Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004920.1 Hibiscus syriacus cultivar Beakdansim tig00011079_pilon, whole genome shotgun sequence
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: 1590857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 6 of 7
Found at i:1157683 original size:8 final size:8
Alignment explanation
Indices: 1157665--1157720 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1157655 CTTGTTTCTC
1157665 TTTTCTTTG
1 TTTT-TTTG
1157674 TTTTTTTG
1 TTTTTTTG
1157682 -TTTTTTG
1 TTTTTTTG
1157689 TTTTTTTTG
1 -TTTTTTTG
*
1157698 CTTTTTTG
1 TTTTTTTG
* *
1157706 CTTCTTTTC
1 -TTTTTTTG
1157715 TTTTTT
1 TTTTTT
1157721 GTTCTTGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 7 0.18
8 16 0.41
9 16 0.41
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1157696 original size:17 final size:16
Alignment explanation
Indices: 1157670--1157723 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1157660 TTCTCTTTTC
1157670 TTTG-TTTTTTTGTTT
1 TTTGTTTTTTTTGTTT
1157685 TTTGTTTTTTTTGCTTT
1 TTTGTTTTTTTTG-TTT
* * *
1157702 TTTGCTTCTTTTCTTT
1 TTTGTTTTTTTTGTTT
1157718 TTTGTT
1 TTTGTT
1157724 CTTGATTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 4 0.12
16 16 0.48
17 13 0.39
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTGTTTTTTTTGTTT
Found at i:1157725 original size:15 final size:16
Alignment explanation
Indices: 1157677--1157726 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1157667 TTCTTTGTTT
* * *
1157677 TTTTGTTTTTTGTTTT
1 TTTTCTTTTTTGCTTC
1157693 TTTTGCTTTTTTGCTTC
1 TTTT-CTTTTTTGCTTC
1157710 TTTTCTTTTTTG-TTC
1 TTTTCTTTTTTGCTTC
1157725 TT
1 TT
1157727 GATTGGATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.17
16 12 0.40
17 13 0.43
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTTGCTTC
Found at i:1166979 original size:30 final size:30
Alignment explanation
Indices: 1166927--1167008 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
1166917 CACTTTATTT
1166927 ATCTTTATTGCTTTGA-TTTTTTTATAGGA
1 ATCTTTATTGCTTTGATTTTTTTTATAGGA
1166956 ATCTTTATTGCTTTGATTTTTTTTATAGGA
1 ATCTTTATTGCTTTGATTTTTTTTATAGGA
*
1166986 ATCTTTATTGCTTTGATATTTTT
1 ATCTTTATTGCTTTGATTTTTTT
1167009 GATCAGTTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 16 0.31
30 35 0.69
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (30 bp):
ATCTTTATTGCTTTGATTTTTTTTATAGGA
Found at i:1170085 original size:23 final size:23
Alignment explanation
Indices: 1170059--1170122 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1170049 CAGCTCATAT
1170059 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1170082 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1170105 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1170123 TATAATAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1170312 original size:103 final size:103
Alignment explanation
Indices: 1170133--1170355 Score: 428
Period size: 103 Copynumber: 2.2 Consensus size: 103
1170123 TATAATAATG
1170133 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
1170198 CACCAGACTTCACACATGTTCCAAATAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1170236 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1170301 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
1170339 TCCCGAAAGACCACATA
1 TCCCGAAGGACCACATA
1170356 GACCCTCGAC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:1171215 original size:64 final size:64
Alignment explanation
Indices: 1171107--1171327 Score: 254
Period size: 64 Copynumber: 3.5 Consensus size: 64
1171097 TAATGAAGGT
* * * *
1171107 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
1171170 G
64 G
* *
1171171 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
1171235 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
1171298 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1171328 ACACCTTCAA
Statistics
Matches: 137, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 127 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:1175538 original size:23 final size:23
Alignment explanation
Indices: 1175501--1175564 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1175491 CAGCTCATAT
*
1175501 AATTGCACCGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1175524 AATTGCATCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1175547 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1175565 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1175754 original size:103 final size:103
Alignment explanation
Indices: 1175575--1175797 Score: 446
Period size: 103 Copynumber: 2.2 Consensus size: 103
1175565 TATAATAATG
1175575 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1175640 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1175678 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1175743 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1175781 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
1175798 GACCCTCGAC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 120 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:1176638 original size:45 final size:45
Alignment explanation
Indices: 1176567--1176673 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
1176557 ATGCACTACT
* * *
1176567 GATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 GATGCATCGATGCACT-AAATGCATTCGATGTT-TCATTATTAATGG
* *
1176612 GATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGG
1 GATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGG
*
1176657 GATGCATTGATGCACTA
1 GATGCATCGATGCACTA
1176674 TTTATGCATC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (45 bp):
GATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGG
Found at i:1176727 original size:64 final size:64
Alignment explanation
Indices: 1176613--1176737 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 64
1176603 TATTACTGGG
* * * *
1176613 ATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGGATGCATTGATGCACTATTT
1 ATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGAGATGCATCGATGCACTATTT
*
1176677 ATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAAATGAG-TGCATCGATGCACTA
1 ATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATT-AATGAGATGCATCGATGCACTA
1176738 CCAATGCATC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 45 0.83
65 9 0.17
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (64 bp):
ATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGAGATGCATCGATGCACTATTT
Found at i:1181155 original size:7 final size:6
Alignment explanation
Indices: 1181121--1181170 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
1181111 GTTTATGGAT
*
1181121 TTAGGG TTAGGG TTAGGG TTAGGG TTAGAGG TTAGAGT TTAGGGG TTAGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAG-GG TTAG-GG TTA-GGG TTAGG
1181171 ATTTTAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 24 0.60
7 15 0.38
8 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (6 bp):
TTAGGG
Found at i:1181551 original size:17 final size:16
Alignment explanation
Indices: 1181529--1181560 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1181519 TTATAAAAAC
1181529 TTTATTGTGAATACTTG
1 TTTATTGTGAA-ACTTG
1181546 TTTATTGTGAAACTT
1 TTTATTGTGAAACTT
1181561 TCAGCACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTATTGTGAAACTTG
Found at i:1185150 original size:6 final size:6
Alignment explanation
Indices: 1185139--1185165 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1185129 ATATTTTGGA
1185139 TTATTG TTATTG TTATTG TTATTG TTA
1 TTATTG TTATTG TTATTG TTATTG TTA
1185166 GAATCAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TTATTG
Found at i:1188252 original size:29 final size:28
Alignment explanation
Indices: 1188190--1188259 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
1188180 TCATAGTCAG
*
1188190 TTTAAAGGGAGATTGAAACCTTTTAGCTC
1 TTTAAAGGGAGACTGAAACC-TTTAGCTC
* *
1188219 ATTAAAGGGATACTGAAACC-TTAGGACTC
1 TTTAAAGGGAGACTGAAACCTTTA-G-CTC
*
1188248 TTTAAAGAGAGA
1 TTTAAAGGGAGA
1188260 TTCAAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 29 0.88
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (28 bp):
TTTAAAGGGAGACTGAAACCTTTAGCTC
Found at i:1199685 original size:23 final size:23
Alignment explanation
Indices: 1199614--1199674 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1199604 TTACTTTGCA
1199614 TTTATAACACGTTTTCTTCTGTT
1 TTTATAACACGTTTTCTTCTGTT
1199637 TTTATAACACGTTTTCTTCTGTT
1 TTTATAACACGTTTTCTTCTGTT
*
1199660 TTTATGACACGTTTT
1 TTTATAACACGTTTT
1199675 TTATGTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (23 bp):
TTTATAACACGTTTTCTTCTGTT
Found at i:1200771 original size:29 final size:28
Alignment explanation
Indices: 1200699--1200771 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 28
1200689 AATAAAGAAT
* *
1200699 TTGTAAAAAATTACAGTAATAAGTTAAA
1 TTGTAAAAAAATAAAGTAATAAGTTAAA
1200727 TTG-AATAAAATATAAAGTCAAT-AGATTAAA
1 TTGTAA-AAAA-ATAAAGT-AATAAG-TTAAA
*
1200757 TTGTAAAAAAGTAAA
1 TTGTAAAAAAATAAA
1200772 CTTATTGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 2 0.05
28 7 0.19
29 11 0.30
30 15 0.41
31 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (28 bp):
TTGTAAAAAAATAAAGTAATAAGTTAAA
Found at i:1202641 original size:20 final size:20
Alignment explanation
Indices: 1202581--1202647 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
1202571 CTTTTAAATA
1202581 AATATATAAAGTTATATTTT
1 AATATATAAAGTTATATTTT
* *
1202601 AATACATTATCGACG-TATATTTT
1 AAT--A-TAT-AAAGTTATATTTT
1202624 AATATATAAAGTTATATTTT
1 AATATATAAAGTTATATTTT
1202644 AATA
1 AATA
1202648 CTTGATCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 18 0.47
21 1 0.03
22 1 0.03
23 14 0.37
24 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
AATATATAAAGTTATATTTT
Found at i:1209079 original size:22 final size:23
Alignment explanation
Indices: 1209048--1209094 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1209038 TAATCGCGAG
1209048 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* * *
1209070 TTTAGCAGATATGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
1209093 TT
1 TT
1209095 GTTTAGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:1213444 original size:2 final size:2
Alignment explanation
Indices: 1213439--1213465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1213429 CTAAAAAACA
1213439 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 A
1213466 ATCTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1223396 original size:42 final size:40
Alignment explanation
Indices: 1223305--1223400 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 40
1223295 TTTTTATATT
* ** *
1223305 ATTA-AAATATATTCTTTAATTATTAAAAATATAAAAATT
1 ATTATAAATATATTATTTAACCATTAAAAATATAAAAATA
* *
1223344 GTTATAAAATATATTATATTAACCATTTAAAATATAATAAATA
1 ATTAT-AAATATATTAT-TTAACCATTAAAAATATAA-AAATA
1223387 ATTATAAATATATT
1 ATTATAAATATATT
1223401 GTTACAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
39 3 0.07
41 10 0.22
42 25 0.54
43 8 0.17
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (40 bp):
ATTATAAATATATTATTTAACCATTAAAAATATAAAAATA
Found at i:1223410 original size:57 final size:57
Alignment explanation
Indices: 1223334--1223441 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
1223324 TTATTAAAAA
*
1223334 TATAAAAATTGTTATAAAATATATTATATTAACCA-TTTAAAATA-TAATAAATAAT
1 TATAAAAATTGTTACAAAATATATTATATTAACCATTTTAAAATATTAATAAATAAT
* **
1223389 TATAAATATATTGTTACAAAATATATTATTTTAATTATTTTAAAATATTAATA
1 TATAAA-A-ATTGTTACAAAATATATTATATTAACCATTTTAAAATATTAATA
1223442 TATTCAGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
55 6 0.13
56 1 0.02
57 24 0.53
58 9 0.20
59 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (57 bp):
TATAAAAATTGTTACAAAATATATTATATTAACCATTTTAAAATATTAATAAATAAT
Found at i:1223759 original size:17 final size:17
Alignment explanation
Indices: 1223737--1223771 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1223727 CCTTAATTTT
1223737 TTTTAAATTATTTTATA
1 TTTTAAATTATTTTATA
*
1223754 TTTTAAATTTTTTTATA
1 TTTTAAATTATTTTATA
1223771 T
1 T
1223772 GTATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAAATTATTTTATA
Found at i:1223767 original size:27 final size:28
Alignment explanation
Indices: 1223729--1223783 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1223719 AGTTGATCCC
*
1223729 TTAATTTTTTTTAAAT-TATTTTATATT
1 TTAAATTTTTTTAAATGTATTTTATATT
* *
1223756 TTAAATTTTTTTATATGTATTTTCTATT
1 TTAAATTTTTTTAAATGTATTTTATATT
1223784 AATAATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TTAAATTTTTTTAAATGTATTTTATATT
Found at i:1231043 original size:42 final size:42
Alignment explanation
Indices: 1230984--1231064 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1230974 TCTTCCTACA
* * *
1230984 TCTACACCTATACCTATATATTCTACAGAAACACAACCTTCT
1 TCTACACCTATACCTATACATACTACAAAAACACAACCTTCT
1231026 TCTACACCTATACCTATACATACTACAAAAACACAACCT
1 TCTACACCTATACCTATACATACTACAAAAACACAACCT
1231065 GCTCTTACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.40, C:0.32, G:0.01, T:0.27
Consensus pattern (42 bp):
TCTACACCTATACCTATACATACTACAAAAACACAACCTTCT
Found at i:1233918 original size:148 final size:149
Alignment explanation
Indices: 1233642--1233935 Score: 581
Period size: 148 Copynumber: 2.0 Consensus size: 149
1233632 TTGCTTGAGT
1233642 ATACTGATTCTTCCATGTTCTACAGATATTTTATTAAAAATATTATTGCATGCAGAATCATTTTG
1 ATACTGATTCTTCCATGTTCTACAGATATTTTATTAAAAATATTATTGCATGCAGAATCATTTTG
1233707 TCGGCTTTTCAGGTAACTTCTAGTAAAGGTGCAAATGGTGTCCTTCAGAATATGAACCAAGCAAC
66 TCGGCTTTTCAGGTAACTTCTAGTAAAGGTGCAAATGGTGTCCTTCAGAATATGAACCAAGCAAC
1233772 AGCCACGACGAGGCTTAGG
131 AGCCACGACGAGGCTTAGG
1233791 ATACTGA-TCTTCCATGTTCTACAGATATTTTATTAAAAATATTATTGCATGCAGAATCATTTTG
1 ATACTGATTCTTCCATGTTCTACAGATATTTTATTAAAAATATTATTGCATGCAGAATCATTTTG
1233855 TCGGCTTTTCAGGTAACTTCTAGTAAAGGTGCAAATGGTGTCCTTCAGAATATGAACCAAGCAAC
66 TCGGCTTTTCAGGTAACTTCTAGTAAAGGTGCAAATGGTGTCCTTCAGAATATGAACCAAGCAAC
1233920 AGCCACGACGAGGCTT
131 AGCCACGACGAGGCTT
1233936 CCAGATGAAC
Statistics
Matches: 145, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 138 0.95
149 7 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (149 bp):
ATACTGATTCTTCCATGTTCTACAGATATTTTATTAAAAATATTATTGCATGCAGAATCATTTTG
TCGGCTTTTCAGGTAACTTCTAGTAAAGGTGCAAATGGTGTCCTTCAGAATATGAACCAAGCAAC
AGCCACGACGAGGCTTAGG
Found at i:1234797 original size:46 final size:46
Alignment explanation
Indices: 1234730--1234822 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1234720 CGGTCGTCAC
1234730 GCTTCAAAAGCGAGCAAACGTCAAGCAAGTTGTTTTTGACAACAGA
1 GCTTCAAAAGCGAGCAAACGTCAAGCAAGTTGTTTTTGACAACAGA
1234776 GCTTCAAAAGCGAGCAAACGTCAAGCAAGTTGTTTTTGACAACAGA
1 GCTTCAAAAGCGAGCAAACGTCAAGCAAGTTGTTTTTGACAACAGA
1234822 G
1 G
1234823 GATACTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (46 bp):
GCTTCAAAAGCGAGCAAACGTCAAGCAAGTTGTTTTTGACAACAGA
Found at i:1239813 original size:28 final size:28
Alignment explanation
Indices: 1239768--1239823 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1239758 AATGTTGTTA
* *
1239768 CTTTCAAGCACTGACTCGACGGTATAAT
1 CTTTCAAGCAATGACTCGACAGTATAAT
*
1239796 CTTTCAAGCAAT-AGCTCGATAGTATAAT
1 CTTTCAAGCAATGA-CTCGACAGTATAAT
1239824 GTAAACAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (28 bp):
CTTTCAAGCAATGACTCGACAGTATAAT
Found at i:1245830 original size:21 final size:21
Alignment explanation
Indices: 1245804--1245848 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1245794 GATTTCTGGG
* *
1245804 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1245825 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1245846 CAA
1 CAA
1245849 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1245918 original size:23 final size:22
Alignment explanation
Indices: 1245874--1245918 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1245864 AATGCCAGAG
*
1245874 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1245896 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1245919 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1247173 original size:32 final size:31
Alignment explanation
Indices: 1247131--1247262 Score: 142
Period size: 31 Copynumber: 4.2 Consensus size: 31
1247121 AGAGTCGAGG
1247131 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
1247162 TTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 -GTTTACCTATGTTC-TACGGA-ACATATGGACA
* *
1247194 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
** * * *
1247225 GTTTACCTGGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1247256 GTTTACC
1 GTTTACC
1247263 GAGGATCTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
31 56 0.67
32 27 0.33
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1247346 original size:29 final size:30
Alignment explanation
Indices: 1247244--1247343 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
1247234 GGTTCTTCGG
*
1247244 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
1247275 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
1247305 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1247334 GACCTCTGGA
1 GACCTCTGGA
1247344 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1250507 original size:21 final size:21
Alignment explanation
Indices: 1250481--1250525 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1250471 GATTTCTGGG
* *
1250481 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
1250502 CAAGGGGAACCGATACCCATT
1 CAAGGGGAACCGATACCCATT
1250523 CAA
1 CAA
1250526 ACGACAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1250595 original size:23 final size:22
Alignment explanation
Indices: 1250551--1250595 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1250541 AATGCCAGAG
*
1250551 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1250573 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1250596 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1251852 original size:32 final size:31
Alignment explanation
Indices: 1251810--1251941 Score: 149
Period size: 31 Copynumber: 4.2 Consensus size: 31
1251800 AGAGTCGAGG
1251810 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
***
1251841 GTTTTACCTATG-TCTTTTGAGACATATGGACA
1 G-TTTACCTATGTTCTACGGA-ACATATGGACA
* *
1251873 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
** * * *
1251904 GTTTACCTGGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1251935 GTTTACC
1 GTTTACC
1251942 GAGGATCTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
31 57 0.68
32 27 0.32
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1252025 original size:29 final size:30
Alignment explanation
Indices: 1251923--1252022 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
1251913 GGTTCTTCGG
*
1251923 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
1251954 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
1251984 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1252013 GACCTCTGGA
1 GACCTCTGGA
1252023 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1253791 original size:21 final size:21
Alignment explanation
Indices: 1253765--1253805 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1253755 GACTATCGTA
*
1253765 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
1253786 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
1253806 AATGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:1253811 original size:21 final size:21
Alignment explanation
Indices: 1253766--1253812 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1253756 ACTATCGTAT
* **
1253766 TGCGATTTTTCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
1253787 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
1253808 TGCGA
1 TGCGA
1253813 ATATGTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:1253827 original size:20 final size:20
Alignment explanation
Indices: 1253802--1253854 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1253792 TTTTCCTAAT
**
1253802 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACATAAA
1253822 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
*
1253842 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1253855 CTGACTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:1253948 original size:20 final size:20
Alignment explanation
Indices: 1253841--1253947 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
1253831 GAATACATAA
*
1253841 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
1253861 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
1253881 ATCGAAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1253901 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1253921 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1253941 ATCGCAA
1 ATCGCAA
1253948 TACTGAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1257268 original size:20 final size:20
Alignment explanation
Indices: 1257243--1257376 Score: 216
Period size: 20 Copynumber: 6.7 Consensus size: 20
1257233 GACATTCATT
*
1257243 TGACTATCGCAACAC-GAATA
1 TGACTATCGCAACGCGGAA-A
* * *
1257263 TGACTATCACAACACGAAAA
1 TGACTATCGCAACGCGGAAA
1257283 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1257303 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1257323 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1257343 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1257363 TGACTATCGCAACG
1 TGACTATCGCAACG
1257377 AGAGAATCGC
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 106 0.98
21 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:1257387 original size:14 final size:14
Alignment explanation
Indices: 1257368--1257421 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1257358 GGAAATGACT
1257368 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1257382 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1257401 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1257415 ATCGCAA
1 ATCGCAA
1257422 TGTGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1257436 original size:34 final size:33
Alignment explanation
Indices: 1257348--1257443 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1257338 GGAAATGACT
* **
1257348 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1257382 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1257415 ATCGCAATGTGAAAATGAAAATCGTAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1257444 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1257499 original size:14 final size:14
Alignment explanation
Indices: 1257480--1257533 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1257470 CATTTTCGCA
1257480 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1257494 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1257511 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1257527 TTGCGAT
1 TTGCGAT
1257534 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1257502 original size:34 final size:34
Alignment explanation
Indices: 1257459--1257553 Score: 156
Period size: 33 Copynumber: 2.8 Consensus size: 34
1257449 TTAGTTTCGT
1257459 GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
1257493 GTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
** *
1257526 GTTGCGATAGTCATTTCCGCATTGCGAT
1 GTTGCGATTTTCATTTTCGCATTGCGAT
1257554 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
Found at i:1259183 original size:42 final size:42
Alignment explanation
Indices: 1259076--1259187 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
1259066 TCTAGAATAT
* * * *
1259076 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCATCTTGAACGA
* * ** *
1259118 TGGGAGGGGACTCTTGAGGGATGATAGGGGCATCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCATCTTGAACGA
1259160 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
1259188 TGAATCAGAT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCATCTTGAACGA
Found at i:1259714 original size:20 final size:20
Alignment explanation
Indices: 1259667--1259733 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1259657 GAAACTTAAA
* *
1259667 ATCGCAACGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
1259687 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
** *
1259707 ATCGCAATGCGAATTTAACT
1 ATCGCAATGCGAAAATGACT
1259727 ATCGCAA
1 ATCGCAA
1259734 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1259805 original size:20 final size:21
Alignment explanation
Indices: 1259780--1259846 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
1259770 AATTCTTTCG
1259780 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTCAAATTTCGCA
* *
1259800 TTGCGATAGTC-ATTTTCGCG
1 TTGCGATAGTCAAATTTCGCA
* *
1259820 TTGCGATAGTC-ATTTTCGCG
1 TTGCGATAGTCAAATTTCGCA
1259840 TTGCGAT
1 TTGCGAT
1259847 TTTGTTGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.09
20 40 0.91
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (21 bp):
TTGCGATAGTCAAATTTCGCA
Found at i:1261212 original size:19 final size:19
Alignment explanation
Indices: 1261188--1261224 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1261178 CAAGTCTTAT
1261188 ACGTGTAAATTCGGCTTCC
1 ACGTGTAAATTCGGCTTCC
1261207 ACGTGTAAATTCGGCTTC
1 ACGTGTAAATTCGGCTTC
1261225 TCCGTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (19 bp):
ACGTGTAAATTCGGCTTCC
Found at i:1261833 original size:20 final size:20
Alignment explanation
Indices: 1261810--1261850 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1261800 TCTGAAACTT
1261810 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
1261830 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
1261850 A
1 A
1261851 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:1261856 original size:20 final size:20
Alignment explanation
Indices: 1261817--1261879 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1261807 CTTAAAATCA
**
1261817 CAACACGAAAATGAAAATCG
1 CAACACGAAAATGACTATCG
1261837 CAACACGAAAATGACTATCG
1 CAACACGAAAATGACTATCG
* *
1261857 CAACGC-AAATTTGACTATCG
1 CAACACGAAA-ATGACTATCG
1261877 CAA
1 CAA
1261880 TGCAAGAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.08
20 35 0.92
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (20 bp):
CAACACGAAAATGACTATCG
Found at i:1262312 original size:22 final size:22
Alignment explanation
Indices: 1262250--1262315 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1262240 TGACTGTGAA
* *
1262250 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1262272 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1262294 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1262316 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1262567 original size:21 final size:21
Alignment explanation
Indices: 1262543--1262582 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1262533 ATTCGCATTG
1262543 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
*
1262564 CGAATTTGGAAAATCGCAA
1 CGAATTAGGAAAATCGCAA
1262583 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:1263122 original size:18 final size:17
Alignment explanation
Indices: 1263092--1263125 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1263082 GTTACTGTTA
*
1263092 TATTTTTTTGAAAATTT
1 TATTTTTTAGAAAATTT
1263109 TATTTTTTAAGAAAATT
1 TATTTTTT-AGAAAATT
1263126 AAAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTTTTAGAAAATTT
Found at i:1268506 original size:21 final size:20
Alignment explanation
Indices: 1268473--1268512 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1268463 AAGTGAAGCA
1268473 TAATTTAAATATAATATTTT
1 TAATTTAAATATAATATTTT
1268493 TAATTTATAATATAATATTT
1 TAATTTA-AATATAATATTT
1268513 AAAATAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATTTAAATATAATATTTT
Found at i:1275055 original size:24 final size:24
Alignment explanation
Indices: 1275019--1275087 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
1275009 CGGAGATATC
*
1275019 AGAAATCAAAACAGAATTCAGATA
1 AGAAATCAGAACAGAATTCAGATA
* * * *
1275043 AGATATCAGAACAGAATCCATATC
1 AGAAATCAGAACAGAATTCAGATA
*
1275067 AGAAATCAGAACAAAATTCAG
1 AGAAATCAGAACAGAATTCAG
1275088 GTAATGTATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (24 bp):
AGAAATCAGAACAGAATTCAGATA
Found at i:1280369 original size:55 final size:54
Alignment explanation
Indices: 1280310--1280462 Score: 159
Period size: 55 Copynumber: 2.8 Consensus size: 54
1280300 AAACTTGAAA
* *
1280310 AATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAAC
1 AATCTTCAAA-AACGAGCCTGCTCCCTATTCATTCAGAG-AGTATAAGACTCGAAC
* * * * *
1280365 AATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAAC
1 AATCTTCA-AAAACGAGCCTGCTCCCTATTCATTCAGAGAGTATAAGACTCGAAC
*
1280420 AATCTTCAATAAAC-AGGTCC-GCTCCCTATTCTTTCAGAGAGTA
1 AATCTTCAA-AAACGA-G-CCTGCTCCCTATTCATTCAGAGAGTA
1280463 CAGGACTCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
54 1 0.01
55 76 0.94
56 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (54 bp):
AATCTTCAAAAACGAGCCTGCTCCCTATTCATTCAGAGAGTATAAGACTCGAAC
Found at i:1280497 original size:51 final size:51
Alignment explanation
Indices: 1280380--1280792 Score: 565
Period size: 51 Copynumber: 8.0 Consensus size: 51
1280370 TCATAAAATG
* * * * ** *
1280380 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAACA
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGAC-T---CAATCTTCAACGAACT
* * * * *
1280435 GGTCCGCTCCCTATTCTTTCAGAGAGTACAGGACTCAATCTTTAACAAACG
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* * * * * *
1280486 TGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
1280537 TGTCCGCTCCCTATTCTTTCATAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
1280588 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
1280639 TGTCCGCTCCCTATTCATTCAGAGATTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
1280690 TGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
1280741 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACT
1 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1280792 T
1 T
1280793 ATTTGCTTCA
Statistics
Matches: 323, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
51 294 0.91
54 1 0.00
55 28 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:1282141 original size:18 final size:19
Alignment explanation
Indices: 1282118--1282172 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1282108 TTTATCTTTT
1282118 TTCATTTTTCTCTTTTC-C
1 TTCATTTTTCTCTTTTCTC
*
1282136 TTCATTTTTCCATTTTTTCTC
1 TTCATTTTT-C-TCTTTTCTC
*
1282157 TTC-TTTTTTTCTTTTC
1 TTCATTTTTCTCTTTTC
1282173 GTTTTTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
20 11 0.35
21 4 0.13
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCATTTTTCTCTTTTCTC
Found at i:1282144 original size:25 final size:25
Alignment explanation
Indices: 1282115--1282206 Score: 70
Period size: 25 Copynumber: 3.8 Consensus size: 25
1282105 TTATTTATCT
1282115 TTTTTCATTTTTCTCTTTTCCTTCA
1 TTTTTCATTTTTCTCTTTTCCTTCA
*
1282140 TTTTTCCATTTTT-TCTCTT-CTT--
1 TTTTT-CATTTTTCTCTTTTCCTTCA
* *
1282162 TTTTTC--TTTTCGTTTTTTCCATCA
1 TTTTTCATTTTTC-TCTTTTCCTTCA
*
1282186 TTTTTTCTTTTTTCTCATTTT
1 -TTTTTCATTTTTCTC-TTTT
1282207 TTCTTCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
19 4 0.08
21 5 0.10
22 7 0.13
24 3 0.06
25 16 0.31
26 8 0.15
27 9 0.17
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.72
Consensus pattern (25 bp):
TTTTTCATTTTTCTCTTTTCCTTCA
Found at i:1282162 original size:46 final size:45
Alignment explanation
Indices: 1282112--1282223 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 45
1282102 CTTTTATTTA
*
1282112 TCTTTTTTCATTTTTCTCTTTTCCTTCATTTTTCCATTTTTTCTC-T
1 TCTTTTTTC-TTTTTCTCTTTTCCATCATTTTTCC-TTTTTTCTCAT
* *
1282158 TCTTTTTT-TCTTTTCGTTTTTTCCATCATTTTTTCTTTTTTCTCAT
1 TCTTTTTTCT-TTTTC-TCTTTTCCATCATTTTTCCTTTTTTCTCAT
1282204 T-TTTTCTTC-TTTTCTCTTTT
1 TCTTTT-TTCTTTTTCTCTTTT
1282224 ATTTCTTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
44 6 0.11
45 23 0.40
46 28 0.49
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.72
Consensus pattern (45 bp):
TCTTTTTTCTTTTTCTCTTTTCCATCATTTTTCCTTTTTTCTCAT
Found at i:1282166 original size:13 final size:13
Alignment explanation
Indices: 1282146--1282193 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1282136 TTCATTTTTC
1282146 CATTTTTTCTCTT
1 CATTTTTTCTCTT
* *
1282159 CTTTTTTTCTTTT
1 CATTTTTTCTCTT
* *
1282172 CGTTTTTTC-CAT
1 CATTTTTTCTCTT
1282184 CATTTTTTCT
1 CATTTTTTCT
1282194 TTTTTCTCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (13 bp):
CATTTTTTCTCTT
Found at i:1282197 original size:20 final size:18
Alignment explanation
Indices: 1282168--1282230 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
1282158 TCTTTTTTTC
1282168 TTTTCGTTTTTTCCATCATT
1 TTTTC-TTTTTTCC-TCATT
1282188 TTTTCTTTTTT-CTCATT
1 TTTTCTTTTTTCCTCATT
*
1282205 TTTTCTTCTTTT-CTCTTT
1 TTTTCTT-TTTTCCTCATT
1282223 TATTTCTT
1 T-TTTCTT
1282231 CTTCAAGCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 12 0.30
18 11 0.28
19 12 0.30
20 5 0.12
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTTTCCTCATT
Found at i:1282197 original size:45 final size:46
Alignment explanation
Indices: 1282114--1282217 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 46
1282104 TTTATTTATC
* * *
1282114 TTTTTTCAT-TTTTC-TCTTTTCCTTCATTTTTCCATTTTTTCTC-
1 TTTTTTCTTCTTTTCGTTTTTTCCATCATTTTTCCATTTTTTCTCA
* *
1282157 TTCTTTTTTTCTTTTCGTTTTTTCCATCATTTTTTC-TTTTTTCTCA
1 TT-TTTTCTTCTTTTCGTTTTTTCCATCATTTTTCCATTTTTTCTCA
1282203 TTTTTTCTTCTTTTC
1 TTTTTTCTTCTTTTC
1282218 TCTTTTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 2 0.04
44 5 0.10
45 26 0.51
46 18 0.35
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (46 bp):
TTTTTTCTTCTTTTCGTTTTTTCCATCATTTTTCCATTTTTTCTCA
Found at i:1282216 original size:27 final size:25
Alignment explanation
Indices: 1282114--1282228 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 25
1282104 TTTATTTATC
*
1282114 TTTTTTCA-TTTTTCTCTTTTCCTTCA
1 TTTTTTCATTTTTTCTCTTTT--TTCT
*
1282140 TTTTTCCATTTTTTCTCTTCTTTT-T
1 TTTTTTCATTTTTTCTCTT-TTTTCT
*
1282165 TTCTTTTCGTTTTTTCCATCATTTTTTCT
1 TT-TTTTCATTTTTT-C-TC-TTTTTTCT
*
1282194 TTTTTCTCATTTTTTCTTCTTTTCTCT
1 TTTTT-TCATTTTTTC-TCTTTTTTCT
1282221 TTTATTTC
1 TTT-TTTC
1282229 TTCTTCAAGC
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
25 2 0.03
26 19 0.26
27 23 0.32
28 16 0.22
29 13 0.18
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (25 bp):
TTTTTTCATTTTTTCTCTTTTTTCT
Found at i:1282228 original size:19 final size:18
Alignment explanation
Indices: 1282183--1282233 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
1282173 GTTTTTTCCA
1282183 TCATTTTTTCTT-TTTTC
1 TCATTTTTTCTTCTTTTC
1282200 TCATTTTTTCTTCTTTTC
1 TCATTTTTTCTTCTTTTC
*
1282218 TCTTTTATTTCTTCTT
1 TCATTT-TTTCTTCTT
1282234 CAAGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTCTTCTTTTC
Found at i:1295875 original size:23 final size:23
Alignment explanation
Indices: 1295831--1295879 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1295821 TAATTTAGAT
* *
1295831 AAAATACATTTATTGAATATATTA
1 AAAATAAATTCATTGAATATA-TA
*
1295855 AAAATAAATTCATTTAA-ATATA
1 AAAATAAATTCATTGAATATATA
1295877 AAA
1 AAA
1295880 TGCATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 5 0.23
23 3 0.14
24 14 0.64
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAATAAATTCATTGAATATATA
Found at i:1297370 original size:582 final size:582
Alignment explanation
Indices: 1296266--1297433 Score: 2102
Period size: 582 Copynumber: 2.0 Consensus size: 582
1296256 AAACAATAAA
1296266 TAACAGGCATTATTAAAATGGTATGCGCGTAAAATTAGAAGGCAAAATAAAAAACTTTAAAGCCC
1 TAACAGGCATTATTAAAATGGTATGCGCGTAAAATTAGAAGGCAAAATAAAAAACTTTAAAGCCC
* *
1296331 CAAAATAGGGATCAAATTACATACATATCGAAAATAAAGGGTGTCTATACATGATATACTCCAAG
66 CAAAATAGGGATCAAATTACATACATATCGAAAATAAAGGGAGTCTATACATGATATACTCCAAA
1296396 AAGGGTGACTAAGACGTAAAAACACGCTTAAAGTTGAGGGACCATTACATGGGTTTCCCTTAAAC
131 AAGGGTGACTAAGACGTAAAAACACGCTTAAAGTTGAGGGACCATTACATGGGTTTCCCTTAAAC
* * * *
1296461 CCGTGACCTAAATGCAAGAACGCACCAAACTTACGGGGACCTATGCGCGATTTGACCCTAAATAA
196 CCATGACCTAAATGCAAGAACGCACCAAACTTACGAGAACCTATGCACGATTTGACCCTAAATAA
1296526 ATGACCACAATGCACAAAGGAGCCTAAAGTCAGGGACTTGTACGTGAATAACCCACGTGGGTTGT
261 ATGACCACAATGCACAAAGGAGCCTAAAGTCAGGGACTTGTACGTGAATAACCCACGTGGGTTGT
*
1296591 TCATGATCTAAACGACGTCGTATTAGTCAGGGTATAAATACCCAAAGGATCGACCTTTTGACCCT
326 TCATGATCTAAACGACGTCGTATTAGTCAAGGTATAAATACCCAAAGGATCGACCTTTTGACCCT
1296656 AAACCCTATTTTCAATTTTTCTCTCTCTCTGAAAGAGAGAACTCTCTCGCTTCTCTCTTCTTTCT
391 AAACCCTATTTTCAATTTTTCTCTCTCTCTGAAAGAGAGAACTCTCTCGCTTCTCTCTTCTTTCT
* * * *
1296721 TCGTCGGGGGAAGGCCGACAACCTCCGACCACCGTTTACTGTAAACCATTTATTGAAATCCTTCT
456 CCGCCGGGGGAAGGCAGACAACCTCCGACCACCGTTTACTGTAAACCATTTATCGAAATCCTTCT
*
1296786 TCTGACGCACACGACGGCCAACGACCTAAAAAGCAACCCCAAAATGACCCTCGACCTTCCTT
521 TCTGACGCACACGACGGCCAACGACCTAAAAAGCAACCCCAAAATGACCCTCGACCTTCCCT
1296848 TAACAGGCATTATTAAAATGGTATGCGCGTAAAATTAGAAGGCAAAATAAAAAACTTTAAAGCCC
1 TAACAGGCATTATTAAAATGGTATGCGCGTAAAATTAGAAGGCAAAATAAAAAACTTTAAAGCCC
1296913 CAAAATAGGGATCAAATTACATACATATCGAAAATAAAGGGAGTCTATACATGATATACTCCAAA
66 CAAAATAGGGATCAAATTACATACATATCGAAAATAAAGGGAGTCTATACATGATATACTCCAAA
* *
1296978 AAGGGTGACTAAGATGTAAAAACACGCTTAAAGTTGAGGGACCATTACATGGTTTTCCCTTAAAC
131 AAGGGTGACTAAGACGTAAAAACACGCTTAAAGTTGAGGGACCATTACATGGGTTTCCCTTAAAC
** *
1297043 CCATGACCTAAATGCAAGAACGCACCAAACTTGTGAGAACCTATGTACGATTTGACCCTAAATAA
196 CCATGACCTAAATGCAAGAACGCACCAAACTTACGAGAACCTATGCACGATTTGACCCTAAATAA
1297108 ATGACCACAATGCACAAAGGAGCCTAAAGTCAGGGACTTGTACGTGAATAACCCACGTGGGTTGT
261 ATGACCACAATGCACAAAGGAGCCTAAAGTCAGGGACTTGTACGTGAATAACCCACGTGGGTTGT
* *
1297173 TCATGATCTAAATGACGTTGTATTAGTCAAGGTATAAATACCCAAAGGATCGACCTTTTGACCCT
326 TCATGATCTAAACGACGTCGTATTAGTCAAGGTATAAATACCCAAAGGATCGACCTTTTGACCCT
*
1297238 AAACCCTATTTTCAGTTTTTCTCTCTCTCTGAAAGAGAGAACTCTCTCGCTTCTCTCTTCTTTCT
391 AAACCCTATTTTCAATTTTTCTCTCTCTCTGAAAGAGAGAACTCTCTCGCTTCTCTCTTCTTTCT
* *
1297303 CCGCCGGGGGAAGGCAGACAACCTCCGGCCACCGTTTACTGTAAACCGTTTATCGAAATCCTTCT
456 CCGCCGGGGGAAGGCAGACAACCTCCGACCACCGTTTACTGTAAACCATTTATCGAAATCCTTCT
* * * *
1297368 TCTGACGCACATGGCGGCCAGCGACCTAAAAAGCACCCCCAAAATGACCCTCGACCTTCCCT
521 TCTGACGCACACGACGGCCAACGACCTAAAAAGCAACCCCAAAATGACCCTCGACCTTCCCT
1297430 TAAC
1 TAAC
1297434 TCGAATCCGA
Statistics
Matches: 560, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
582 560 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (582 bp):
TAACAGGCATTATTAAAATGGTATGCGCGTAAAATTAGAAGGCAAAATAAAAAACTTTAAAGCCC
CAAAATAGGGATCAAATTACATACATATCGAAAATAAAGGGAGTCTATACATGATATACTCCAAA
AAGGGTGACTAAGACGTAAAAACACGCTTAAAGTTGAGGGACCATTACATGGGTTTCCCTTAAAC
CCATGACCTAAATGCAAGAACGCACCAAACTTACGAGAACCTATGCACGATTTGACCCTAAATAA
ATGACCACAATGCACAAAGGAGCCTAAAGTCAGGGACTTGTACGTGAATAACCCACGTGGGTTGT
TCATGATCTAAACGACGTCGTATTAGTCAAGGTATAAATACCCAAAGGATCGACCTTTTGACCCT
AAACCCTATTTTCAATTTTTCTCTCTCTCTGAAAGAGAGAACTCTCTCGCTTCTCTCTTCTTTCT
CCGCCGGGGGAAGGCAGACAACCTCCGACCACCGTTTACTGTAAACCATTTATCGAAATCCTTCT
TCTGACGCACACGACGGCCAACGACCTAAAAAGCAACCCCAAAATGACCCTCGACCTTCCCT
Found at i:1298183 original size:22 final size:23
Alignment explanation
Indices: 1298158--1298201 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1298148 TTGGGCCGAG
*
1298158 CCGA-TTTGCTTGTAAATGGGCT
1 CCGAGTTTACTTGTAAATGGGCT
*
1298180 CCGAGTTTACTTGTAATTGGGC
1 CCGAGTTTACTTGTAAATGGGC
1298202 CTAATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (23 bp):
CCGAGTTTACTTGTAAATGGGCT
Found at i:1298398 original size:16 final size:16
Alignment explanation
Indices: 1298377--1298408 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1298367 TGGAGTGATC
1298377 AAATTATGAATAATTT
1 AAATTATGAATAATTT
1298393 AAATTATGAATAATTT
1 AAATTATGAATAATTT
1298409 GAAAGTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
AAATTATGAATAATTT
Found at i:1299200 original size:2 final size:2
Alignment explanation
Indices: 1299193--1299223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1299183 AATAAAAATA
1299193 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
1299224 AAAATTTTAC
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:1301758 original size:2 final size:2
Alignment explanation
Indices: 1301753--1301777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1301743 TGTGTGTGTG
1301753 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 T
1301778 TAAAAATACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1301877 original size:7 final size:7
Alignment explanation
Indices: 1301865--1301904 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1301855 TGATGAAAAT
1301865 CCTAAAC
1 CCTAAAC
1301872 CCTAAAC
1 CCTAAAC
* *
1301879 CATAAAT
1 CCTAAAC
*
1301886 CATAAAC
1 CCTAAAC
1301893 CCTAAAC
1 CCTAAAC
1301900 CCTAA
1 CCTAA
1301905 CCATTCTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:1301891 original size:21 final size:21
Alignment explanation
Indices: 1301861--1301900 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1301851 TTGTTGATGA
*
1301861 AAATCCTAAACCCTAAACCAT
1 AAATCATAAACCCTAAACCAT
1301882 AAATCATAAACCCTAAACC
1 AAATCATAAACCCTAAACC
1301901 CTAACCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
AAATCATAAACCCTAAACCAT
Found at i:1302080 original size:7 final size:7
Alignment explanation
Indices: 1302068--1302132 Score: 62
Period size: 7 Copynumber: 9.4 Consensus size: 7
1302058 TAATCAATTA
1302068 TTAGGGT
1 TTAGGGT
1302075 TTAGGGT
1 TTAGGGT
*
1302082 TTAGGAT
1 TTAGGGT
1302089 TATA--GT
1 T-TAGGGT
1302095 TTAGGGT
1 TTAGGGT
*
1302102 TTAGAGT
1 TTAGGGT
**
1302109 TTAGATT
1 TTAGGGT
*
1302116 TTAGTGT
1 TTAGGGT
1302123 TTAGGGT
1 TTAGGGT
1302130 TTA
1 TTA
1302133 AGATTTTCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
7 42 0.88
8 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:1302105 original size:27 final size:27
Alignment explanation
Indices: 1302068--1302132 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1302058 TAATCAATTA
*
1302068 TTAGGGTTTAGGGTTTAGGATTATA-GT
1 TTAGGGTTTAGAGTTTA-GATTATAGGT
*
1302095 TTAGGGTTTAGAGTTTAGATTTTAGTGT
1 TTAGGGTTTAGAGTTTAGATTATAG-GT
1302123 TTAGGGTTTA
1 TTAGGGTTTA
1302133 AGATTTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 6 0.18
27 16 0.47
28 12 0.35
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.48
Consensus pattern (27 bp):
TTAGGGTTTAGAGTTTAGATTATAGGT
Found at i:1302111 original size:14 final size:14
Alignment explanation
Indices: 1302068--1302132 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
1302058 TAATCAATTA
*
1302068 TTAGGGTTTAGGGT
1 TTAGGGTTTAGAGT
* *
1302082 TTA-GGATTATAGT
1 TTAGGGTTTAGAGT
1302095 TTAGGGTTTAGAGT
1 TTAGGGTTTAGAGT
** *
1302109 TTAGATTTTAGTGT
1 TTAGGGTTTAGAGT
1302123 TTAGGGTTTA
1 TTAGGGTTTA
1302133 AGATTTTCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 10 0.25
14 30 0.75
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTAGAGT
Found at i:1302124 original size:21 final size:22
Alignment explanation
Indices: 1302074--1302139 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
1302064 ATTATTAGGG
*
1302074 TTTAGGGTTTAG-GATTATAG--
1 TTTAGGGTTTAGAGTTTA-AGAT
1302094 TTTAGGGTTTAGAGTTT-AGAT
1 TTTAGGGTTTAGAGTTTAAGAT
* *
1302115 TTTAGTGTTTAGGGTTTAAGAT
1 TTTAGGGTTTAGAGTTTAAGAT
1302137 TTT
1 TTT
1302140 CATCAACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.05
20 12 0.31
21 18 0.46
22 7 0.18
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTTAGAGTTTAAGAT
Found at i:1302389 original size:7 final size:7
Alignment explanation
Indices: 1302377--1302414 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1302367 TGGTTATTGA
1302377 AAATCCT
1 AAATCCT
1302384 AAATCCT
1 AAATCCT
1302391 AAATCCT
1 AAATCCT
*
1302398 AAACCCT
1 AAATCCT
*
1302405 AAACCCT
1 AAATCCT
1302412 AAA
1 AAA
1302415 CTCTAACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
AAATCCT
Found at i:1302396 original size:14 final size:14
Alignment explanation
Indices: 1302377--1302420 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1302367 TGGTTATTGA
*
1302377 AAATCCTAAATCCT
1 AAATCCTAAACCCT
1302391 AAATCCTAAACCCT
1 AAATCCTAAACCCT
* *
1302405 AAACCCTAAACTCT
1 AAATCCTAAACCCT
1302419 AA
1 AA
1302421 CCATTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCTAAACCCT
Found at i:1302415 original size:7 final size:7
Alignment explanation
Indices: 1302381--1302420 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1302371 TATTGAAAAT
*
1302381 CCTAAAT
1 CCTAAAC
*
1302388 CCTAAAT
1 CCTAAAC
1302395 CCTAAAC
1 CCTAAAC
1302402 CCTAAAC
1 CCTAAAC
1302409 CCTAAAC
1 CCTAAAC
*
1302416 TCTAA
1 CCTAA
1302421 CCATTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:1302621 original size:21 final size:21
Alignment explanation
Indices: 1302595--1302634 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1302585 GAATGGTTAG
1302595 GGTTTAGGATTTAAGATTTAT
1 GGTTTAGGATTTAAGATTTAT
* *
1302616 GGTTTAGGGTTTAGGATTT
1 GGTTTAGGATTTAAGATTT
1302635 TAATCAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
GGTTTAGGATTTAAGATTTAT
Found at i:1302734 original size:2 final size:2
Alignment explanation
Indices: 1302727--1302758 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1302717 TATATTTTAT
1302727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1302759 CATACAAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1304041 original size:23 final size:21
Alignment explanation
Indices: 1303989--1304041 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
1303979 AATTCTACAT
1303989 ATTTAA-TTATATTATTTTTA
1 ATTTAATTTATATTATTTTTA
*
1304009 AATTATATTTATTATTATATTTTA
1 ATTTA-ATTTA-TATTAT-TTTTA
1304033 ATTTAATTT
1 ATTTAATTT
1304042 TAATTACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 3 0.11
23 10 0.37
24 9 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTTATATTATTTTTA
Found at i:1308751 original size:25 final size:22
Alignment explanation
Indices: 1308718--1308775 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
1308708 TTCACTTCAC
*
1308718 ACCTTTAAAATTTTGTAATTTAAT
1 ACCTTT-AAATTTT-TAATATAAT
1308742 ACCTCTTAAATTTTTAATATAAT
1 ACCT-TTAAATTTTTAATATAAT
*
1308765 TCC-TTAAATTT
1 ACCTTTAAATTT
1308776 GTACCCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.26
23 10 0.32
24 11 0.35
25 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
ACCTTTAAATTTTTAATATAAT
Found at i:1309298 original size:2 final size:2
Alignment explanation
Indices: 1309216--1309286 Score: 64
Period size: 2 Copynumber: 37.5 Consensus size: 2
1309206 GTTCTACTTC
1309216 AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT GA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* *
1309255 AGT AG A- AC AT -T AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1309287 AGGGATTATA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
1 6 0.10
2 51 0.86
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1319231 original size:3 final size:3
Alignment explanation
Indices: 1319223--1319247 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1319213 GAATAATTTA
1319223 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1319248 TATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1322888 original size:31 final size:31
Alignment explanation
Indices: 1322813--1322904 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
1322803 TTACATGGTA
* * ** *
1322813 GAAAATATTAATAAAATATACCATGTCATTG
1 GAAAATATTAATACAGTATGTCATATCATTG
1322844 GAAAATATTAATACAGTATGTCATATCATTG
1 GAAAATATTAATACAGTATGTCATATCATTG
*
1322875 GAAAATATTAATACGGTATGTCATATCATT
1 GAAAATATTAATACAGTATGTCATATCATT
1322905 TTAGAGTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
GAAAATATTAATACAGTATGTCATATCATTG
Found at i:1326302 original size:2 final size:2
Alignment explanation
Indices: 1326295--1326327 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1326285 ATTAAATAAT
1326295 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 T
1326328 GGATTTTGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1332705 original size:15 final size:14
Alignment explanation
Indices: 1332684--1332729 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1332674 ATTTGAGTAT
1332684 TTATTTTTAAAATA
1 TTATTTTTAAAATA
* **
1332698 TTATTTTTTGAAGGA
1 TTA-TTTTTAAAATA
1332713 TTATTTTTAAAATA
1 TTATTTTTAAAATA
1332727 TTA
1 TTA
1332730 AAAAGAAGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTATTTTTAAAATA
Found at i:1337326 original size:6 final size:6
Alignment explanation
Indices: 1337317--1337378 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
1337307 TTGCGAAAAT
1337317 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1337365 GACCAC GACCAC GA
1 GACCAC GACCAC GA
1337379 GACGAGACGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.34, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1337385 original size:5 final size:5
Alignment explanation
Indices: 1337375--1337402 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1337365 GACCACGACC
1337375 ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1337403 GCGGCGGCGG
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:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:1338024 original size:22 final size:22
Alignment explanation
Indices: 1337997--1338049 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1337987 AATTTGGAAA
1337997 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
1338019 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1338041 ATCGCAACG
1 ATCGCAACG
1338050 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1338087 original size:41 final size:41
Alignment explanation
Indices: 1338038--1338216 Score: 295
Period size: 41 Copynumber: 4.4 Consensus size: 41
1338028 ACAACTGTAG
1338038 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1338079 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *** * *
1338120 ACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1338161 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1338202 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
1338217 TTTTCAACTA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1338212 original size:103 final size:103
Alignment explanation
Indices: 1338102--1338291 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 103
1338092 GAAATGGAAA
* *** * *
1338102 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCGACTATA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
1338167 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
66 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* *
1338205 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATC
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
1338270 GCAACGCGAAATGGAAAATCGC
66 GCAACGCGAAATGGAAAATCGC
1338292 GTTCTATCTC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (103 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:1338250 original size:41 final size:41
Alignment explanation
Indices: 1338205--1338291 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
1338195 ATTTTCAACT
1338205 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
1338246 ATCGCAACGCGATTTTCAATTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1338287 ATCGC
1 ATCGC
1338292 GTTCTATCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1338253 original size:82 final size:82
Alignment explanation
Indices: 1338038--1338257 Score: 205
Period size: 82 Copynumber: 2.7 Consensus size: 82
1338028 ACAACTGTAG
* ** *
1338038 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCG-ATTTTC-AACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAAT-CAACAATCGCAACGCGCA-AATCGAA-AATCGCAACGCGAAATGGA
1338100 AAATCGCAACGCGATTTTCA
63 AAATCGCAACGCGATTTTCA
** *** *** ** *
1338120 ACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCGACTATAGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGAAATGGAAAA
1338185 TCGCAACGCGATTTTCA
66 TCGCAACGCGATTTTCA
** * *
1338202 ACTATCGCAACGCGATTTTCAACTATCGCAACGCG-AAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGA-AATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGA
1338258 TTTTCAATTA
Statistics
Matches: 112, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
81 2 0.02
82 98 0.88
83 12 0.11
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGAAATGGAAAA
TCGCAACGCGATTTTCA
Found at i:1338278 original size:62 final size:62
Alignment explanation
Indices: 1338038--1338278 Score: 261
Period size: 62 Copynumber: 3.9 Consensus size: 62
1338028 ACAACTGTAG
** **
1338038 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
* ** ** * ** ** * *** * *
1338100 A-AATCGCAACGCGATTTTCAACTATCGCAACGCGA-AATGGACAATCGCGTTGCGCTTTTCG
1 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
*
1338161 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
*
1338223 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
1338279 AATGGAAAAT
Statistics
Matches: 137, Mismatches: 39, Indels: 6
0.75 0.21 0.03
Matches are distributed among these distances:
61 40 0.29
62 97 0.71
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:1340221 original size:2 final size:2
Alignment explanation
Indices: 1340214--1340238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1340204 TTTAAATAAA
1340214 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
1340239 AATTGAATCT
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:1340567 original size:3 final size:3
Alignment explanation
Indices: 1340559--1340586 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1340549 AATTAGTAGC
1340559 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1340587 TTGATATAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1343901 original size:46 final size:48
Alignment explanation
Indices: 1343829--1343926 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 48
1343819 GAATATAGAA
*
1343829 TATAATAATATTATTTAATACAAAAAATAC-TTTTATTTTTAAAATAT
1 TATAATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAAAATAT
**
1343876 TATAATAAT-TTAGTTAATATTAAAAATACTTTTTATTTTTAAAATAT
1 TATAATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAAAATAT
1343923 TATA
1 TATA
1343927 GATATTAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 17 0.36
47 30 0.64
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (48 bp):
TATAATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAAAATAT
Found at i:1354345 original size:36 final size:36
Alignment explanation
Indices: 1354259--1354419 Score: 182
Period size: 36 Copynumber: 4.4 Consensus size: 36
1354249 TAGAGCAAAG
* *
1354259 TCAATATTAAGCCTTCACCGAAGAGGAGTGAAGCAGA
1 TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA-A
* * * *
1354296 TCAATCTGAAGCCTTCACCGGAGAATAGTGAACCAA
1 TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
* * *
1354332 ACAATCTTCAGCCTTCACCAAAGAGTAGTGAAGCAA
1 TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
*
1354368 TTC-ATCTTAAGCCTTCACCGAAGAGGAGTGAAGCGAA
1 -TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AA
1354405 TC-ATCTGTAAGCCTT
1 TCAATCT-TAAGCCTT
1354420 TAGAGCAGGA
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
36 64 0.62
37 40 0.38
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (36 bp):
TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
Found at i:1354419 original size:73 final size:73
Alignment explanation
Indices: 1354260--1354399 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
1354250 AGAGCAAAGT
* * * *
1354260 CAATATTAAGCCTTCACCGAAGAGGAGTGAAGCAGATCAATCTGAAGCCTTCACCGGAGAATAGT
1 CAATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAGATCAATCTGAAGCCTTCACCGAAGAAGAGT
1354325 GAACCAAA
66 GAACCAAA
* * * *
1354333 CAATCTTCAGCCTTCACCAAAGAGTAGTGAAGCA-ATTC-ATCTTAAGCCTTCACCGAAGAGGAG
1 CAATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAGA-TCAATCTGAAGCCTTCACCGAAGAAGAG
1354396 TGAA
65 TGAA
1354400 GCGAATCATC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 26 0.45
73 32 0.55
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (73 bp):
CAATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAGATCAATCTGAAGCCTTCACCGAAGAAGAGT
GAACCAAA
Found at i:1354782 original size:207 final size:207
Alignment explanation
Indices: 1354498--1356159 Score: 2560
Period size: 207 Copynumber: 8.0 Consensus size: 207
1354488 GAAAATGAAA
1354498 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
1 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
*
1354563 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGGGCATGATG-TCTAAATCCTTCGGGTCATCT
66 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCT-TAAATCCTTCGGGTCATCT
*
1354627 GTAAGCCTTTAAAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTT
130 GTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTT
*
1354692 TCACCTGAAATTG
195 TCACATGAAATTG
*
1354705 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACCAT
1 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
*
1354770 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATACTTCGGGTCATCTG
66 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
1354835 TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
131 TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
1354900 CACATGAAATTG
196 CACATGAAATTG
* *
1354912 AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACCAT
1 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
* *
1354977 TTATAAATCCTTCGGGCTATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
66 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
*
1355042 TAAGTCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
131 TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
1355107 CACATGAAATTG
196 CACATGAAATTG
* * *
1355119 AAAATGATGTTTTAAGAAGATGGAATTTTTAAAAACGAAGAATACGATTTTCAAAATTTCACCAT
1 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
*
1355184 TTATAAGTCCTTCGGGCTATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
66 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
* *
1355249 TAAGTCTTTAGAGCAAGATGATAAGTCATTCGGGCTATCCATAAAACCTTCGGGTAGGATGTTTT
131 TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
1355314 CACATGAAATTG
196 CACATGAAATTG
* *
1355326 AAAATGATGTTTTAAGAAGATGGAATTTTTTAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
1 AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
* *
1355391 TTATAAGTCCTTCGGGCTATCAATAAGTCTATCGAGCATGATGCTTAAATCCTTCGGGTCATC-G
66 TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
*
1355455 TAAGTCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCAGGGTAGGATGTTT
131 TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTC-GGGTAGGATGTTT
*
1355520 TCACATGAATTTG
195 TCACATGAAATTG
*
1355533 AAAATGAAAAAATGATGTTTTAAGACGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAAT
1 AAAATG-----AT-A--TTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAAT
* * * *
1355598 TTCACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGG
58 TTCACCATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGG
* * *
1355663 GTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAG
123 GTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAG
*
1355728 GATGTTTTCACATGAATTTG
188 GATGTTTTCACATGAAATTG
* ** * * * * *
1355748 AGAATGA-A--AAAATGATGTTGGAATTTTTGAAGACGAATAATGCGATTTTCAAAATTTCACAA
1 AAAATGATATTTTAA-GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCA
* * * * * * *
1355810 TGTATAAGTCCCTCAGGCTATCAGTAAGTCTTTCGAGCAAGATGTTTAAATCCTTCGGGTCATCT
65 TTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCT
* *
1355875 GTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTT
130 GTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTT
* * *
1355940 TTAAATGAATTTG
195 TCACATGAAATTG
*
1355953 AAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAAT
1 AAAATG-----AT-A--TTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAAT
* * * *
1356018 TTCACGATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG
58 TTCACCATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGG
* * * * *
1356083 GTCATCTGTAAGCCTTTAGAGCAGGATGATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAG
123 GTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAG
1356148 GATGTTTATCAC
188 GATGTTT-TCAC
1356160 CAGGATAATA
Statistics
Matches: 1360, Mismatches: 71, Indels: 39
0.93 0.05 0.03
Matches are distributed among these distances:
204 2 0.00
205 184 0.14
206 51 0.04
207 758 0.56
208 2 0.00
210 2 0.00
212 3 0.00
215 304 0.22
216 54 0.04
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (207 bp):
AAAATGATATTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACCAT
TTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
TAAGCCTTTAGAGCAAGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
CACATGAAATTG
Found at i:1355046 original size:42 final size:42
Alignment explanation
Indices: 1354980--1355061 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1354970 TCACCATTTA
* *
1354980 TAAATCCTTCGGGCTATCAATAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGCTATCAATAAGTCTTTAGAGCAAGATGCT
**
1355022 TAAATCCTTCGGG-TCATCTGTAAGTCTTTAGAGCAAGATG
1 TAAATCCTTCGGGCT-ATCAATAAGTCTTTAGAGCAAGATG
1355062 ATAAGTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGCTATCAATAAGTCTTTAGAGCAAGATGCT
Found at i:1355675 original size:42 final size:41
Alignment explanation
Indices: 1355616--1355709 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
1355606 TTATAAGTCA
* * *
1355616 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCC
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG-ATAAATCC
* * *
1355658 TTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCC
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAATCC
1355699 TTCGGGCCATC
1 TTCGGGCCATC
1355710 CATAAGACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAATCC
Found at i:1355892 original size:42 final size:41
Alignment explanation
Indices: 1355833--1355914 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
1355823 CAGGCTATCA
* * * *
1355833 GTAAGTCTTTCGAGCAAGATGTTTAAATCCTTCGGGTCATCT
1 GTAAGCCTTTAGAGCAAGATG-ATAAATCCTTCGGGCCATCT
*
1355875 GTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATC
1 GTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATC
1355915 CATAAGACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 16 0.46
42 19 0.54
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (41 bp):
GTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATCT
Found at i:1356127 original size:41 final size:42
Alignment explanation
Indices: 1356029--1356129 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1356019 TCACGATTTG
* * * * *
1356029 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAGGATGCA
* * *
1356071 TAAATCCTTCAGGTCATCTGTAAGCCTTTAGAGCAGGATG-A
1 TAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAGGATGCA
1356112 TAAGTCCTTCGGGTCATC
1 TAAGTCCTTCGGGTCATC
1356130 CATAAGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAGGATGCA
Found at i:1363170 original size:41 final size:44
Alignment explanation
Indices: 1363086--1363181 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 44
1363076 TGTTAATGAT
* *
1363086 TTAAAAAATATATAATATATTAAGTTATAATCCTATTTTAATTA
1 TTAAAAAATATATAATATATTAAATTATAATCCTATTTAAATTA
*
1363130 TTAAAAAAT-TATTATAT-TTAAATTATAAT-C-ATCTTAAATTA
1 TTAAAAAATATATAATATATTAAATTATAATCCTAT-TTAAATTA
1363171 TTAAAAGAATA
1 TTAAAA-AATA
1363182 GGATTAAGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 2 0.04
41 14 0.30
42 14 0.30
43 7 0.15
44 9 0.20
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (44 bp):
TTAAAAAATATATAATATATTAAATTATAATCCTATTTAAATTA
Found at i:1363827 original size:16 final size:16
Alignment explanation
Indices: 1363806--1363837 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1363796 GTCCGAATGT
1363806 ACTTACTCTTTTTAAA
1 ACTTACTCTTTTTAAA
1363822 ACTTACTCTTTTTAAA
1 ACTTACTCTTTTTAAA
1363838 GAATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTTACTCTTTTTAAA
Found at i:1365534 original size:25 final size:25
Alignment explanation
Indices: 1365469--1365535 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
1365459 TATCCGACCT
* * *
1365469 AAAT-AAATATATTTTTATAAAGTA
1 AAATAAAATATATATTTAAAAAATA
1365493 AAATAAGGAAT-TA-ATTTAAAAAATA
1 AAATAA--AATATATATTTAAAAAATA
1365518 AAATAAAATATATATTTA
1 AAATAAAATATATATTTA
1365536 TTATAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
23 3 0.09
24 6 0.17
25 21 0.60
26 2 0.06
27 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATAAAATATATATTTAAAAAATA
Found at i:1367432 original size:21 final size:21
Alignment explanation
Indices: 1367406--1367451 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1367396 ATTAATAACA
* *
1367406 CTAAACCTTAACCCATAACTT
1 CTAAACCCTAAACCATAACTT
* *
1367427 CTAAACCCTAAACCTTAATTT
1 CTAAACCCTAAACCATAACTT
1367448 CTAA
1 CTAA
1367452 CTTAAAACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
CTAAACCCTAAACCATAACTT
Found at i:1370127 original size:14 final size:13
Alignment explanation
Indices: 1370099--1370124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1370089 TCTGGCTTTG
1370099 GTTTCAGTATTTT
1 GTTTCAGTATTTT
1370112 GTTTCAGTATTTT
1 GTTTCAGTATTTT
1370125 TGTCCTTTCA
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:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
GTTTCAGTATTTT
Found at i:1378489 original size:59 final size:59
Alignment explanation
Indices: 1378423--1378542 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 59
1378413 AAATATGTCT
**
1378423 TTGAACTTTT-AAATGTTCTAATTTCATCCGTAAACTATGA-CTATCATTCT-AATTAATCC
1 TTGAACTTTTAAAAT-TTC-AATTTCATCCCCAAACTATGACCT-TCATTCTAAATTAATCC
* *
1378482 TTGAACTTTTGAAAATTTCAATTTCATCCCCAAACTCTGACCTTCATTCTAAATTGATCC
1 TTGAACTTTT-AAAATTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATTAATCC
1378542 T
1 T
1378543 CACACTTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 35 0.66
60 14 0.26
61 4 0.08
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (59 bp):
TTGAACTTTTAAAATTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATTAATCC
Found at i:1380314 original size:2 final size:2
Alignment explanation
Indices: 1380307--1380334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1380297 ATCATTAACA
1380307 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
1380335 TCGTACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1389102 original size:20 final size:20
Alignment explanation
Indices: 1389077--1389116 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1389067 ATCGATTGAA
*
1389077 ATTTTTGAATATCTCTTGTT
1 ATTTTTGAATATCTATTGTT
1389097 ATTTTTGAATATCTATTGTT
1 ATTTTTGAATATCTATTGTT
1389117 TGTGATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (20 bp):
ATTTTTGAATATCTATTGTT
Found at i:1395075 original size:21 final size:20
Alignment explanation
Indices: 1394989--1395146 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1394979 AAATGACCAA
**
1394989 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1395008 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1395028 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1395048 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1395069 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* ** *
1395090 CAAATTCGCATTGTGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1395110 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1395131 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1395147 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1395175 original size:20 final size:20
Alignment explanation
Indices: 1395113--1395342 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
1395103 TGATTTTCCA
* ** *
1395113 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1395133 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
1395153 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1395173 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1395193 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1395213 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1395233 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1395253 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1395273 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1395293 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1395313 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1395333 AAATCACAAC
1 AAATCGCAAC
1395343 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1396263 original size:12 final size:12
Alignment explanation
Indices: 1396246--1396270 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1396236 ATATAATCCT
1396246 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1396258 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1396270 G
1 G
1396271 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1398575 original size:19 final size:19
Alignment explanation
Indices: 1398553--1398821 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
1398543 CGGAAATTAC
*
1398553 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1398572 AATCACAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1398586 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1398606 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1398620 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398639 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1398658 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1398672 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398691 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1398710 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1398724 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398743 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1398762 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
1398776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398795 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398814 AATCGCAA
1 AATCGCAA
1398822 CGAGAGAATC
Statistics
Matches: 212, Mismatches: 12, Indels: 52
0.77 0.04 0.19
Matches are distributed among these distances:
14 52 0.25
15 5 0.02
16 7 0.03
17 6 0.03
18 6 0.03
19 123 0.58
20 13 0.06
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Done.