Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2713
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: 368274
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
File 3 of 3
Found at i:303756 original size:40 final size:40
Alignment explanation
Indices: 303701--303782 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
303691 GACTTTGCAC
*
303701 TTTTTTTCTGTGTTTTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTCTGTGTTTTTTTTTTTGTTTGTTTGTTTTTTTT
*
303741 TTTTTTTGTGTGTTTTTTTTTTTGTTTGTTTGTTTTTTTT
1 TTTTTTTCTGTGTTTTTTTTTTTGTTTGTTTGTTTTTTTT
303781 TT
1 TT
303783 ATCACCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (40 bp):
TTTTTTTCTGTGTTTTTTTTTTTGTTTGTTTGTTTTTTTT
Found at i:303794 original size:1 final size:1
Alignment explanation
Indices: 303713--303782 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
303703 TTTTTCTGTG
* * * * * * * *
303713 TTTTTTTTTTTGTTTTTTTGTTTTTTTTTTTTTTTGTGTGTTTTTTTTTTTGTTTGTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
303778 TTTTT
1 TTTTT
303783 ATCACCTTTT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:310755 original size:52 final size:52
Alignment explanation
Indices: 310685--310805 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
310675 GAAAATTTAT
*
310685 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
310737 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
310789 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
310806 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:310818 original size:52 final size:51
Alignment explanation
Indices: 310685--310825 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
310675 GAAAATTTAT
310685 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
310737 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
310789 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
310826 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:310832 original size:13 final size:13
Alignment explanation
Indices: 310814--310838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
310804 CAAAGATCAG
310814 TGTATCGATACAA
1 TGTATCGATACAA
310827 TGTATCGATACA
1 TGTATCGATACA
310839 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:310921 original size:13 final size:13
Alignment explanation
Indices: 310903--310927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
310893 ACAAAAAATA
310903 TGTATCGATACAT
1 TGTATCGATACAT
310916 TGTATCGATACA
1 TGTATCGATACA
310928 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:310923 original size:32 final size:33
Alignment explanation
Indices: 310882--310947 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
310872 AGTAGCTTAA
310882 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
310914 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
310947 A
1 A
310948 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:316045 original size:79 final size:80
Alignment explanation
Indices: 315936--316128 Score: 232
Period size: 79 Copynumber: 2.4 Consensus size: 80
315926 GAAAAATTTA
* * * * * *
315936 ATATTTTGAAGATAAAGA-CGGGGTTGGAGTATCCCT-TCAAAAATCACGGGG-CTGGAGTATCT
1 ATATTCTGAAAATAAA-ACCGGGGTTAGAGTATCCCTCTCAAAAATAACGGGGTC-GAAGTATCC
315998 CCGATTGTGAAAAATCG
64 CCGATTGTGAAAAATCG
* * *
316015 ATGTTCTGAAAATAAAACCGGGGTTTGAGTAT-TCTCTCAAAAATAACGGGGTCGAAGTATCCCC
1 ATATTCTGAAAATAAAACCGGGGTTAGAGTATCCCTCTCAAAAATAACGGGGTCGAAGTATCCCC
316079 GATTGTGAAAAATCG
66 GATTGTGAAAAATCG
* **
316094 ATATTCTGAAAATAAAATCAAGGTTAGAGTATCCC
1 ATATTCTGAAAATAAAACCGGGGTTAGAGTATCCC
316129 CGATGGTGGG
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
78 3 0.03
79 91 0.95
80 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (80 bp):
ATATTCTGAAAATAAAACCGGGGTTAGAGTATCCCTCTCAAAAATAACGGGGTCGAAGTATCCCC
GATTGTGAAAAATCG
Found at i:316125 original size:51 final size:52
Alignment explanation
Indices: 316070--316181 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 52
316060 ACGGGGTCGA
*
316070 AGTATCCCCGATTGTGAAAAATCGATATTCTGAAAAT-AAAATCAAGGTTAG
1 AGTATCCCCGATGGTGAAAAATCGATATTCTGAAAATAAAAATCAAGGTTAG
** * * * * * *
316121 AGTATCCCCGATGGTGGGAAATTGGTGTTTTGGAAATAAAAATCGAGGTTAG
1 AGTATCCCCGATGGTGAAAAATCGATATTCTGAAAATAAAAATCAAGGTTAG
316173 AGTATCCCC
1 AGTATCCCC
316182 TAAAAAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 29 0.57
52 22 0.43
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
AGTATCCCCGATGGTGAAAAATCGATATTCTGAAAATAAAAATCAAGGTTAG
Found at i:316269 original size:79 final size:79
Alignment explanation
Indices: 316115--316656 Score: 475
Period size: 79 Copynumber: 6.8 Consensus size: 79
316105 ATAAAATCAA
* ** * * * *
316115 GGTTAGAGTATCCCCGATGGTGGGAAATTGGTGTTTTGGAAATAAAAATCGAGGTTAGAGTATCC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAAT-AAAATCGAGGTTGGAGTATCC
* * *
316180 CCTAAAAAATAACAG
65 CCTCAGAAATAACGG
* * * * *
316195 GGTTGGAGTATCTCCGATTGTGGCAAATCAGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
316260 CTCAGAAATAACGG
66 CTCAGAAATAACGG
* * ** * * * * *
316274 GGCTGGAGTATGCCCGATGGTGGAAAA-TCGATGATTTGAAAATAAAA-CCAGAGTTAGAGCATC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAG-TGTTTTGAAAATAAAATCGAG-GTTGGAGTATC
* * *
316337 CCCTCGGAAATAATGA
64 CCCTCAGAAATAACGG
* * * *
316353 GATTGGAGTATCCTCGATTATGGAAAATTGGTG-TTTGAGAAATAAAATCGGGGTTGGAGTAT-C
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAAAATCGAGGTTGGAGTATCC
** *
316416 CCTTTGAAAATAATGG
65 CCTCAG-AAATAACGG
* * * * *
316432 GGTTGGAGTATCCCCGATTAT-GAAAAATCGATATTTTGAAAATAAAATCG-GAGTTAGAGCATC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAG-TGTTTTGAAAATAAAATCGAG-GTTGGAGTATC
** *
316495 CTTTCGGAAATAACGG
64 CCCTCAGAAATAACGG
* * * * *
316511 GGTTGGAGAATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGAAGTATCCC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
*
316576 CTCAAAAATAACGG
66 CTCAGAAATAACGG
* * ** * * * *
316590 GGCTGAAGTATCTTCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCTAAGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
316655 CT
66 CT
316657 TGGAAGTAAA
Statistics
Matches: 373, Mismatches: 77, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
78 22 0.06
79 297 0.80
80 54 0.14
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
CTCAGAAATAACGG
Found at i:316303 original size:210 final size:210
Alignment explanation
Indices: 315957--316339 Score: 504
Period size: 210 Copynumber: 1.8 Consensus size: 210
315947 ATAAAGACGG
* * * * *
315957 GGTTGGAGTATCCCTTCAAAAATCACGGGGCTGGAGTATCTCCGATTGTGAAAAATCGATGTTCT
1 GGTTAGAGTATCCCCTAAAAAATAACAGGGCTGGAGTATCTCCGATTGTGAAAAATCGATGTTCT
* * * * * *
316022 GAAAATAAAACCGGGGTTTGAGTATTCTCTCAAAAATAACGGGGTCGAAGTATCCCCGATTGTGA
66 AAAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTCGAAGTATCCCCGATGGTGA
*
316087 AAAATCGAT-ATTCTGAAAATAAAATCAAG-GTTAGAGTATCCCCGATGGTGGGAAATTGGTGTT
131 AAAATCGATGATT-TGAAAATAAAA-CAAGAGTTAGAGCATCCCCGATGGTGGGAAATTGGTGTT
316150 TTGGAAATAAAAATCGA
194 TTGGAAATAAAAATCGA
* ** *
316167 GGTTAGAGTATCCCCTAAAAAATAACAGGGTTGGAGTATCTCCGATTGTGGCAAATC-AGTGTTT
1 GGTTAGAGTATCCCCTAAAAAATAACAGGGCTGGAGTATCTCCGATTGTGAAAAATCGA-TGTTC
* * * *
316231 TAAAAATAAAATCGAGGTTGGAGTATCCCCTCAGAAATAACGGGG-CTGGAGTATGCCCGATGGT
65 TAAAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTC-GAAGTATCCCCGATGGT
* *
316295 GGAAAATCGATGATTTGAAAATAAAACCAGAGTTAGAGCATCCCC
129 GAAAAATCGATGATTTGAAAATAAAACAAGAGTTAGAGCATCCCC
316340 TCGGAAATAA
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
209 5 0.03
210 139 0.95
211 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (210 bp):
GGTTAGAGTATCCCCTAAAAAATAACAGGGCTGGAGTATCTCCGATTGTGAAAAATCGATGTTCT
AAAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTCGAAGTATCCCCGATGGTGA
AAAATCGATGATTTGAAAATAAAACAAGAGTTAGAGCATCCCCGATGGTGGGAAATTGGTGTTTT
GGAAATAAAAATCGA
Found at i:316360 original size:158 final size:157
Alignment explanation
Indices: 316197--316661 Score: 524
Period size: 158 Copynumber: 2.9 Consensus size: 157
316187 AATAACAGGG
* * * *
316197 TTGGAGTATCTCCGATTGTGGCAAATCAGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCCT
1 TTGGAGTATC-CCGATTATGGAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCT
* * *
316262 CAGAAATAACGGGGCTGGAGTATGCCCGATGGTGGAAAATCGATGA-TTTGAAAATAAAACCAGA
65 CAGAAATAACGGGGCTGGAGTATCCCCGATGATGAAAAATCGAT-ATTTTGAAAATAAAACCAGA
*
316326 GTTAGAGCATCCCCTCGGAAATAATGAGA
129 GTTAGAGCATCCCCTCGGAAATAACGAGA
* * *
316355 TTGGAGTATCCTCGATTATGGAAAATTGGTGTTTGAGAAATAAAATCGGGGTTGGAGTAT-CCCT
1 TTGGAGTATCC-CGATTATGGAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCT
** * * * * *
316419 TTGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCGGA
65 CAG-AAATAACGGGGCTGGAGTATCCCCGATGATGAAAAATCGATATTTTGAAAATAAAACCAGA
** * *
316484 GTTAGAGCATCCTTTCGGAAATAACGGGG
129 GTTAGAGCATCCCCTCGGAAATAACGAGA
* * *
316513 TTGGAGAATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGAAGTATCCCCT
1 TTGGAGTAT-CCCGATTATGGAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCT
* * ** * * *
316578 CAAAAATAACGGGGCTGAAGTATCTTCGATTATGAAAAAT-TAGTGTTTTGAAAATAAAACCTA-
65 CAGAAATAACGGGGCTGGAGTATCCCCGATGATGAAAAATCGA-TATTTTGAAAATAAAACC-AG
* * *
316641 AGTTGGAGTATCCCCTTGGAA
128 AGTTAGAGCATCCCCTCGGAA
316662 GTAAAAACAT
Statistics
Matches: 255, Mismatches: 45, Indels: 14
0.81 0.14 0.04
Matches are distributed among these distances:
157 8 0.03
158 241 0.95
159 6 0.02
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (157 bp):
TTGGAGTATCCCGATTATGGAAAATTAGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTC
AGAAATAACGGGGCTGGAGTATCCCCGATGATGAAAAATCGATATTTTGAAAATAAAACCAGAGT
TAGAGCATCCCCTCGGAAATAACGAGA
Found at i:316555 original size:237 final size:238
Alignment explanation
Indices: 316120--316656 Score: 548
Period size: 237 Copynumber: 2.3 Consensus size: 238
316110 ATCAAGGTTA
* ** * *
316120 GAGTATCCCCGATGGTGGGAAATTGGTGTTTTG-GAAATAAAAATCGAGGTTAGAGTATCCCCTA
1 GAGTATCCTCGATTATGGAAAATTGGTGTTTTGAGAAAT-AAAATCGAGGTTGGAGTATCCCCTA
* * ** *
316184 AAAAATAACAGGGTTGGAGTATCTCCGATTGTGGCAAATCAGTGTTTTAAAAATAAAATCGAGGT
65 AAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCAGTATTTTAAAAATAAAATCGAGGT
* * * * * * * *
316249 TGGAGTATCCCCTCAGAAATAACGGGGCTGGAGTATGCCCGATGGTGGAAAATCGATGATTTGAA
130 TAGAGCATCCCCTCAGAAATAACGGGGCTGGAGAATCCCCGATGATGAAAAATAGATGATTTAAA
** * *
316314 AATAAAACCAGAGTT-AGAGCATCCCCTCGGAAATAATGAGATTG
195 AATAAAACCAGAGTTGA-AGCATCCCCTCAAAAATAACGAGACTG
* * **
316358 GAGTATCCTCGATTATGGAAAATTGGTG-TTTGAGAAATAAAATCGGGGTTGGAGTATCCCTTTG
1 GAGTATCCTCGATTATGGAAAATTGGTGTTTTGAGAAATAAAATCGAGGTTGGAGTATCCCCTAA
** *
316422 AAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATC-GATATTTTGAAAATAAAATCG-GAG
66 AAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCAG-TATTTTAAAAATAAAATCGAG-G
** * * * *
316485 TTAGAGCATCCTTTCGGAAATAACGGGGTTGGAGAATCCCCGATTATGAAAAATTAG-TGTTTTA
129 TTAGAGCATCCCCTCAGAAATAACGGGGCTGGAGAATCCCCGATGATGAAAAA-TAGATGATTTA
* * * * * *
316549 AAAATAAAATCGGGGTTGAAGTATCCCCTCAAAAATAACGGGGCTG
193 AAAATAAAACCAGAGTTGAAGCATCCCCTCAAAAATAACGAGACTG
* * * * * * *
316595 AAGTATCTTCGATTATGAAAAATTAGTGTTTTGA-AAATAAAACCTAAGTTGGAGTATCCCCT
1 GAGTATCCTCGATTATGGAAAATTGGTGTTTTGAGAAATAAAATCGAGGTTGGAGTATCCCCT
316657 TGGAAGTAAA
Statistics
Matches: 243, Mismatches: 50, Indels: 13
0.79 0.16 0.04
Matches are distributed among these distances:
236 2 0.01
237 204 0.84
238 37 0.15
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (238 bp):
GAGTATCCTCGATTATGGAAAATTGGTGTTTTGAGAAATAAAATCGAGGTTGGAGTATCCCCTAA
AAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCAGTATTTTAAAAATAAAATCGAGGTT
AGAGCATCCCCTCAGAAATAACGGGGCTGGAGAATCCCCGATGATGAAAAATAGATGATTTAAAA
ATAAAACCAGAGTTGAAGCATCCCCTCAAAAATAACGAGACTG
Found at i:319129 original size:24 final size:20
Alignment explanation
Indices: 319067--319121 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
319057 TAAAACCCAA
*
319067 AATGTATCAATACAATGAAT
1 AATGTATCGATACAATGAAT
319087 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAT
319107 AATGTATCGATACAA
1 AATGTATCGATACAA
319122 CTTGTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAT
Found at i:319397 original size:21 final size:21
Alignment explanation
Indices: 319373--319419 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
319363 TTTTTTAAAA
* * * *
319373 ATTTTGAAAATATTTTTTTAT
1 ATTTTAAAAATAATTATTAAT
319394 ATTTTAAAAATAATTATTAAT
1 ATTTTAAAAATAATTATTAAT
319415 ATTTT
1 ATTTT
319420 TAATTTTTTT
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:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTAAAAATAATTATTAAT
Found at i:320662 original size:33 final size:33
Alignment explanation
Indices: 320625--320693 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
320615 AAATATCGTT
** * *
320625 TTTATCT-TAATTTTAAGTATATTACAAATGAAA
1 TTTATCTCTAA-TTTAACAATATTAAAAATAAAA
320658 TTTATCTCTAATTTAACAATATTAAAAATAAAA
1 TTTATCTCTAATTTAACAATATTAAAAATAAAA
320691 TTT
1 TTT
320694 TTCAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (33 bp):
TTTATCTCTAATTTAACAATATTAAAAATAAAA
Found at i:320736 original size:13 final size:14
Alignment explanation
Indices: 320711--320751 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
320701 AAGATGATGG
320711 TTAAAAATAATTTT
1 TTAAAAATAATTTT
320725 TTAAAAAT-A---T
1 TTAAAAATAATTTT
320735 TTAAAAATAATTTT
1 TTAAAAATAATTTT
320749 TTA
1 TTA
320752 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 1 0.04
14 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAAATAATTTT
Found at i:320775 original size:30 final size:30
Alignment explanation
Indices: 320722--320784 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
320712 TAAAAATAAT
* *
320722 TTTTTAAAAATATTTAAAAATAATTTTTTA
1 TTTTTAAAAATAATTAAAAATAATTTTTAA
***
320752 TTTTTAAAAATAATTATTGATAATTTTTAA
1 TTTTTAAAAATAATTAAAAATAATTTTTAA
320782 TTT
1 TTT
320785 CTTTAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTAAAAATAATTAAAAATAATTTTTAA
Found at i:322056 original size:31 final size:31
Alignment explanation
Indices: 322021--322079 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
322011 CTTTAATTTA
322021 ATAAT-ACTAAAAATAAATATTTTTAAAAAAG
1 ATAATGACTAAAAAT-AATATTTTTAAAAAAG
** *
322052 ATAATGGTTAAAAATAATTTTTTTAAAA
1 ATAATGACTAAAAATAATATTTTTAAAA
322080 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (31 bp):
ATAATGACTAAAAATAATATTTTTAAAAAAG
Found at i:322122 original size:30 final size:31
Alignment explanation
Indices: 322066--322132 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
322056 TGGTTAAAAA
* *
322066 TAATTTTTTTAAAATATTTAAAAATAATTTT
1 TAATTTTTTAAAAATATTTAAAAATAATCTT
* **
322097 TTATTTTTTAAAAAT-TTTATTAATAATCTT
1 TAATTTTTTAAAAATATTTAAAAATAATCTT
322127 TAATTT
1 TAATTT
322133 AATTTTATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
TAATTTTTTAAAAATATTTAAAAATAATCTT
Found at i:323015 original size:16 final size:16
Alignment explanation
Indices: 322986--323088 Score: 61
Period size: 16 Copynumber: 6.4 Consensus size: 16
322976 GTTAAAAAGC
*
322986 TCAAACTT-ACAATAAT
1 TCAAACTTGA-AAAAAT
* *
323002 TCGAACTTGAAATAACT
1 TCAAACTTGAAA-AAAT
* *
323019 T-GAACTT-AAAAGAAC
1 TCAAACTTGAAAA-AAT
* *
323034 TCAAAC-TCAAAAGAAC
1 TCAAACTTGAAAA-AAT
*
323050 TCAAACTTGAAAAAAA
1 TCAAACTTGAAAAAAT
323066 TCAAACTTGAAAAAAT
1 TCAAACTTGAAAAAAT
*
323082 TCGAACT
1 TCAAACT
323089 CAAGAGAACC
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.01
15 6 0.08
16 55 0.77
17 9 0.13
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.23
Consensus pattern (16 bp):
TCAAACTTGAAAAAAT
Found at i:323081 original size:15 final size:16
Alignment explanation
Indices: 323050--323080 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
323040 TCAAAAGAAC
323050 TCAAACTTGAAAAAAA
1 TCAAACTTGAAAAAAA
323066 TCAAACTTGAAAAAA
1 TCAAACTTGAAAAAA
323081 TTCGAACTCA
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:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (16 bp):
TCAAACTTGAAAAAAA
Found at i:323552 original size:2 final size:2
Alignment explanation
Indices: 323536--323579 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
323526 ATATGAAAGC
323536 TA TA -A TA TA -A 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 TA TA TA TA TA
323576 TA TA
1 TA TA
323580 AAATGAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:325965 original size:87 final size:88
Alignment explanation
Indices: 325815--325992 Score: 252
Period size: 87 Copynumber: 2.0 Consensus size: 88
325805 TCTAAACTTA
* * **
325815 ATTCCCATGTTAATTTTATCACCCAATTAATATGCATATGTCCAAAAACTATTTACTGCAACCCA
1 ATTCCCATGTTAATTTTATCACCCAATTAATATGCATATGTCCAAAAAATAATTACTAAAACCCA
*
325880 ATG-CCCTTAGAATCT-ATAATTC
66 ATGAACCTTA-AATCTAATAATTC
* * *
325902 ATTCCCATGTTAATTTTATCATCCAATTAATTTGCATATTTCCAAAAAATAATTACTAAAACCCA
1 ATTCCCATGTTAATTTTATCACCCAATTAATATGCATATGTCCAAAAAATAATTACTAAAACCCA
*
325967 ATGAACTTTAAATCTAATAATTC
66 ATGAACCTTAAATCTAATAATTC
325990 ATT
1 ATT
325993 TTTTTTAGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
87 66 0.82
88 14 0.17
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (88 bp):
ATTCCCATGTTAATTTTATCACCCAATTAATATGCATATGTCCAAAAAATAATTACTAAAACCCA
ATGAACCTTAAATCTAATAATTC
Found at i:329500 original size:77 final size:78
Alignment explanation
Indices: 329396--329547 Score: 261
Period size: 77 Copynumber: 2.0 Consensus size: 78
329386 GGCAGCAAAA
* *
329396 GGCCTATGATATTTATGTTGGTGTCTGTCTTAATACTATTTGTATTATTAGTTATGTAATGCATG
1 GGCCTATAATATTTATGTTGGTGTCTGTCTTAATACTAATTGTATTATTAGTTATGTAATGCATG
329461 TCACATTAAGAAT
66 TCACATTAAGAAT
*
329474 GGCCTATAATA-TTATGTTGGTGTCTGTCTTAATACTAATTGTATTATTAGTTGTGTAATGCATG
1 GGCCTATAATATTTATGTTGGTGTCTGTCTTAATACTAATTGTATTATTAGTTATGTAATGCATG
*
329538 TCATATTAAG
66 TCACATTAAG
329548 CATTATAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
77 60 0.86
78 10 0.14
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (78 bp):
GGCCTATAATATTTATGTTGGTGTCTGTCTTAATACTAATTGTATTATTAGTTATGTAATGCATG
TCACATTAAGAAT
Found at i:334200 original size:79 final size:78
Alignment explanation
Indices: 334052--334327 Score: 249
Period size: 79 Copynumber: 3.5 Consensus size: 78
334042 ATTTTTGGTG
* *
334052 AAAATCGGGGTTGGAGTATCCCCTC--AAA-GATAGTGGGTTGAAGTATCCTCGAGATG-AAAAT
1 AAAAT-GGGGTTGGAGTATCCCCTCAGAAATGAT-G-GGGTTGAAGTATCC-CCA-ATGTAAAAA
* *
334113 TTTAATA-TTTCGAAAGTA
61 ATTAATATTTTGGAAA-TA
*
334131 AAAATGGGGTTGGAGTATCCCCTC-GAAAATGATGGGGTTGGAGTATCCCCAATAGTAAAAAATT
1 AAAATGGGGTTGGAGTATCCCCTCAG-AAATGATGGGGTTGAAGTATCCCCAAT-GTAAAAAATT
*
334195 GATATTTTGGAAATA
64 AATATTTTGGAAATA
*** * * ** ** *
334210 AAAACATGGATAGAGTATATCCTCAGAAATGATGGGGTTGAAGTATCCCCGACGGTAAAAAATCA
1 AAAATGGGGTTGGAGTATCCCCTCAGAAATGATGGGGTTGAAGTATCCCC-AATGTAAAAAATTA
334275 ATATTTTGGAAATA
65 ATATTTTGGAAATA
* * * *
334289 AAAATGAGGTTGGACTATCCCCTCAGAGATAATGGGGTT
1 AAAATGGGGTTGGAGTATCCCCTCAGAAATGATGGGGTT
334328 AGAGTGTCCC
Statistics
Matches: 161, Mismatches: 28, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
77 2 0.01
78 22 0.14
79 121 0.75
80 13 0.08
81 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (78 bp):
AAAATGGGGTTGGAGTATCCCCTCAGAAATGATGGGGTTGAAGTATCCCCAATGTAAAAAATTAA
TATTTTGGAAATA
Found at i:334464 original size:79 final size:79
Alignment explanation
Indices: 334372--334584 Score: 279
Period size: 79 Copynumber: 2.7 Consensus size: 79
334362 TCCTTGAAAG
*
334372 TGAAAAATCGATATTTT-AGAAATAAAAACGGGGTTTGAGTATCCCCTTGAAAATGATGGGGTCG
1 TGAAAAATCGATATTTTGA-AAATAAAAACGGGGTTGGAGTATCCCCTTGAAAATGATGGGGTCG
* *
334436 GAGTGTCCCCGACAA
65 GAATATCCCCGACAA
* * *
334451 TGAAAAATTGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCC-TCAGAAATGATGGGGTTG
1 TGAAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTTGA-AAATGATGGGGTCG
* **
334515 GAATATTCCCGATGA
65 GAATATCCCCGACAA
* *
334530 TAAAAAATCGATATTTTGAAAATAAAAACGAGGTTGGAGTAT-CCCTTCGAAAATG
1 TGAAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTT-GAAAATG
334585 GTAGGGTTGT
Statistics
Matches: 117, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
78 5 0.04
79 110 0.94
80 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (79 bp):
TGAAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTTGAAAATGATGGGGTCGG
AATATCCCCGACAA
Found at i:334620 original size:79 final size:77
Alignment explanation
Indices: 334374--334621 Score: 259
Period size: 79 Copynumber: 3.1 Consensus size: 77
334364 CTTGAAAGTG
* *
334374 AAAAATCGATATTTT-AGAAATAAAAACGGGGTTTGAGTATCCCCTT-GAAAATGATGGGGTCGG
1 AAAAATCGATATTTTGA-AAATAAAAACGGGGTTGGAGTAT-CCCTTCGAAAATGATGGGGTTGG
* * **
334437 AGTGTCCCCGACAAT
64 AGTAT-CCCAATGAT
* *
334452 GAAAAATTGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTC-AGAAATGATGGGGTTGG
1 -AAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTTCGA-AAATGATGGGGTTGG
* *
334516 AATATTCCCGATGAT
64 AGTA-TCCCAATGAT
* * * *
334531 AAAAAATCGATATTTTGAAAATAAAAACGAGGTTGGAGTATCCCTTCGAAAATGGTAGGGTTGTA
1 -AAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTTCGAAAATGATGGGGTTGGA
334596 GTATCCCTAATGGAT
65 GTATCCC-AAT-GAT
*
334611 AAAATTCGATA
1 AAAAATCGATA
334622 AAATATTTTA
Statistics
Matches: 144, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
78 9 0.06
79 129 0.90
80 6 0.04
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (77 bp):
AAAAATCGATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCTTCGAAAATGATGGGGTTGGAG
TATCCCAATGAT
Found at i:336952 original size:52 final size:52
Alignment explanation
Indices: 336869--337006 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 52
336859 AATTACTTGC
** * *
336869 ATGTATTGATACTTTGAAGAATGTATCGATACATGT-GGGTCAAAAACTCAGA
1 ATGTATTGATACAATGAAAAATGTATCGATACATGTAGGGT-AAAAACCCAGA
* * * * *
336921 ATGTATTGATACAATGAAAAATGTTTTGATACATTTAGGGTTAAAACCCATA
1 ATGTATTGATACAATGAAAAATGTATCGATACATGTAGGGTAAAAACCCAGA
* * * *
336973 ATGTATCGATACAATAAAAAATGTGTCAATACAT
1 ATGTATTGATACAATGAAAAATGTATCGATACAT
337007 TTTCTTTCCA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 67 0.94
53 4 0.06
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (52 bp):
ATGTATTGATACAATGAAAAATGTATCGATACATGTAGGGTAAAAACCCAGA
Found at i:340682 original size:27 final size:27
Alignment explanation
Indices: 340652--340720 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
340642 GAAAAAACGG
*
340652 GGTTAGAGTATCCCCTCAGAAGAATGA
1 GGTTAAAGTATCCCCTCAGAAGAATGA
*
340679 GGTTAAAGTATCCCTTCAGAAGAATGA
1 GGTTAAAGTATCCCCTCAGAAGAATGA
340706 GGTTAAAGTATCCCC
1 GGTTAAAGTATCCCC
340721 AATGATGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (27 bp):
GGTTAAAGTATCCCCTCAGAAGAATGA
Found at i:349242 original size:79 final size:79
Alignment explanation
Indices: 349143--349332 Score: 231
Period size: 79 Copynumber: 2.4 Consensus size: 79
349133 AATTATTGAT
* * *
349143 TTTTAATTTCCAAAAAATCAATTTTTTACCATCGGAGATACTCGAATCCC-ATTATTTATAAGGG
1 TTTT-ATTTCCAAAATATCAATTTTTCACCATCGGAGATACTCGAA-CCCTATTATTTACAAGGG
*
349207 GATACTCTAACCCCAA
64 GATACTCAAACCCCAA
* * * * * *
349223 TTTTATTTTCAAAATATCAAATTTTCACCATCGGGGATACTCTAACCCTGTTATTTCCAAGGGGA
1 TTTTATTTCCAAAATATCAATTTTTCACCATCGGAGATACTCGAACCCTATTATTTACAAGGGGA
* *
349288 TACTCAAATCCCAT
66 TACTCAAACCCCAA
349302 TTTTATTTCCAAAATATTC-ATTTTTCACCAT
1 TTTTATTTCCAAAATA-TCAATTTTTCACCAT
349333 TGATGATACT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
78 3 0.03
79 85 0.90
80 6 0.06
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (79 bp):
TTTTATTTCCAAAATATCAATTTTTCACCATCGGAGATACTCGAACCCTATTATTTACAAGGGGA
TACTCAAACCCCAA
Found at i:349361 original size:130 final size:130
Alignment explanation
Indices: 349206--349480 Score: 374
Period size: 130 Copynumber: 2.1 Consensus size: 130
349196 ATTTATAAGG
* *
349206 GGATACTCTAACCCCAATTTTATTTTCAAAATATCAAATTTTCACCATCGGGGATACTCTAACC-
1 GGATACTCCAACCCCAATTTTATTTTCAAAATATCAAATTTTCACCATCGGGGATACTCCAACCT
* * *
349270 CTGTTATTTCCAAGGGGATACTCAAATCCCATTTTTATTTCCAAAATATTC-ATTTTTCACCATT
66 C-ATTATTTCCAAGGGGATACTCAAACCCCATTTTTACTTCCAAAATA-TCAATTTTTCACCATT
349334 GA
129 GA
* * * ** *
349336 TGATACTCCAACCTCGATTTTATTTTCAAAATATTGATTTTTCACCATCGGGGATACTCCAACCT
1 GGATACTCCAACCCCAATTTTATTTTCAAAATATCAAATTTTCACCATCGGGGATACTCCAACCT
* * * *
349401 CATTATTTTCAAGGGGATACTCCAACCCCGTTTTTACTTCCAAAATATCAAATTTTTCACCATTT
66 CATTATTTCCAAGGGGATACTCAAACCCCATTTTTACTTCCAAAATATC-AATTTTTCACCATTG
349466 A
130 A
349467 GGATACTCCAACCC
1 GGATACTCCAACCC
349481 TCATTATTTC
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
129 2 0.02
130 96 0.77
131 27 0.22
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (130 bp):
GGATACTCCAACCCCAATTTTATTTTCAAAATATCAAATTTTCACCATCGGGGATACTCCAACCT
CATTATTTCCAAGGGGATACTCAAACCCCATTTTTACTTCCAAAATATCAATTTTTCACCATTGA
Found at i:349366 original size:51 final size:50
Alignment explanation
Indices: 349285--349412 Score: 154
Period size: 51 Copynumber: 2.6 Consensus size: 50
349275 ATTTCCAAGG
* * *
349285 GGATACTCAAATCC-CATTTTTATTTCCAAAATATTCATTTTTCACCATTGA
1 GGATACTCCAA-CCTCA-TTTTATTTTCAAAATATTCATTTTTCACCATCGA
* * *
349336 TGATACTCCAACCTCGATTTTATTTTCAAAATATTGATTTTTCACCATCGG
1 GGATACTCCAACCTC-ATTTTATTTTCAAAATATTCATTTTTCACCATCGA
349387 GGATACTCCAACCTCA--TTATTTTCAA
1 GGATACTCCAACCTCATTTTATTTTCAA
349413 GGGGATACTC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
48 10 0.15
50 3 0.04
51 54 0.79
52 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (50 bp):
GGATACTCCAACCTCATTTTATTTTCAAAATATTCATTTTTCACCATCGA
Found at i:349420 original size:79 final size:81
Alignment explanation
Indices: 349337--349489 Score: 211
Period size: 79 Copynumber: 1.9 Consensus size: 81
349327 CACCATTGAT
* * * ** *
349337 GATACTCCAACCTCGATTTTATTTTCAAAATAT-TGATTTTTCACCATCGGGGATACTCCAA-CC
1 GATACTCCAACCCCGATTTTACTTCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAACCC
349400 TCATTATTTTCAAGGG
66 TCATTATTTTCAAGGG
* **
349416 GATACTCCAACCCCGTTTTTACTTCCAAAATATCAAATTTTTCACCATTTAGGATACTCCAACCC
1 GATACTCCAACCCCGATTTTACTTCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAACCC
349481 TCATTATTT
66 TCATTATTT
349490 CTAAAAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 29 0.46
80 23 0.37
81 11 0.17
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (81 bp):
GATACTCCAACCCCGATTTTACTTCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAACCC
TCATTATTTTCAAGGG
Found at i:349517 original size:81 final size:80
Alignment explanation
Indices: 349338--349540 Score: 187
Period size: 81 Copynumber: 2.5 Consensus size: 80
349328 ACCATTGATG
* * * * ** *
349338 ATACTCCAACCTCGATTTTATTTTCAAAATAT-TGATTTTTCACCATCGGGGATACTCCAACCTC
1 ATACTCCAACCCCAATTTTATCTCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAACCTC
****
349402 ATTATTTTCAAGGGG
66 ATTATTTTCAAAAAA
** **
349417 ATACTCCAACCCCGTTTTTA-CTTCCAAAATATCAAATTTTTCACCATTTAGGATACTCCAACCC
1 ATACTCCAACCCCAATTTTATC-TCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAA-CC
349481 TCATTA-TTTCTAAAAAA
64 TCATTATTTTC-AAAAAA
* * * *
349498 ATACTCTAACCCCAATTTTATCTCCTAAATATTAAATCTTTCA
1 ATACTCCAACCCCAATTTTATCTCCAAAATATCAAATTTTTCA
349541 TCGGGGGATG
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
79 27 0.27
80 27 0.27
81 45 0.45
82 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (80 bp):
ATACTCCAACCCCAATTTTATCTCCAAAATATCAAATTTTTCACCATCGAGGATACTCCAACCTC
ATTATTTTCAAAAAA
Found at i:354833 original size:20 final size:20
Alignment explanation
Indices: 354796--354833 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
354786 ATAAGGTCCA
**
354796 GTATCGATACATTCACTTAT
1 GTATCGATACATGAACTTAT
354816 GTATCGATACATGAACTT
1 GTATCGATACATGAACTT
354834 GTTGTACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
GTATCGATACATGAACTTAT
Found at i:360611 original size:28 final size:28
Alignment explanation
Indices: 360452--361064 Score: 676
Period size: 28 Copynumber: 21.6 Consensus size: 28
360442 TTTAAAAAAA
* *
360452 GTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAATG
360482 AGTTGCCACTGACTTGTGTGGGCTTTGAAA-G
1 -G-TGCCACTGAC-T-TGTGGGCTTTGAAATG
* * * *
360513 GATGTCACTGACTTGTGGGTTTTAAAAAG
1 G-TGCCACTGACTTGTGGGCTTTGAAATG
* * * *
360542 AGTACCACTGACTTGTGGGATTTAAAAGG
1 -GTGCCACTGACTTGTGGGCTTTGAAATG
*
360571 GAATGCCACTGACTTATGGGCTTTGAAATG
1 G--TGCCACTGACTTGTGGGCTTTGAAATG
*
360601 GTGCCACTGACTTGTGGGCTTTGCAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
*
360629 ATGCCACTGACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
360657 GTGCCACTGACTTGTGGACTTTGAATTG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
*
360685 ATGCCACTGACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* ** *
360713 GTGCCACTGACTTATAAGCTTTGAAATT
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* ** * *
360741 ATGCCACAAACTTGTGGGCATTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
*
360769 ATGCCACTGACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* * *
360797 ATGCCACGGACTTATGGGCTTTGAAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
360824 GATGCCACTGACTTATGCGCTTTGAAATG
1 G-TGCCACTGACTTGTGGGCTTTGAAATG
*
360853 GTACCACTGACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
360881 GTGCCACTAACTTGTGAGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
360909 ATGCCACTGACTTATGGGCTTTGAAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
360936 GATGCTACTAACTTGTGGGCTTTGAAATG
1 G-TGCCACTGACTTGTGGGCTTTGAAATG
* *
360965 ATGCCACTAACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
*
360993 GTGCCACTGATTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* * *
361021 ATGCCACTGACTTGTGGACTTT-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAATG
* *
361048 GTGCCACGGAGTTGTGG
1 GTGCCACTGACTTGTGG
361065 ACTTAAATAG
Statistics
Matches: 500, Mismatches: 73, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
27 20 0.04
28 390 0.78
29 28 0.06
30 34 0.07
31 2 0.00
32 26 0.05
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAATG
Found at i:361062 original size:27 final size:27
Alignment explanation
Indices: 361020--361423 Score: 461
Period size: 27 Copynumber: 14.8 Consensus size: 27
361010 GCTTTGAAAT
* * *
361020 GATGCCACTGACTTGTGGACTTTAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
361047 GGTGCCACGGAGTTGTGGACTTAAATAG
1 GATGCCACGGAGTTGTGGACTTAAA-AG
* * ** *
361075 G-TACTATAGAGTTGTGGACCTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * *
361101 GGTGCCACGAAGTGGTGGACTTTAAAA-
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
*
361128 GAGTGCCACAGAGTTGTGGACTTAAAAG
1 GA-TGCCACGGAGTTGTGGACTTAAAAG
*
361156 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
*
361184 GGTGCCACGGAGTTGTGGACCTTAAAAG
1 GATGCCACGGAGTTGTGGA-CTTAAAAG
* *
361212 GATGCCACAGAGTTATGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
361239 GATGCCACAGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
361266 GATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * ** * * *
361293 AAGGCCACAAAGTTATGGACTCAAGAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
361320 GATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
**
361347 GATGCCATAGAGTTGTGGACTTTAAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
*
361375 GATGCCACGGAGTTGTAGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * *
361402 GATGCCACTGAATCGTGGACTT
1 GATGCCACGGAGTTGTGGACTT
361424 TGAAGAGGTC
Statistics
Matches: 319, Mismatches: 50, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.01
27 218 0.68
28 97 0.30
29 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (27 bp):
GATGCCACGGAGTTGTGGACTTAAAAG
Found at i:361102 original size:54 final size:54
Alignment explanation
Indices: 361020--361423 Score: 497
Period size: 55 Copynumber: 7.4 Consensus size: 54
361010 GCTTTGAAAT
* * * *
361020 GATGCCACTGACTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAATAG
1 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAA-AG
* * * * * * *
361075 G-TACTATAGAGTTGTGGACCTAAAAGGGTGCCACGAAGTGGTGGACTTTAAAA-
1 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAG
*
361128 GAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG
1 GA-TGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
361184 GGTGCCACGGAGTTGTGGACCTTAAAAGGATGCCACAGAGTTATGGACTTAAAAG
1 GATGCCACAGAGTTGTGGA-CTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
361239 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
* * * * * *
361293 AAGGCCACAAAGTTATGGACTCAAGAGGATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
* *
361347 GATGCCATAGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTAGACTTAAAAG
1 GATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
* * *
361402 GATGCCACTGAATCGTGGACTT
1 GATGCCACAGAGTTGTGGACTT
361424 TGAAGAGGTC
Statistics
Matches: 301, Mismatches: 42, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.00
54 135 0.45
55 139 0.46
56 26 0.09
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (54 bp):
GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
Found at i:363711 original size:13 final size:13
Alignment explanation
Indices: 363693--363730 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
363683 CTATTTATAG
*
363693 TGTATCGATACAC
1 TGTATCGATACAA
363706 TGTATCGATACAA
1 TGTATCGATACAA
363719 TGTATCGATACA
1 TGTATCGATACA
363731 TGAATAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:365675 original size:13 final size:13
Alignment explanation
Indices: 365657--365681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365647 ACTGAAGCAA
365657 TGTATCGATACAT
1 TGTATCGATACAT
365670 TGTATCGATACA
1 TGTATCGATACA
365682 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:367316 original size:83 final size:84
Alignment explanation
Indices: 367208--367371 Score: 203
Period size: 83 Copynumber: 2.0 Consensus size: 84
367198 CATTTTCCAC
* *
367208 TTGCAACTCATTTCTTTTCTCCTCTAATTCAT-TTATTTTCTTTTTAAAAGAAT-T-ATT-TCTA
1 TTGCAACTCATTTCTATTCTCCTCTAATTC-TCTTAATTTC-TTTT-AAAGAATATCATTCTCTA
367269 AACTCATTGATTTACTTTCATT
63 AACTCATTGATTTACTTTCATT
* * *
367291 TTGCAACTC-TTTCATATTCTTCTCTAATTCTCTTAATTTCTTTTCAAGAATATCATTCTCTACA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCTCTTAATTTCTTTTAAAGAATATCATTCTCTAAA
*
367355 CTCATTGATTTATTTTC
65 CTCATTGATTTACTTTC
367372 TTCTTTGAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
81 6 0.09
82 10 0.14
83 33 0.47
84 21 0.30
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCTCTTAATTTCTTTTAAAGAATATCATTCTCTAAAC
TCATTGATTTACTTTCATT
Done.