Matches: 316, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
123 110 0.35
124 1 0.00
125 3 0.01
126 2 0.01
127 1 0.00
128 3 0.01
130 190 0.60
131 3 0.01
132 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (126 bp):
AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
GATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAGAGG
Found at i:1246250 original size:253 final size:252
Alignment explanation
Indices: 1245796--1246283 Score: 663
Period size: 253 Copynumber: 1.9 Consensus size: 252
1245786 AGCCGAGTGA
* * *
1245796 AATTTTGAAGGGATATTTGATTATTTTAAACAATCGAGGAATTGCTACCCAACACGTTAGGGCAC
1 AATTTCGAAGGGAAATTTGATTATTTTAAACAATCGA-GAATTGCAACCCAACACGTTAGGGCAC
* * * * * * *
1245861 GATCCCACAAATTGCCAAATACCGAATATCGCCTTTGTTTTAGGGATTTTAAAAGACACGAGCGA
65 GATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACGA
* * *
1245926 AATTTCAAAGTGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
130 AATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCAC
1245991 GATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
195 GATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
* *
1246049 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGA-AATTGCAACCCAACACGTTAGGGCA
1 AATTTCGAAGGGAAATTTGATTATTTTAAAC-AAT-CGAGAATTGCAACCCAACACGTTAGGGCA
* * * * * * * * *
1246113 CGATTCCGCGAATTGCTAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAATGAATG
64 CGATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACG
* * *
1246178 GAATTTCGAAGGGAAATTTGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
129 AAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
* * * *
1246243 TGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
194 CGATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTT
1246284 TGAAGAATTT
Statistics
Matches: 202, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
253 196 0.97
254 3 0.01
255 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (252 bp):
AATTTCGAAGGGAAATTTGATTATTTTAAACAATCGAGAATTGCAACCCAACACGTTAGGGCACG
ATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACGAA
ATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCACG
ATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
Found at i:1258600 original size:6 final size:7
Alignment explanation
Indices: 1258584--1258608 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1258574 TCTATATTTA
1258584 TTTTAAT
1 TTTTAAT
1258591 TTTTAAT
1 TTTTAAT
1258598 TTTTAAT
1 TTTTAAT
1258605 TTTT
1 TTTT
1258609 GAGAAAAACG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:1267718 original size:3 final size:3
Alignment explanation
Indices: 1267710--1267737 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1267700 ACAATGTAAC
1267710 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1267738 TGCTGCCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1273597 original size:127 final size:127
Alignment explanation
Indices: 1273366--1273597 Score: 299
Period size: 127 Copynumber: 1.8 Consensus size: 127
1273356 TGTGGACGAA
** * ** * *
1273366 ATTTTAAAGGGATGTTTGATTCTTTGGATAAACAGAAAATCGAAACCCAGCACATTAGGGCACGA
1 ATTTTAAAGGGAAATTTGATTATTTAAATAAACAGAAAATCAAAACCCAACACATTAGGGCACGA
* * *
1273431 TTTCCCGAATTCCCAAACATCAATCATCGCTTTCGTTTTAAAGTTTAGGAAACGCGGACAGG
66 TTCCCCGAATTCCCAAACATCAAACATCGCTTTCATTTTAAAGTTTAGGAAACGCGGACAGG
*
1273493 ATTTTAAAGGGAAATTTGATTATTTAAATAAAC-GAAAGATCAAAACCCAATACATTAGGGCACG
1 ATTTTAAAGGGAAATTTGATTATTTAAATAAACAGAAA-ATCAAAACCCAACACATTAGGGCACG
* *
1273557 A-TCCCTCGAATTTCTAAACATCAAACATCGCATTT-ATTTTA
65 ATTCCC-CGAATTCCCAAACATCAAACATCGC-TTTCATTTTA
1273598 TAAAGTCAAC
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
126 7 0.08
127 79 0.89
128 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (127 bp):
ATTTTAAAGGGAAATTTGATTATTTAAATAAACAGAAAATCAAAACCCAACACATTAGGGCACGA
TTCCCCGAATTCCCAAACATCAAACATCGCTTTCATTTTAAAGTTTAGGAAACGCGGACAGG
Found at i:1274335 original size:50 final size:49
Alignment explanation
Indices: 1274241--1274336 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
1274231 ATAAATAGTT
* * *
1274241 TATAAAGCAATTTAAAGTAAACAATATATAAAATAATTTAAAACAATAA
1 TATAAAACAATTGAAAGTAAACAATATATAAAACAATTTAAAACAATAA
* *
1274290 TATAAAACAAATTGAAA-TAAATAATATGATATAACAATTTAAAACAA
1 TATAAAAC-AATTGAAAGTAAACAATAT-ATAAAACAATTTAAAACAA
1274337 ATGCTATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
49 16 0.40
50 24 0.60
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.28
Consensus pattern (49 bp):
TATAAAACAATTGAAAGTAAACAATATATAAAACAATTTAAAACAATAA
Found at i:1274338 original size:27 final size:25
Alignment explanation
Indices: 1274121--1274338 Score: 103
Period size: 26 Copynumber: 8.8 Consensus size: 25
1274111 AAAGTACGAA
*
1274121 ATAAA-AAGTTTAAAATAAATAATAT
1 ATAAACAA-TTTAAAACAAATAATAT
* *
1274146 ATAAAAAAGTTTAAAA-TAATAATAT
1 ATAAACAA-TTTAAAACAAATAATAT
* * * * *
1274171 ATGAAACAGTTCAGAATAAACAATAT
1 AT-AAACAATTTAAAACAAATAATAT
* * *
1274197 AT-AA-ATTTTAAAA-TAA-AGTAT
1 ATAAACAATTTAAAACAAATAATAT
* * * * *
1274218 A-AATCAATTTGAAATAAATAGTTT
1 ATAAACAATTTAAAACAAATAATAT
** *
1274242 ATAAAGCAATTTAAAGTAAACAATAT
1 ATAAA-CAATTTAAAACAAATAATAT
*
1274268 ATAAAATAATTTAAAAC-AATAATAT
1 AT-AAACAATTTAAAACAAATAATAT
* * *
1274293 A-AAACAAATTGAAATAAATAATAT
1 ATAAACAATTTAAAACAAATAATAT
1274317 GATATAACAATTTAAAACAAAT
1 -ATA-AACAATTTAAAACAAAT
1274339 GCTATGTGGA
Statistics
Matches: 145, Mismatches: 34, Indels: 26
0.71 0.17 0.13
Matches are distributed among these distances:
21 6 0.04
22 9 0.06
23 18 0.12
24 15 0.10
25 31 0.21
26 49 0.34
27 17 0.12
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.30
Consensus pattern (25 bp):
ATAAACAATTTAAAACAAATAATAT
Found at i:1274438 original size:22 final size:22
Alignment explanation
Indices: 1274411--1274452 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1274401 GATTTATAAT
1274411 AAATAAAAAT-ACAATATAATGA
1 AAAT-AAAATGACAATATAATGA
*
1274433 AAATAAGATGACAATATAAT
1 AAATAAAATGACAATATAAT
1274453 AATGTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (22 bp):
AAATAAAATGACAATATAATGA
Found at i:1274473 original size:20 final size:20
Alignment explanation
Indices: 1274448--1274632 Score: 68
Period size: 20 Copynumber: 9.4 Consensus size: 20
1274438 AGATGACAAT
*
1274448 ATAATAATGTATTAATAAGA
1 ATAATAATATATTAATAAGA
* *
1274468 ATAATAATATATTAGTAATA
1 ATAATAATATATTAATAAGA
* * * * *
1274488 ATAATCATGGAAAATGATAATA
1 ATAATAAT--ATATTAATAAGA
* *
1274510 ATACTAATATTTTAAATAAG-
1 ATAATAATATATT-AATAAGA
1274530 ATAATAATA-A-TAGAT-AGA
1 ATAATAATATATTA-ATAAGA
* * **
1274548 A-AGTAGTAGTAGCAAT-AGTA
1 ATAATAATA-TATTAATAAG-A
* * *
1274568 ATAATAATAAAATAATAATA
1 ATAATAATATATTAATAAGA
*
1274588 ATAATAATA-A-TAATAATA
1 ATAATAATATATTAATAAGA
1274606 ATAATAATA-A-TAATAA-A
1 ATAATAATATATTAATAAGA
1274623 TATAATAATA
1 -ATAATAATA
1274633 AAAATAATTA
Statistics
Matches: 127, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
17 9 0.07
18 37 0.29
19 6 0.05
20 51 0.40
21 10 0.08
22 14 0.11
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (20 bp):
ATAATAATATATTAATAAGA
Found at i:1274572 original size:3 final size:3
Alignment explanation
Indices: 1274561--1274640 Score: 119
Period size: 3 Copynumber: 27.0 Consensus size: 3
1274551 TAGTAGTAGC
*
1274561 AAT AGT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1274608 AAT AAT AAT AAT AA- ATAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
1274641 TAATTTGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
2 3 0.04
3 66 0.94
4 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1290249 original size:16 final size:17
Alignment explanation
Indices: 1290216--1290253 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1290206 GAATCACTGT
1290216 TAAAAAATAATAAATATA
1 TAAAAAATAAT-AATATA
*
1290234 TAAAAAATAAT-TTATA
1 TAAAAAATAATAATATA
1290250 TAAA
1 TAAA
1290254 TATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATAATAATATA
Found at i:1297280 original size:21 final size:18
Alignment explanation
Indices: 1297234--1297282 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 18
1297224 TAATGTCAAA
*
1297234 TTTAGTTTTTATTATTCAC
1 TTTA-TTTTTATTATTAAC
1297253 TTTATTTTTATTAATTTAAC
1 TTTATTTTTATT-A-TTAAC
1297273 TATTATTTTT
1 T-TTATTTTT
1297283 TTGAGCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 5 0.19
21 8 0.31
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTTTATTATTAAC
Found at i:1301296 original size:16 final size:18
Alignment explanation
Indices: 1301260--1301298 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1301250 AATCCAGTTT
1301260 GTTTT-GGTTTCGGATCA
1 GTTTTAGGTTTCGGATCA
1301277 -TTTTAGGTTT-GGAT-A
1 GTTTTAGGTTTCGGATCA
1301292 GTTTTAG
1 GTTTTAG
1301299 TATAGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 14 0.70
17 5 0.25
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.51
Consensus pattern (18 bp):
GTTTTAGGTTTCGGATCA
Found at i:1303143 original size:16 final size:16
Alignment explanation
Indices: 1303122--1303152 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1303112 GATGTTTTAT
1303122 ATTTTTTTTAAAAATA
1 ATTTTTTTTAAAAATA
1303138 ATTTTTTTTAAAAAT
1 ATTTTTTTTAAAAAT
1303153 GTATACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTTTAAAAATA
Found at i:1304420 original size:32 final size:30
Alignment explanation
Indices: 1304350--1304421 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
1304340 ACTAATTATT
* *
1304350 ATTTCATCATTTTTGAAGGGAATAAACATA
1 ATTTTATCATTTTTGAAGGGAATAAACACA
*
1304380 ATTTTATCATTTTTGAAAGGAGACA-AAATACA
1 ATTTTATCATTTTTG-AAGG-GA-ATAAACACA
1304412 ATTTTATCAT
1 ATTTTATCAT
1304422 ACATTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 14 0.39
31 4 0.11
32 17 0.47
33 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (30 bp):
ATTTTATCATTTTTGAAGGGAATAAACACA
Found at i:1305466 original size:31 final size:29
Alignment explanation
Indices: 1305428--1305507 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1305418 ACATTAAAAC
1305428 TATATATGAAATTTGATTTAATGTATAATGT
1 TATATATGAAATTTGATTT--TGTATAATGT
* *
1305459 TATATATGAATTTTGATTTTGTATAATTT
1 TATATATGAAATTTGATTTTGTATAATGT
*
1305488 TATACATGAAATTTTGATTT
1 TATATATGAAA-TTTGATTT
1305508 GATTTGATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.41
30 8 0.18
31 18 0.41
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (29 bp):
TATATATGAAATTTGATTTTGTATAATGT
Found at i:1305481 original size:29 final size:30
Alignment explanation
Indices: 1305428--1305507 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
1305418 ACATTAAAAC
*
1305428 TATATATGAAATTTGATTTAATGTATAATGT
1 TATATATGAATTTTGATTT-ATGTATAATGT
*
1305459 TATATATGAATTTTGATTT-TGTATAATTT
1 TATATATGAATTTTGATTTATGTATAATGT
*
1305488 TATACATGAAATTTTGATTT
1 TATATATG-AATTTTGATTT
1305508 GATTTGATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.36
30 11 0.24
31 18 0.40
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (30 bp):
TATATATGAATTTTGATTTATGTATAATGT
Found at i:1306016 original size:2 final size:2
Alignment explanation
Indices: 1306009--1306038 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1305999 TTTAATATGA
1306009 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
1306039 GTATTCGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1306526 original size:22 final size:22
Alignment explanation
Indices: 1306498--1306563 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1306488 AATATATATT
1306498 TGTATTGTACCTATAAATATAC
1 TGTATTGTACCTATAAATATAC
*
1306520 TGTATTGTACGTATAAATATAC
1 TGTATTGTACCTATAAATATAC
*
1306542 TCTATTGTACCTATAAAATATA
1 TGTATTGTACCTAT-AAATATA
1306564 GTTTAAGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 33 0.82
23 7 0.17
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (22 bp):
TGTATTGTACCTATAAATATAC
Found at i:1316735 original size:4 final size:4
Alignment explanation
Indices: 1316721--1316750 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1316711 ATTAAGACTT
*
1316721 AAAG TAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1316751 GTGATAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:1319665 original size:17 final size:18
Alignment explanation
Indices: 1319639--1319672 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1319629 TTTCAATTAA
*
1319639 ATAAATATTA-AAAATTC
1 ATAAAAATTATAAAATTC
1319656 ATAAAAATTATAAAATT
1 ATAAAAATTATAAAATT
1319673 GATTCAACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTATAAAATTC
Found at i:1321029 original size:2 final size:2
Alignment explanation
Indices: 1321022--1321063 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1321012 GATGCTGCTG
*
1321022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1321064 TCATACCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1327244 original size:50 final size:50
Alignment explanation
Indices: 1327185--1327324 Score: 253
Period size: 50 Copynumber: 2.8 Consensus size: 50
1327175 TAATGTGAAA
1327185 AAACTCAGTTCAATTAACCCAAATTCACACTTGGAAATAGGAGAATTCAT
1 AAACTCAGTTCAATTAACCCAAATTCACACTTGGAAATAGGAGAATTCAT
* *
1327235 AAACTCAGTTCAATTAACCTAAATTCACACTTGGAAATAAGAGAATTCAT
1 AAACTCAGTTCAATTAACCCAAATTCACACTTGGAAATAGGAGAATTCAT
*
1327285 AAACTCAATTCAATTAACCCAAATTCACACTTGGAAATAG
1 AAACTCAGTTCAATTAACCCAAATTCACACTTGGAAATAG
1327325 TAGTATTCGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (50 bp):
AAACTCAGTTCAATTAACCCAAATTCACACTTGGAAATAGGAGAATTCAT
Found at i:1335223 original size:22 final size:23
Alignment explanation
Indices: 1335181--1335223 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1335171 GTATGGTTTG
*
1335181 AAATTAATAAAGTATACATAATA
1 AAATTAATAAAGTATAAATAATA
*
1335204 AAATTAA-AATGTATAAATAA
1 AAATTAATAAAGTATAAATAA
1335224 ATCAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATTAATAAAGTATAAATAATA
Found at i:1336984 original size:34 final size:34
Alignment explanation
Indices: 1336943--1337007 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1336933 AAACACTACG
*
1336943 ATAAATATAATAAATATTTTATTTTATTAAAAAA
1 ATAAATATAATAAATATTTTATTATATTAAAAAA
1336977 ATAAATATAATAAATATTTTATTATATTAAA
1 ATAAATATAATAAATATTTTATTATATTAAA
1337008 TATAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
ATAAATATAATAAATATTTTATTATATTAAAAAA
Found at i:1337002 original size:17 final size:17
Alignment explanation
Indices: 1336948--1337010 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
1336938 CTACGATAAA
1336948 TATAATAAATATTTTAT
1 TATAATAAATATTTTAT
* * * ** * *
1336965 TTTATTAAAAAAATAAA
1 TATAATAAATATTTTAT
1336982 TATAATAAATATTTTAT
1 TATAATAAATATTTTAT
*
1336999 TATATTAAATAT
1 TATAATAAATAT
1337011 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATAATAAATATTTTAT
Found at i:1342607 original size:2 final size:2
Alignment explanation
Indices: 1342590--1342629 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1342580 GAAAATAACA
* * *
1342590 AT AT AT AC AT AA AT AT AT AT AT AC 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
1342630 GTTGATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1342609 original size:16 final size:16
Alignment explanation
Indices: 1342590--1342628 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1342580 GAAAATAACA
1342590 ATATATACATAAATAT
1 ATATATACATAAATAT
*
1342606 ATATATACATATATAT
1 ATATATACATAAATAT
1342622 ATATATA
1 ATATATA
1342629 TGTTGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATACATAAATAT
Found at i:1342919 original size:28 final size:28
Alignment explanation
Indices: 1342892--1342956 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
1342882 TATAATAATA
*
1342892 ACATGTACATAATAC-GGTATTAAAAAT
1 ACATATACATAATACAGGTATTAAAAAT
* * * *
1342919 ATATATATATAATACAGTTATTAAAAAA
1 ACATATACATAATACAGGTATTAAAAAT
*
1342947 ATATATACAT
1 ACATATACAT
1342957 GAGATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (28 bp):
ACATATACATAATACAGGTATTAAAAAT
Found at i:1343244 original size:21 final size:21
Alignment explanation
Indices: 1343218--1343319 Score: 79
Period size: 21 Copynumber: 4.9 Consensus size: 21
1343208 AGTTATTAAT
*
1343218 AATATATATATAATATAATAA
1 AATATATACATAATATAATAA
*
1343239 AATATATGA-ATAATAGGATATAAA
1 AATATAT-ACATAATA-TA-AT-AA
*
1343263 AATATAAACATAATAT-ATAA
1 AATATATACATAATATAATAA
* *
1343283 AAAATATAC-T-ATTTAA-AA
1 AATATATACATAATATAATAA
1343301 AATAATATACATAATATAA
1 AAT-ATATACATAATATAA
1343320 GAGTATTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
18 7 0.11
19 8 0.12
20 10 0.16
21 20 0.31
22 2 0.03
23 3 0.05
24 14 0.22
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AATATATACATAATATAATAA
Found at i:1343497 original size:24 final size:24
Alignment explanation
Indices: 1343446--1343499 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1343436 GTATAACAAT
1343446 GATAA-AAAAATAATAATAGTGAAA
1 GATAATAAAAATAATAATAG-GAAA
*
1343470 -ATAATAAATATAATAATA-GAAA
1 GATAATAAAAATAATAATAGGAAA
1343492 CGATAATA
1 -GATAATA
1343500 CTATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (24 bp):
GATAATAAAAATAATAATAGGAAA
Found at i:1343588 original size:28 final size:29
Alignment explanation
Indices: 1343557--1343612 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1343547 ATTAATAATG
* *
1343557 AATAT-AATATTATAAT-ACTAATAATAAC
1 AATATGAA-ATTAAAATAACTAAAAATAAC
1343585 AATATGAAATTAAAATAACTAAAAATAA
1 AATATGAAATTAAAATAACTAAAAATAA
1343613 TACCATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (29 bp):
AATATGAAATTAAAATAACTAAAAATAAC
Found at i:1343701 original size:18 final size:18
Alignment explanation
Indices: 1343672--1343717 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1343662 TGGCATAAAA
*
1343672 AATAATAGTATT-GATAAT
1 AATAATAATATTAGA-AAT
*
1343690 ATTAATAATATTAGAAAT
1 AATAATAATATTAGAAAT
1343708 AATAATAATA
1 AATAATAATA
1343718 ACAATACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (18 bp):
AATAATAATATTAGAAAT
Found at i:1344383 original size:21 final size:21
Alignment explanation
Indices: 1344328--1344383 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
1344318 TATATGAATG
1344328 AAAAAAATGAGAAGATGAAAAA
1 AAAAAAATGA-AAGATGAAAAA
* * *
1344350 AAAAGATTCGAAATATGAAAAA
1 AAAAAAAT-GAAAGATGAAAAA
1344372 AAAAAAATGAAA
1 AAAAAAATGAAA
1344384 ATCACCTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.12
Consensus pattern (21 bp):
AAAAAAATGAAAGATGAAAAA
Found at i:1348527 original size:32 final size:33
Alignment explanation
Indices: 1348491--1348561 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
1348481 GATAATTAGA
1348491 TAATTAAATCAAGCCTTAA-TATAGAATTGA-TT
1 TAATTAAATCAAGCCTTAATTA-AGAATTGATTT
* *
1348523 TAATTAAATCAAGGCTTAATTAAGCATTGATTT
1 TAATTAAATCAAGCCTTAATTAAGAATTGATTT
1348556 TAATTA
1 TAATTA
1348562 CCAATAGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (33 bp):
TAATTAAATCAAGCCTTAATTAAGAATTGATTT
Found at i:1354420 original size:14 final size:14
Alignment explanation
Indices: 1354401--1354429 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1354391 AAAAAGAAAC
1354401 TAAATTGGAGTTTA
1 TAAATTGGAGTTTA
1354415 TAAATTGGAGTTTA
1 TAAATTGGAGTTTA
1354429 T
1 T
1354430 CTAAATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TAAATTGGAGTTTA
Found at i:1362636 original size:16 final size:16
Alignment explanation
Indices: 1362615--1362654 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1362605 ATGCTAGTAA
1362615 ATAATGATAATGGACT
1 ATAATGATAATGGACT
1362631 ATAATGATAATGGACT
1 ATAATGATAATGGACT
1362647 ATAATGAT
1 ATAATGAT
1362655 GATAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (16 bp):
ATAATGATAATGGACT
Found at i:1362693 original size:3 final size:3
Alignment explanation
Indices: 1362685--1362742 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
1362675 AATAACAATT
* * * *
1362685 TAA TAA TAA TAA CAA TAA TTA TAA TAT TAA -CA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1362730 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
1362743 GTGTAATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.93
4 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1362962 original size:67 final size:66
Alignment explanation
Indices: 1362883--1363024 Score: 177
Period size: 63 Copynumber: 2.2 Consensus size: 66
1362873 AAATTATAAA
* * *
1362883 AATAAGTAAATAAGTAAAAATAAA-AAGAT-TCATGAAAGGCTAAAATTTCAATAATAAATGAAC
1 AATAA-TAAA-AA-TAAAAATAAATAA-ATCTCATGAAAAGCTAAAATTGCAATAATAAATAAAC
1362946 AAAT-
62 AAATG
*
1362950 AATAAT-AAAAT-AAAATAAATAAATCTCATGAAAAGCTAAAATTGCAATAATAAATAAATAAAT
1 AATAATAAAAATAAAAATAAATAAATCTCATGAAAAGCTAAAATTGCAATAATAAATAAACAAAT
1363013 G
66 G
1363014 AATAATAAAAA
1 AATAATAAAAA
1363025 AATAAAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
62 10 0.15
63 37 0.55
64 8 0.12
65 6 0.09
66 1 0.01
67 5 0.07
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.24
Consensus pattern (66 bp):
AATAATAAAAATAAAAATAAATAAATCTCATGAAAAGCTAAAATTGCAATAATAAATAAACAAAT
G
Found at i:1362982 original size:63 final size:62
Alignment explanation
Indices: 1362899--1363086 Score: 210
Period size: 63 Copynumber: 3.1 Consensus size: 62
1362889 TAAATAAGTA
* *
1362899 AAAATAAAAAGATTCATGAAAGGCTAAAATTTCAATAATAAATGAACAAAT-AATAATAAAAT
1 AAAATAAAAA-ATTCATGAAAGGCTAAAATTTCAATAATAAATAAATAAATAAATAATAAAAT
* * *
1362961 AAAATAAATAAATCTCATGAAAAGCTAAAATTGCAATAATAAATAAATAAATGAATAAT-AAA-
1 AAAATAAA-AAAT-TCATGAAAGGCTAAAATTTCAATAATAAATAAATAAATAAATAATAAAAT
* * *
1363023 AAAATAAAAAAATTTATGAAAGACTCAAAA-TT--A-AATAAATAAATAAGTAAATAATAAAAT
1 AAAAT-AAAAAATTCATGAAAGGCT-AAAATTTCAATAATAAATAAATAAATAAATAATAAAAT
1363083 AAAA
1 AAAA
1363087 CAGCTTGTAA
Statistics
Matches: 109, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
58 20 0.18
59 4 0.04
60 4 0.04
61 10 0.09
62 23 0.21
63 42 0.39
64 6 0.06
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.24
Consensus pattern (62 bp):
AAAATAAAAAATTCATGAAAGGCTAAAATTTCAATAATAAATAAATAAATAAATAATAAAAT
Found at i:1363065 original size:62 final size:60
Alignment explanation
Indices: 1362898--1363079 Score: 206
Period size: 62 Copynumber: 2.9 Consensus size: 60
1362888 GTAAATAAGT
* * * *
1362898 AAAAATAAAAAGATTCATGAAAGGCTAAAATTTCAATAATAAATGAACAAATAATAATAAA
1 AAAAATAAAAAAATTCATGAAAGACTAAAA-TTCAATAATAAATAAATAAATAATAATAAA
*
1362959 ATAAAATAAATAAATCTCATGAAA-AGCTAAAATTGCAATAATAAATAAATAAATGAATAAT-AA
1 A-AAAATAAAAAAAT-TCATGAAAGA-CTAAAATT-CAATAATAAATAAATAAAT-AATAATAAA
* * *
1363022 AAAAATAAAAAAATTTATGAAAGACTCAAAATTAAATAAATAAATAAGTAAATAATAA
1 AAAAATAAAAAAATTCATGAAAGACT-AAAATTCAAT-AATAAATAAATAAATAATAA
1363080 AATAAAACAG
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
61 18 0.17
62 46 0.44
63 34 0.33
64 6 0.06
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (60 bp):
AAAAATAAAAAAATTCATGAAAGACTAAAATTCAATAATAAATAAATAAATAATAATAAA
Found at i:1364368 original size:7 final size:7
Alignment explanation
Indices: 1364336--1364366 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1364326 ACTTTAATGG
1364336 ATTTATT
1 ATTTATT
1364343 ATTTATT
1 ATTTATT
1364350 ATTTATT
1 ATTTATT
1364357 ATTT-TT
1 ATTTATT
1364363 ATTT
1 ATTT
1364367 TTGGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:1367943 original size:39 final size:41
Alignment explanation
Indices: 1367857--1367943 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 41
1367847 TACGTACATG
* *
1367857 TATATATATAGTATTATCTTTTATTACTTTATTTTATTATA
1 TATATATATAGTATGATCTTTTATTACTTCATTTTATTATA
* *
1367898 TATATATATAGTATGGT-TTTTAATTACTTCATTATTTTTAT-
1 TATATATATAGTATGATCTTTT-ATTACTTCATT-TTATTATA
1367939 TATAT
1 TATAT
1367944 TTTATTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
40 4 0.10
41 30 0.75
42 6 0.15
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (41 bp):
TATATATATAGTATGATCTTTTATTACTTCATTTTATTATA
Found at i:1367950 original size:19 final size:19
Alignment explanation
Indices: 1367928--1367966 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1367918 TAATTACTTC
1367928 ATTATTTTTATTATATTTT
1 ATTATTTTTATTATATTTT
* *
1367947 ATTATTTTTTTTGTATTTT
1 ATTATTTTTATTATATTTT
1367966 A
1 A
1367967 AAACCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
ATTATTTTTATTATATTTT
Found at i:1368704 original size:2 final size:2
Alignment explanation
Indices: 1368697--1368721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1368687 ACATACTTTA
1368697 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 A
1368722 GCACCATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1371528 original size:132 final size:131
Alignment explanation
Indices: 1371266--1371527 Score: 328
Period size: 132 Copynumber: 2.0 Consensus size: 131
1371256 TCTCGCTTTG
* * * * * * * *
1371266 GAAAACGTGAATGAAATTTAAAGGGATATTCGATTATTTTGCATAAACGAGAAATTGCAACCCAG
1 GAAAACATGAACGAAATTTAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTACAACCCAG
* * * * *
1371331 CACGATAGGGCACGTTTCCCCGAATTGCCGAACGTCAAACATTTCCTTCGTTTTAAAAATTTTTT
66 CACGATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATGTCCTCCGTTTTAAAAATTTTTT
1371396 A
131 A
**
1371397 GAAAACATGAACGAAATTCTAAAGAGACATCCGATTATTTTGGGCAAACAAGAAATTACAACCCA
1 GAAAACATGAACGAAATT-TAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTACAACCCA
* * *
1371462 GCATGATAGGGCACGATTCCCCGAATTGCTAAACATCGAACATCGT-CTCCGTTTTAAAGAATTT
65 GCACGATAGGGCACGATTCCCCGAATTGCCAAACATCAAACAT-GTCCTCCGTTTTAAA-AATTT
1371526 TT
128 TT
1371528 AAACGAATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
131 16 0.15
132 86 0.78
133 8 0.07
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (131 bp):
GAAAACATGAACGAAATTTAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTACAACCCAG
CACGATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATGTCCTCCGTTTTAAAAATTTTTT
A
Found at i:1371829 original size:3 final size:3
Alignment explanation
Indices: 1371823--1371857 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1371813 TAATAATAAT
1371823 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1371858 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1371862 original size:3 final size:3
Alignment explanation
Indices: 1371856--1371904 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
1371846 CAACAACAAC
*
1371856 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1371902 AAT
1 AAT
1371905 GCAATGATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Done.