Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold40
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1915636
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 67970 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:267581 original size:67 final size:68
Alignment explanation
Indices: 267466--267615 Score: 196
Period size: 67 Copynumber: 2.2 Consensus size: 68
267456 CCTAGTTCAC
* * * *
267466 TGTCCTAGTGGACTTCATTTGTTGCCATAGCCCTGCTATAGTCTTACATAGTATGAT-CCATGTT
1 TGTCCTGGTGGACTTCATATGTTGCCATAGCCCTGCTATAGTATTACATAGTATAATCCCATGTT
267530 TAT
66 TAT
* * * *
267533 TTTCTTGGTGGACTTCATATGTTGCCATAG-CTTAGCTATCGTATTACATAGTATAATCCCATGT
1 TGTCCTGGTGGACTTCATATGTTGCCATAGCCCT-GCTATAGTATTACATAGTATAATCCCATGT
267597 TTAT
65 TTAT
*
267601 TGTCCTGGTAGACTT
1 TGTCCTGGTGGACTT
267616 TTGATTCCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
66 2 0.03
67 46 0.66
68 22 0.31
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (68 bp):
TGTCCTGGTGGACTTCATATGTTGCCATAGCCCTGCTATAGTATTACATAGTATAATCCCATGTT
TAT
Found at i:270417 original size:11 final size:10
Alignment explanation
Indices: 270362--270415 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 10
270352 CAAATAAATC
270362 ATTTCTCT-A
1 ATTTCTCTCA
270371 ATATTCTCTCA
1 AT-TTCTCTCA
270382 ATTTCCTCTCA
1 ATTT-CTCTCA
*
270393 ATTTCCTCTGAA
1 ATTT-CTCT-CA
270405 ATTTCTCTCA
1 ATTTCTCTCA
270415 A
1 A
270416 ATCCCTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 10 0.26
11 22 0.56
12 5 0.13
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (10 bp):
ATTTCTCTCA
Found at i:271604 original size:7 final size:7
Alignment explanation
Indices: 271592--271617 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
271582 TAGTCGATTG
271592 GTATTTA
1 GTATTTA
271599 GTATTTA
1 GTATTTA
271606 GTATTTA
1 GTATTTA
271613 GTATT
1 GTATT
271618 ATGTCTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:272295 original size:18 final size:18
Alignment explanation
Indices: 272272--272314 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
272262 TGCCAAGTGC
* *
272272 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
272290 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
272308 GTCTCCT
1 GTATCCT
272315 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:276147 original size:126 final size:126
Alignment explanation
Indices: 275922--276194 Score: 510
Period size: 126 Copynumber: 2.2 Consensus size: 126
275912 GCCATGCTCC
275922 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGACAAAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGACAAAGCATCCTGCT
**
275987 TAAAGTGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCGGGAGCT
66 TAAAGCATTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCGGGAGCT
* *
276048 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGTACTTCTGCTGACAAAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGACAAAGCATCCTGCT
276113 TAAAGCATTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCGGGAGCT
66 TAAAGCATTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCGGGAGCT
276174 ACTGTAGCAAAAGCGCGTCCA
1 ACTGTAGCAAAAGCGCGTCCA
276195 AACCTAATCT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 143 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (126 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGACAAAGCATCCTGCT
TAAAGCATTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCGGGAGCT
Found at i:286522 original size:16 final size:17
Alignment explanation
Indices: 286490--286522 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
286480 CCATACCTTC
286490 GATTTTGAACCTGTTACG
1 GATTTTGAA-CTGTTACG
286508 GATTTTGAA-TGTTAC
1 GATTTTGAACTGTTAC
286523 CATTGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (17 bp):
GATTTTGAACTGTTACG
Found at i:287127 original size:20 final size:20
Alignment explanation
Indices: 287063--287141 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
287053 TATACCATGA
*
287063 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTGCCCCTAT
* * *
287083 TTGTACTTCCGTACCCCTGA-
1 TTGCACTTCGGTGCCCCT-AT
*
287103 ATGCA-TATCGGTGCCCCTAT
1 TTGCACT-TCGGTGCCCCTAT
287123 TTGCACTTCGGTGCCCCTA
1 TTGCACTTCGGTGCCCCTA
287142 GTCACACATC
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.07
20 42 0.91
21 1 0.02
ACGTcount: A:0.14, C:0.34, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTAT
Found at i:287355 original size:16 final size:16
Alignment explanation
Indices: 287334--287371 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
287324 ATGATCAAAG
287334 TATGAATATTCATGAT
1 TATGAATATTCATGAT
287350 TATGAATATTCATGAT
1 TATGAATATTCATGAT
287366 TATGAA
1 TATGAA
287372 AAGTATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (16 bp):
TATGAATATTCATGAT
Found at i:290036 original size:19 final size:19
Alignment explanation
Indices: 290014--290054 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
290004 CCATAAAATA
290014 TTTTTT-ATTTTTTTTTAT
1 TTTTTTCATTTTTTTTTAT
* *
290032 TTTTTTCGTTTTTTTTTGT
1 TTTTTTCATTTTTTTTTAT
290051 TTTT
1 TTTT
290055 GCACTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (19 bp):
TTTTTTCATTTTTTTTTAT
Found at i:290450 original size:13 final size:13
Alignment explanation
Indices: 290434--290458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290424 TAAAGAAAGC
290434 AATTAAGATAGAT
1 AATTAAGATAGAT
290447 AATTAAGATAGA
1 AATTAAGATAGA
290459 AAAAAATTTA
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:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (13 bp):
AATTAAGATAGAT
Found at i:309989 original size:42 final size:42
Alignment explanation
Indices: 309930--310212 Score: 397
Period size: 42 Copynumber: 6.7 Consensus size: 42
309920 TAATCGTCCT
309930 TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
1 TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
*
309972 TATAGATCAGGACCTTTAGCGGCGCTTTCCCATAAACGCCGC
1 TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
310014 TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
1 TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
* * *
310056 TATAGAGCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGC
1 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGC
* * * *
310099 TATAGATTAGGGCCTTTAGCGGCGCTTTTCCCAGAAACGCCGT
1 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGC
* * * * *
310142 TATAGCTCAAGACCTTTAGCGACGCTTTTCCCACAAATGCCAC
1 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGC
*
310185 TATAGGTCAAGG-CCTTTAGCGGCGCTTT
1 TATAGATC-AGGACCTTTAGCGGCGCTTT
310213 TTTCACAAAC
Statistics
Matches: 215, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
42 107 0.50
43 106 0.49
44 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (42 bp):
TATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAACGCCGC
Found at i:310100 original size:43 final size:43
Alignment explanation
Indices: 309930--310254 Score: 406
Period size: 43 Copynumber: 7.7 Consensus size: 43
309920 TAATCGTCCT
*
309930 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* *
309972 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCATAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
*
310014 TATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* *
310056 TATAGAGCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* * * * *
310099 TATAGATTAGGGCCTTTAGCGGCGCTTTTCCCAGAAACGCCGT
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* * * *
310142 TATAGCTCAAGACCTTTAGCGACGCTTTTCCCACAAATGCCAC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* * ** * *
310185 TATAGGTCAAGGCCTTTAGCGGCGCTTTTTTCACAAACGTCAC
1 TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
* * *
310228 TATAAACCAA-ACCTTTAGCGACGCTTT
1 TATAGATCAAGACCTTTAGCGGCGCTTT
310255 CGTAAAAACG
Statistics
Matches: 249, Mismatches: 33, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
42 119 0.48
43 130 0.52
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (43 bp):
TATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGC
Found at i:315511 original size:7 final size:7
Alignment explanation
Indices: 315501--315554 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
315491 CCCCAGCCTT
315501 TAAACCA
1 TAAACCA
*
315508 TAAACCC
1 TAAACCA
315515 TAAACCA
1 TAAACCA
* *
315522 TAATCCC
1 TAAACCA
315529 TAAACTCA
1 TAAAC-CA
*
315537 TAATCCA
1 TAAACCA
*
315544 TAAACCT
1 TAAACCA
315551 TAAA
1 TAAA
315555 ATGGTAACAC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:315518 original size:14 final size:14
Alignment explanation
Indices: 315501--315612 Score: 64
Period size: 14 Copynumber: 7.4 Consensus size: 14
315491 CCCCAGCCTT
315501 TAAACCATAAACCC
1 TAAACCATAAACCC
*
315515 TAAACCATAATCCC
1 TAAACCATAAACCC
* *
315529 TAAACTCATAATCCA
1 TAAAC-CATAAACCC
*
315544 TAAACCTTAAAATGGTAACACC
1 TAAACC-----AT--AAAC-CC
*
315566 TAAA-CATTAAACTC
1 TAAACCA-TAAACCC
*
315580 TAAACCATATACCC
1 TAAACCATAAACCC
*
315594 TAAACCAAAAACCC
1 TAAACCATAAACCC
315608 TAAAC
1 TAAAC
315613 TATAGTGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
14 46 0.61
15 18 0.24
16 1 0.01
17 1 0.01
19 2 0.03
21 3 0.04
22 5 0.07
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:315540 original size:15 final size:14
Alignment explanation
Indices: 315501--315549 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
315491 CCCCAGCCTT
*
315501 TAAACCATAAACCC
1 TAAACCATAATCCC
315515 TAAACCATAATCCC
1 TAAACCATAATCCC
*
315529 TAAACTCATAATCCA
1 TAAAC-CATAATCCC
315544 TAAACC
1 TAAACC
315550 TTAAAATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:315835 original size:41 final size:41
Alignment explanation
Indices: 315782--316021 Score: 365
Period size: 41 Copynumber: 5.9 Consensus size: 41
315772 TAAATCCCTA
*
315782 AGCATTAGCGGCGCTTTC-CAAAAAACGCCGCTAAAGACCCT
1 AGCATTAGCGGCGCTTTCTC-AAAAACGCCGCTAAAGACCCG
*
315823 AGCATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
315864 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* * * * *
315905 AGAATTAGCGACGCTTTCTCAAAAATGCAGCTAAAGACCAG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* *
315946 AGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCAG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* *
315987 AGCATTAGCGGCGCTTTCCCAAAAATGCCGCTAAA
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAA
316022 TCTCCGAAAG
Statistics
Matches: 184, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 183 0.99
42 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (41 bp):
AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
Found at i:316148 original size:40 final size:40
Alignment explanation
Indices: 316101--316194 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
316091 AATGCTTATA
* *
316101 TTTAGCGGCGTTTTCCATGAAA-CTCCACTAATGCTCGATC
1 TTTAGCGGCGTTTTCCA-AAAAGCACCACTAATGCTCGATC
* *
316141 TTTAGCGGCGTTTTCCAAAAAGCACCGCTAATGCTTGATC
1 TTTAGCGGCGTTTTCCAAAAAGCACCACTAATGCTCGATC
* *
316181 TTTAGTGGTGTTTT
1 TTTAGCGGCGTTTT
316195 TTATCCAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.06
40 44 0.94
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTAGCGGCGTTTTCCAAAAAGCACCACTAATGCTCGATC
Found at i:320275 original size:19 final size:18
Alignment explanation
Indices: 320239--320290 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
320229 AGTTTCACAT
*
320239 TTCATTTCATCATTTCATA
1 TTCATTTC-TCATCTCATA
*
320258 TTACCTTTCTCATCTCATA
1 TT-CATTTCTCATCTCATA
320277 TTCATTTCTCATCT
1 TTCATTTCTCATCT
320291 TTTCCATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 13 0.45
20 5 0.17
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (18 bp):
TTCATTTCTCATCTCATA
Found at i:326112 original size:7 final size:7
Alignment explanation
Indices: 326100--326148 Score: 89
Period size: 7 Copynumber: 6.9 Consensus size: 7
326090 CTGATATATA
326100 TTTTTTC
1 TTTTTTC
326107 TTTTTTC
1 TTTTTTC
326114 TTTTTTC
1 TTTTTTC
326121 TTTTTTC
1 TTTTTTC
326128 TTTTTTC
1 TTTTTTC
326135 TTTTTTTC
1 -TTTTTTC
326143 TTTTTT
1 TTTTTT
326149 TTCCTTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 34 0.83
8 7 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:327195 original size:6 final size:6
Alignment explanation
Indices: 327186--327245 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
327176 AATTAAAATT
* *
327186 AAAAAC AAAAAA AGTAAAAGC AAAAGC AAAAAC AAAAAC AAAAAC -AAAAC
1 AAAAAC AAAAAC A--AAAA-C AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
327236 AAAAAC AAAA
1 AAAAAC AAAA
327246 TAAAATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 33 0.72
7 3 0.07
8 4 0.09
9 1 0.02
ACGTcount: A:0.80, C:0.13, G:0.05, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:327234 original size:11 final size:11
Alignment explanation
Indices: 327201--327250 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
327191 CAAAAAAAGT
*
327201 AAAAGCAAAAGC
1 AAAAACAAAA-C
327213 AAAAACAAAAAC
1 AAAAAC-AAAAC
327225 AAAAACAAAAC
1 AAAAACAAAAC
*
327236 AAAAACAAAAT
1 AAAAACAAAAC
327247 AAAA
1 AAAA
327251 TAAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
11 19 0.54
12 12 0.34
13 4 0.11
ACGTcount: A:0.80, C:0.14, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:327270 original size:17 final size:17
Alignment explanation
Indices: 327250--327283 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
327240 ACAAAATAAA
327250 ATAAAAATAAATAAAAT
1 ATAAAAATAAATAAAAT
* *
327267 ATAAAATTAAATGAAAT
1 ATAAAAATAAATAAAAT
327284 CACTTTGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAAAATAAATAAAAT
Found at i:327333 original size:14 final size:14
Alignment explanation
Indices: 327305--327336 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
327295 AGGTAGGAAG
327305 AAAACAAAAGAAAA
1 AAAACAAAAGAAAA
327319 AAAATCAAAAGAAAA
1 AAAA-CAAAAGAAAA
327334 AAA
1 AAA
327337 CCTAGCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.03
Consensus pattern (14 bp):
AAAACAAAAGAAAA
Found at i:327814 original size:7 final size:8
Alignment explanation
Indices: 327791--327824 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
327781 ATTTTTTCAG
327791 ATTTTGTTT
1 ATTTT-TTT
327800 ATTTTTTT
1 ATTTTTTT
327808 ATTTTTTT
1 ATTTTTTT
327816 ATTTTTTT
1 ATTTTTTT
327824 A
1 A
327825 AAAAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.80
9 5 0.20
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:330073 original size:19 final size:20
Alignment explanation
Indices: 330040--330082 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
330030 CAAACAAATG
330040 AAAA-ATTAAATTAAAAACA
1 AAAATATTAAATTAAAAACA
*
330059 AAAATATTAAA-TAAAAATA
1 AAAATATTAAATTAAAAACA
330078 AAAAT
1 AAAAT
330083 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATATTAAATTAAAAACA
Found at i:331876 original size:31 final size:31
Alignment explanation
Indices: 331841--331901 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
331831 GTACAAAATA
*
331841 AATCTAGCTATAATCTCTTATTTTAATAATG
1 AATCTAGCCATAATCTCTTATTTTAATAATG
331872 AATCTAGCCATAATCTCTTATTTTAATAAT
1 AATCTAGCCATAATCTCTTATTTTAATAAT
331902 ATTCATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (31 bp):
AATCTAGCCATAATCTCTTATTTTAATAATG
Found at i:332374 original size:11 final size:11
Alignment explanation
Indices: 332353--332377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
332343 TAAAAATTAG
332353 AAAAAAATCAT
1 AAAAAAATCAT
332364 AAAAAAATCAT
1 AAAAAAATCAT
332375 AAA
1 AAA
332378 TTTTAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATCAT
Found at i:332387 original size:18 final size:19
Alignment explanation
Indices: 332366--332401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
332356 AAAATCATAA
332366 AAAAATCA-TAAATTTTAG
1 AAAAATCATTAAATTTTAG
*
332384 AAAAATTATTAAATTTTA
1 AAAAATCATTAAATTTTA
332402 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATCATTAAATTTTAG
Found at i:332646 original size:19 final size:20
Alignment explanation
Indices: 332618--332674 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
332608 AATGTTACAA
332618 ATATAAAAATCGTAAAAATT
1 ATATAAAAATCGTAAAAATT
*
332638 ATA-AAAAATTTGT-AAAATT
1 ATATAAAAA-TCGTAAAAATT
* *
332657 TTATAAAAATCATAAAAA
1 ATATAAAAATCGTAAAAA
332675 AAAATAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (20 bp):
ATATAAAAATCGTAAAAATT
Found at i:332666 original size:20 final size:19
Alignment explanation
Indices: 332619--332666 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
332609 ATGTTACAAA
332619 TATAAAAA-TCGTAAAAAT
1 TATAAAAATTCGTAAAAAT
* *
332637 TATAAAAAATTTGTAAAATTT
1 TAT-AAAAATTCGTAAAA-AT
332658 TATAAAAAT
1 TATAAAAAT
332667 CATAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.12
19 5 0.20
20 13 0.52
21 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TATAAAAATTCGTAAAAAT
Found at i:332840 original size:20 final size:20
Alignment explanation
Indices: 332815--332871 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
332805 TACGATAATT
332815 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
332835 TTTAT-ATTTCTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
332853 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
332872 CTTTATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:345310 original size:14 final size:14
Alignment explanation
Indices: 345291--345318 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
345281 AGAATCATAG
345291 ACCTCATCAACTGT
1 ACCTCATCAACTGT
345305 ACCTCATCAACTGT
1 ACCTCATCAACTGT
345319 GAGAGATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
ACCTCATCAACTGT
Found at i:346829 original size:20 final size:21
Alignment explanation
Indices: 346788--346829 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
346778 ATGAGGGATC
*
346788 ACTATACTCTAAGGTATGCCA
1 ACTATACTCTAAGGTATCCCA
346809 ACTATA-TCTAAAGGT-TCCCA
1 ACTATACTCT-AAGGTATCCCA
346829 A
1 A
346830 TACATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (21 bp):
ACTATACTCTAAGGTATCCCA
Found at i:351908 original size:23 final size:23
Alignment explanation
Indices: 351882--351925 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
351872 ATAAGTGCCA
*
351882 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
351905 CACTGAAATGTAGTCGAAGCT
1 CACTGAAATGTAGCCGAAGCT
351926 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:355359 original size:28 final size:28
Alignment explanation
Indices: 355328--355398 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
355318 TTAATTATTT
*
355328 TTATTATCTAAAAAATTA-AATCTA-AATA
1 TTATTAT-TAAAAAATTATAATATAGAA-A
*
355356 TTA-TATGTAAAATATTATAATATAGAAA
1 TTATTAT-TAAAAAATTATAATATAGAAA
355384 TTATTATTACAAAAA
1 TTATTATTA-AAAAA
355399 AAACATACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 12 0.34
28 14 0.40
29 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (28 bp):
TTATTATTAAAAAATTATAATATAGAAA
Found at i:364856 original size:6 final size:6
Alignment explanation
Indices: 364845--364876 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
364835 AAACCTAGAG
*
364845 AAACCT AAACCT AAACCT AAACCT AAAACT AA
1 AAACCT AAACCT AAACCT AAACCT AAACCT AA
364877 GCTAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (6 bp):
AAACCT
Found at i:369740 original size:94 final size:94
Alignment explanation
Indices: 369579--369810 Score: 284
Period size: 94 Copynumber: 2.5 Consensus size: 94
369569 TGAAAGACTA
** * * * * * ** * *
369579 TTCATGATCACAAATCAATGAATTTAGGCTATGATCATAAATTAGCGAGTTGTTTGGAGTAGTGA
1 TTCATGATCGTAAATAAATGAACTTAGGCTGTGATCATAAATCAACGAACTGTTTGAAGTAGCGA
369644 TAGTAAATCAGCTAACTCATAGAAAATTG
66 TAGTAAATCAGCTAACTCATAGAAAATTG
* * * **
369673 TTCATGGTCGTAAATCAATGAACTTAGGTTGTGATTGTAAATCAACGAACTGTTTGAAGTAGCGA
1 TTCATGATCGTAAATAAATGAACTTAGGCTGTGATCATAAATCAACGAACTGTTTGAAGTAGCGA
* * *
369738 TAGTAAATTAGTTAACTCATAGAAGATTG
66 TAGTAAATCAGCTAACTCATAGAAAATTG
*
369767 TTTATGATCGTAAATAAATGAACTTAGGCTGTGATCATAAATCA
1 TTCATGATCGTAAATAAATGAACTTAGGCTGTGATCATAAATCA
369811 GCAAGCCTTA
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
94 115 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (94 bp):
TTCATGATCGTAAATAAATGAACTTAGGCTGTGATCATAAATCAACGAACTGTTTGAAGTAGCGA
TAGTAAATCAGCTAACTCATAGAAAATTG
Found at i:379050 original size:10 final size:10
Alignment explanation
Indices: 379035--379059 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
379025 TGAATTTTTT
379035 TCTTTTATTA
1 TCTTTTATTA
379045 TCTTTTATTA
1 TCTTTTATTA
379055 TCTTT
1 TCTTT
379060 GATTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (10 bp):
TCTTTTATTA
Found at i:385937 original size:3 final size:3
Alignment explanation
Indices: 385929--385961 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
385919 TTATAAGTGT
385929 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
385962 ATAAACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:388260 original size:41 final size:39
Alignment explanation
Indices: 388196--388275 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 39
388186 GTATATGTTG
388196 ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
1 ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
* *
388235 ATTGTTGAACTCTGTCTTAGTATCTTATTACTCGGGTCCAC
1 ATTGTTGAA-T-TGTCTTAGCATCTTATTACTCGAGTCCAC
388276 CAACCGGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 9 0.24
40 1 0.03
41 27 0.73
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (39 bp):
ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
Found at i:388351 original size:14 final size:13
Alignment explanation
Indices: 388315--388360 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
388305 CATCCAGCCT
388315 AAAACCAAAAATA
1 AAAACCAAAAATA
*
388328 AATAAACAAAACATA
1 AA-AACCAAAA-ATA
388343 AAAACCAAAAAATA
1 AAAACC-AAAAATA
388357 AAAA
1 AAAA
388361 ATCCAAGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.78, C:0.13, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:389591 original size:61 final size:61
Alignment explanation
Indices: 389495--389613 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
389485 TGTCCTAGGG
* *
389495 TTGGGAATATTTTCCCATTCGCCCCTGCTCTTTTTTCGC-TCGTTATATTTTAGTCATTTAT
1 TTGGGAATATATTCCCATTCGCCCCTGCTCTTTTTTCGCGT-GTTACATTTTAGTCATTTAT
* *
389556 TTGGGAATATATTCCTATTCGGCCCCTGTTC-TTTTTCGCGTGTTACATTTTAGTCATT
1 TTGGGAATATATTCCCATTC-GCCCCTGCTCTTTTTTCGCGTGTTACATTTTAGTCATT
389614 AGTAATTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
61 42 0.81
62 10 0.19
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (61 bp):
TTGGGAATATATTCCCATTCGCCCCTGCTCTTTTTTCGCGTGTTACATTTTAGTCATTTAT
Found at i:389823 original size:3 final size:3
Alignment explanation
Indices: 389817--389842 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
389807 ATTATTATTC
389817 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
389843 ATTTATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:402256 original size:44 final size:44
Alignment explanation
Indices: 402193--402546 Score: 247
Period size: 44 Copynumber: 8.0 Consensus size: 44
402183 CACCATAGTG
* * *
402193 AATCTTATCTCCCTAAAGTTACAGTGGAGAAGATTAAAGCTACA
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGCTACA
** * *
402237 AATCTTATCTTTTTAAAGTTGCAGTGGAGCATATTGAAGCTACA
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGCTACA
* *
402281 AATCTTATCTCCTTGAAGTTGTAGTGGA-ACAGATTGAAGCTACA
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGA-AGATTGAAGCTACA
* * *
402325 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGT-CA
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGC-TACA
* * * ** * *
402369 AATCCTAT-ACCTCTAAAGATGCAGTAGG-TTAGATTAAATCTACCA
1 AATCTTATCTCCT-TAAAGTTGCAGT-GGAGAAGATTGAAGCTA-CA
* * * * *
402414 TAGCGAGTCTCATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCTACA
1 -A---A-TCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGCTACA
* * * * * *
402463 AACCTTATCTCCCTGAAGTAGCAGTAGA-ACAGATTGAAGCTACG
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGA-AGATTGAAGCTACA
* * * *
402507 AATCTCATCTCCCTAAA---GCAGCGGAGAAGATTGAAACTAC
1 AATCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGCTAC
402547 CCCTGAAGTT
Statistics
Matches: 246, Mismatches: 48, Indels: 35
0.75 0.15 0.11
Matches are distributed among these distances:
41 18 0.07
42 1 0.00
43 3 0.01
44 185 0.75
45 6 0.02
46 1 0.00
48 1 0.00
49 5 0.02
50 24 0.10
51 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCTTAAAGTTGCAGTGGAGAAGATTGAAGCTACA
Found at i:402497 original size:94 final size:88
Alignment explanation
Indices: 402196--402520 Score: 275
Period size: 88 Copynumber: 3.6 Consensus size: 88
402186 CATAGTGAAT
* * * *** *
402196 CTTATCTCCCTAAAGTTA-CAGTGGAGA-AGATTAAAGCTACAAATCTTATCTTTTTAAAGTTGC
1 CTTATCTCCCTGAAG-TAGCAGTAGA-ACAGATTAAAGCTACAAATCTCATCTCCCTGAAGTTGC
* *
402259 AGTGGAGCATATTGAAGCTACAAAT
64 AGTGGAGCAGATTGAAGCTACAAAC
* * * * * *
402284 CTTATCTCCTTGAAGTTGTAGTGGAACAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTAGCAGTAGAACAGATTAAAGCTACAAATCTCATCTCCCTGAAGTTGCAG
402349 TGGAGCAGATTGAAGCGT-CAAATC
66 TGGAGCAGATTGAAGC-TACAAA-C
* * *** *
402373 C-TATAC-CTCTAAAG-ATGCAGTAGGTTAGATTAAATCTACCATAGCGAGTCTCATCTCCCTGA
1 CTTAT-CTCCCTGAAGTA-GCAGTAGAACAGATTAAAGCTA-CA-A---A-TCTCATCTCCCTGA
* *
402435 AGTTGTAGTGGAGTAGATTGAAGCTACAAAC
58 AGTTGCAGTGGAGCAGATTGAAGCTACAAAC
* *
402466 CTTATCTCCCTGAAGTAGCAGTAGAACAGATTGAAGCTACGAATCTCATCTCCCT
1 CTTATCTCCCTGAAGTAGCAGTAGAACAGATTAAAGCTACAAATCTCATCTCCCT
402521 AAAGCAGCGG
Statistics
Matches: 188, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
87 2 0.01
88 106 0.56
89 6 0.03
90 1 0.01
92 1 0.01
93 6 0.03
94 65 0.35
95 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (88 bp):
CTTATCTCCCTGAAGTAGCAGTAGAACAGATTAAAGCTACAAATCTCATCTCCCTGAAGTTGCAG
TGGAGCAGATTGAAGCTACAAAC
Found at i:404109 original size:3 final size:3
Alignment explanation
Indices: 404103--404137 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
404093 ATTATTATTA
404103 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
404138 ATTTATCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:421763 original size:2 final size:2
Alignment explanation
Indices: 421756--421791 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
421746 TTCCACCAAA
421756 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
421792 TTATAGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:428581 original size:31 final size:31
Alignment explanation
Indices: 428540--428601 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
428530 AGGCAAATTA
428540 CAAGACTAATTGAATCCTAATAAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAACTCTTT
*
428571 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAACTCTTT
428602 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (31 bp):
CAAGACTAATTGAATCCTAATAAAACTCTTT
Found at i:435530 original size:31 final size:32
Alignment explanation
Indices: 435489--435551 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
435479 AGGCAAATTA
435489 CAAGACTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAAACTCTTT
*
435520 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAAACTCTTT
435552 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (32 bp):
CAAGACTAATTGAATCCTAATAAAAACTCTTT
Found at i:438800 original size:20 final size:21
Alignment explanation
Indices: 438769--438807 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
438759 TTTATCGTTT
438769 TAAATAATTTTTGGGTAAAAA
1 TAAATAATTTTTGGGTAAAAA
*
438790 TAAAT-ATTTTTGGTTAAA
1 TAAATAATTTTTGGGTAAA
438808 TTGGAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (21 bp):
TAAATAATTTTTGGGTAAAAA
Found at i:443090 original size:46 final size:47
Alignment explanation
Indices: 443023--443116 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
443013 ACTCCTCTCA
443023 CAGTTTAGAGTTGCTCAATTATAGACCCTTG-CCACAGATTCAAATT
1 CAGTTTAGAGTTGCTCAATTATAGACCCTTGACCACAGATTCAAATT
443069 CAGTTTAGAGTTGCTCAATTATAGACCCTTGACCCACAGATTCAAATT
1 CAGTTTAGAGTTGCTCAATTATAGACCCTTGA-CCACAGATTCAAATT
443117 GAGTCTCGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 31 0.67
48 15 0.33
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (47 bp):
CAGTTTAGAGTTGCTCAATTATAGACCCTTGACCACAGATTCAAATT
Found at i:452173 original size:12 final size:11
Alignment explanation
Indices: 452156--452188 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
452146 AGCAAATCCT
452156 CTCTCATATTTC
1 CTCTCA-ATTTC
452168 CTCTCAA-TTC
1 CTCTCAATTTC
452178 CTCTCAATTTC
1 CTCTCAATTTC
452189 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:452203 original size:22 final size:22
Alignment explanation
Indices: 452173--452228 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
452163 ATTTCCTCTC
*
452173 AATTCCTCTCAATTTCTTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
452196 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
452218 AATTCTCTCAA
1 AATTCTCTCAA
452229 ATCCATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:452276 original size:22 final size:22
Alignment explanation
Indices: 452251--452301 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
452241 TTTCAATTTC
452251 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
452273 CTCTTAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
452295 CTCTCAA
1 CTCTCAA
452302 ATCCATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:452282 original size:73 final size:72
Alignment explanation
Indices: 452171--452315 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 72
452161 ATATTTCCTC
*
452171 TCAATTCCTCTCAATTTCTTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATA
1 TCAATTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATA
452236 TTTAATT
66 TTTAATT
*
452243 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTTAATTTCCTTCCAAAATTCTCTCAAATCCAT
1 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCAT
452308 ATTTAATT
65 ATTTAATT
452316 ATTAATTTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 4 0.06
73 66 0.94
ACGTcount: A:0.29, C:0.28, G:0.00, T:0.43
Consensus pattern (72 bp):
TCAATTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATA
TTTAATT
Found at i:453223 original size:7 final size:7
Alignment explanation
Indices: 453211--453236 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
453201 TAGTCGATTG
453211 GTATTTA
1 GTATTTA
453218 GTATTTA
1 GTATTTA
453225 GTATTTA
1 GTATTTA
453232 GTATT
1 GTATT
453237 ATTATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:454421 original size:29 final size:29
Alignment explanation
Indices: 454380--455714 Score: 1769
Period size: 29 Copynumber: 46.4 Consensus size: 29
454370 GAAGTTTATT
*
454380 CCTAACCCTAACCCAATTTAATTAAAAAT
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454409 CCTAACCCTAACCTAATTCAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454438 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
********** * *
454467 CCTANNNNNNNNNNNAACTTAATTAAAAAA
1 CCTA-ACCCTAACCCAATTTAATTAAAAAC
454497 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454526 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454555 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
454584 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454613 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454642 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
454671 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454700 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454729 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
454758 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454787 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454816 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
454845 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454874 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454903 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
454932 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
454961 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
454990 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455019 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455048 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455077 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455106 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455135 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455164 CCTAACCCTAACCCAATTCAATTAAAAAA
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455193 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455222 CCTAACCCTAGCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
*
455251 CCTAACCCTAACCCAATTCAATT--AAA-
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455277 ---AACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455303 CCTAACCCTAACCTAA-TCAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455331 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455360 CCTAACCCTAATCCAATTCAACTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455389 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455418 TCTAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455447 CCTAACCCTAACCTAATTCAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455476 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455505 CCTAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455534 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* *
455563 CTTAACCCTAACCCAATTCAATT--AAA-
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455589 ---AACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
** * *
455615 CCTAACCCTAACATAACTCAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
* * *
455644 CCTAACGCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
*
455673 CCTAACCCTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCCAATTTAATTAAAAAC
455702 CCTAACCCTAACC
1 CCTAACCCTAACC
455715 AGGTGCGAGA
Statistics
Matches: 1138, Mismatches: 154, Indels: 28
0.86 0.12 0.02
Matches are distributed among these distances:
23 38 0.03
25 6 0.01
27 6 0.01
28 27 0.02
29 1043 0.92
30 18 0.02
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.22
Consensus pattern (29 bp):
CCTAACCCTAACCCAATTTAATTAAAAAC
Found at i:454617 original size:87 final size:87
Alignment explanation
Indices: 454380--455714 Score: 2031
Period size: 87 Copynumber: 15.5 Consensus size: 87
454370 GAAGTTTATT
* * * *
454380 CCTAACCCTAACCCAATTTAATTAAAAATCCTAACCCTAACCTAATTCAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
* *
454445 CTAACCTAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
**********
454467 CCTANNNNNNNNNNNAACTT-AATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAA
1 CCTA-ACCCTAACCCAA-TTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAA
454531 CCCTAGCCAAACTTAATTAAAAAC
64 CCCTAGCCAAACTTAATTAAAAAC
454555 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
454620 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
454642 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
454707 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
454729 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
454794 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
454816 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
454881 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
454903 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
454968 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
454990 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
455055 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
455077 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
455142 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
455164 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
455229 CTAGCCAAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
455251 CCTAACCCTAACCCAATTCAATT---AAA---AACCCTAACCCAATTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
* * *
455310 CTAACCTAA-TCAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
* * * * *
455331 CCTAACCCTAACCTAACTT-AATTAAAAACCCTAACCCTAATCCAATTCAACTAAAAACCCTAAC
1 CCTAACCCTAACCCAA-TTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAAC
* * *
455395 CCTAACCCAATTTAATTAAAAAC
65 CCTAGCCAAACTTAATTAAAAAC
* * * * *
455418 TCTAACCCTAACCAAACTT-AATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAC
1 CCTAACCCTAACCCAA-TTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAAC
* *
455482 CCTAACCTAACTTAATTAAAAAC
65 CCTAGCCAAACTTAATTAAAAAC
* * * * *
455505 CCTAACCCTAACCAAACTT-AATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCTTAAC
1 CCTAACCCTAACCCAA-TTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAAC
* *
455569 CCTAACCCAA-TTCAATT--AAA-
65 CCTAGCCAAACTT-AATTAAAAAC
* * ** * * *
455589 ---AACCCTAACCCAATTTAATTAAAAACCCTAACCCTAACATAACTCAATTAAAAACCCTAACG
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
* *
455651 CTAACCTAACTTAATTAAAAAC
66 CTAGCCAAACTTAATTAAAAAC
*
455673 CCTAACCCTAACCCAATTCAATTAAAAACCCTAACCCTAACC
1 CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACC
455715 AGGTGCGAGA
Statistics
Matches: 1173, Mismatches: 55, Indels: 40
0.93 0.04 0.03
Matches are distributed among these distances:
80 32 0.03
81 108 0.09
82 2 0.00
83 5 0.00
84 3 0.00
85 3 0.00
86 42 0.04
87 907 0.77
88 69 0.06
89 2 0.00
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.22
Consensus pattern (87 bp):
CCTAACCCTAACCCAATTCAATTAAAAAACCTAACCCTAACCCAATTTAATTAAAAACCCTAACC
CTAGCCAAACTTAATTAAAAAC
Found at i:462529 original size:22 final size:25
Alignment explanation
Indices: 462486--462534 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 25
462476 AAATAAGTTA
* *
462486 TAATTGTTTTATATAATTTAAATAC
1 TAATTGTTTTATATAATATAAAAAC
462511 TAATT-TTTT-TATAA-ATAAAAAC
1 TAATTGTTTTATATAATATAAAAAC
462533 TA
1 TA
462535 GAACACGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 4 0.18
25 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATTGTTTTATATAATATAAAAAC
Found at i:465628 original size:45 final size:46
Alignment explanation
Indices: 465471--465643 Score: 258
Period size: 46 Copynumber: 3.8 Consensus size: 46
465461 ATGCTATAAA
* * *
465471 TCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCATAAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACAAC
* * * * *
465517 TCACTATGGCTTTCGTTACTAAAATACCATACCTACTTCTCACAAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACAAC
465563 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACAAC
*
465609 -CAGTATGGTTTTCTTTACTGAAATATCATACCTAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
465644 GTTCCACACT
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 34 0.30
46 79 0.70
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACAAC
Found at i:469180 original size:2 final size:2
Alignment explanation
Indices: 469173--469200 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
469163 AACTAAATAT
469173 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
469201 TGAGGGTGTA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:473783 original size:11 final size:11
Alignment explanation
Indices: 473767--473834 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
473757 TCCTCTCTCA
473767 AATTTCCT-TT
1 AATTTCCTCTT
*
473777 CAATTTCCTCTA
1 -AATTTCCTCTT
473789 AATTTCCTCTT
1 AATTTCCTCTT
*
473800 AATTTGCTCTT
1 AATTTCCTCTT
473811 AATTTCCTCTT
1 AATTTCCTCTT
473822 AAATTT-CTCTT
1 -AATTTCCTCTT
473833 AA
1 AA
473835 ATCCCTATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
10 2 0.04
11 43 0.84
12 6 0.12
ACGTcount: A:0.24, C:0.24, G:0.01, T:0.51
Consensus pattern (11 bp):
AATTTCCTCTT
Found at i:473794 original size:22 final size:21
Alignment explanation
Indices: 473760--473836 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 21
473750 AAATTAATCC
473760 TCTCTCAAATTTCCT-TTCAATT
1 TCTCT-AAATTTCCTCTT-AATT
473782 TCCTCTAAATTTCCTCTTAATT
1 T-CTCTAAATTTCCTCTTAATT
*
473804 TGCTCTTAATTTCCTCTTAAATT
1 T-CTCTAAATTTCCTCTT-AATT
473827 TCTCTTAAAT
1 TCTC-TAAAT
473837 CCCTATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 33 0.69
23 15 0.31
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (21 bp):
TCTCTAAATTTCCTCTTAATT
Found at i:473835 original size:11 final size:11
Alignment explanation
Indices: 473760--473836 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
473750 AAATTAATCC
*
473760 TCTCTCAAATT
1 TCTCTTAAATT
*
473771 TC-CTTTCAATT
1 TCTC-TTAAATT
473782 TC-CTCTAAATT
1 TCTCT-TAAATT
473793 TCCTCTT-AATT
1 T-CTCTTAAATT
473804 TGCTCTT-AATT
1 T-CTCTTAAATT
473815 TCCTCTTAAATT
1 T-CTCTTAAATT
473827 TCTCTTAAAT
1 TCTCTTAAAT
473837 CCCTATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.04
11 45 0.80
12 7 0.12
13 2 0.04
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (11 bp):
TCTCTTAAATT
Found at i:474795 original size:11 final size:11
Alignment explanation
Indices: 474779--474846 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
474769 TCCTCTCTCA
474779 AATTTCCT-TT
1 AATTTCCTCTT
*
474789 CAATTTCCTCTA
1 -AATTTCCTCTT
474801 AATTTCCTCTT
1 AATTTCCTCTT
*
474812 AATTTGCTCTT
1 AATTTCCTCTT
474823 AATTTCCTCTT
1 AATTTCCTCTT
474834 AAATTT-CTCTT
1 -AATTTCCTCTT
474845 AA
1 AA
474847 ATCCCTATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
10 2 0.04
11 43 0.84
12 6 0.12
ACGTcount: A:0.24, C:0.24, G:0.01, T:0.51
Consensus pattern (11 bp):
AATTTCCTCTT
Found at i:474806 original size:22 final size:21
Alignment explanation
Indices: 474772--474848 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 21
474762 AAATTAATCC
474772 TCTCTCAAATTTCCT-TTCAATT
1 TCTCT-AAATTTCCTCTT-AATT
474794 TCCTCTAAATTTCCTCTTAATT
1 T-CTCTAAATTTCCTCTTAATT
*
474816 TGCTCTTAATTTCCTCTTAAATT
1 T-CTCTAAATTTCCTCTT-AATT
474839 TCTCTTAAAT
1 TCTC-TAAAT
474849 CCCTATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 33 0.69
23 15 0.31
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (21 bp):
TCTCTAAATTTCCTCTTAATT
Found at i:474847 original size:11 final size:11
Alignment explanation
Indices: 474772--474848 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
474762 AAATTAATCC
*
474772 TCTCTCAAATT
1 TCTCTTAAATT
*
474783 TC-CTTTCAATT
1 TCTC-TTAAATT
474794 TC-CTCTAAATT
1 TCTCT-TAAATT
474805 TCCTCTT-AATT
1 T-CTCTTAAATT
474816 TGCTCTT-AATT
1 T-CTCTTAAATT
474827 TCCTCTTAAATT
1 T-CTCTTAAATT
474839 TCTCTTAAAT
1 TCTCTTAAAT
474849 CCCTATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.04
11 45 0.80
12 7 0.12
13 2 0.04
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (11 bp):
TCTCTTAAATT
Found at i:476537 original size:18 final size:18
Alignment explanation
Indices: 476495--476537 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
476485 TGCCAGGTGC
* *
476495 GTTTCCTAGCCCTTTTAT
1 GTTTCCTAACCCTTATAT
* *
476513 GTATCCTAACCCTTATCT
1 GTTTCCTAACCCTTATAT
476531 GTTTCCT
1 GTTTCCT
476538 TTTTCGAGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.30, G:0.09, T:0.47
Consensus pattern (18 bp):
GTTTCCTAACCCTTATAT
Found at i:477119 original size:15 final size:15
Alignment explanation
Indices: 477099--477146 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
477089 ACAAACCCTA
477099 AACCCTTAACTTAAT
1 AACCCTTAACTTAAT
*
477114 AACCC-TAAC--CAT
1 AACCCTTAACTTAAT
*
477126 AACCCTTAACTTAAA
1 AACCCTTAACTTAAT
477141 AACCCT
1 AACCCT
477147 AACCCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 4 0.15
15 12 0.44
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (15 bp):
AACCCTTAACTTAAT
Found at i:477129 original size:27 final size:27
Alignment explanation
Indices: 477099--477150 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
477089 ACAAACCCTA
*
477099 AACCCTTAACTTAATAACCCTAACCAT
1 AACCCTTAACTTAAAAACCCTAACCAT
477126 AACCCTTAACTTAAAAACCCTAACC
1 AACCCTTAACTTAAAAACCCTAACC
477151 CTTAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (27 bp):
AACCCTTAACTTAAAAACCCTAACCAT
Found at i:477644 original size:22 final size:21
Alignment explanation
Indices: 477120--477638 Score: 489
Period size: 21 Copynumber: 24.2 Consensus size: 21
477110 TAATAACCCT
*
477120 AACCATAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
477141 AACCCTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
* *
477162 AACCACAAACCCTTAACCT-AA
1 AACC-CTAACCCTTAACTTAAA
**
477183 AGTCCTAAACCCTTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
*
477204 AACCCTAAACTCTTAACTTAAAA
1 AACCCT-AACCCTTAACTT-AAA
*
477227 TCCTAACTCTAACCCTTAACTTAAA
1 ----AACCCTAACCCTTAACTTAAA
* * *
477252 AACACTAACCCTTAAATTTAA
1 AACCCTAACCCTTAACTTAAA
477273 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
477295 AACCCTTAACCCTAAACCTAAA
1 AACCC-TAACCCTTAACTTAAA
* *
477317 AACCATAA-CCTTAAACCCT--A
1 AACCCTAACCCTT-AA-CTTAAA
* *
477337 AACCCTAACCCTTAAATAAAA
1 AACCCTAACCCTTAACTTAAA
* * *
477358 AACACTAACACTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
*
477379 AACCCTAACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
*
477400 AACCCTAAACTCTTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
*
477421 AACCCTAACTCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
477442 AACCCTAAACCCTTAATTTAAA
1 AACCCT-AACCCTTAACTTAAA
* * *
477464 AACCCTAACCGTAAAGCCT--A
1 AACCCTAACCCTTAA-CTTAAA
*
477484 AACCCTAACCCTTAA-ATAAA
1 AACCCTAACCCTTAACTTAAA
*
477504 AACACTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
477525 AACCCTAACCCTTAACTTTAAA
1 AACCCTAACCCTTAAC-TTAAA
*
477547 AATCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
** *
477569 AACACAAAATCCTTAACTTAAA
1 AAC-CCTAACCCTTAACTTAAA
*
477591 AACCCTAACTCTTAACTTTAAA
1 AACCCTAACCCTTAAC-TTAAA
477613 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
477635 AACC
1 AACC
477639 ATAAACTATT
Statistics
Matches: 413, Mismatches: 58, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
18 1 0.00
20 55 0.13
21 181 0.44
22 134 0.32
23 23 0.06
25 3 0.01
26 11 0.03
27 5 0.01
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:477876 original size:126 final size:126
Alignment explanation
Indices: 477650--478021 Score: 568
Period size: 126 Copynumber: 3.0 Consensus size: 126
477640 TAAACTATTT
* *
477650 GCATCCTGCTTGAAGCGTTTTTTTTAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTC
1 GCATCCTGCTTGAAGCG-TTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
477715 CAGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATA
65 CAGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-A
* * * * *
477777 GCATCCTGCTTGAAGTGTTTTTAAAACTATTTGCTCAGAAACGTCAGCTCGAAACTATTTCTTCT
1 GCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCC
477842 AGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
66 AGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
* * *
477903 GCATCCTGCTTGAAGCGTTTTTTATACTATTTTCTTAGAAACGTCAACTCGAAATTATTT-TTCC
1 GCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCC
* * * * * *
477967 AGGACCTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATCCTTCT
66 AGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCT
478022 TGTCGAAACC
Statistics
Matches: 223, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
125 52 0.23
126 153 0.69
127 18 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (126 bp):
GCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCC
AGGACCTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
Found at i:479142 original size:15 final size:14
Alignment explanation
Indices: 479114--479146 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
479104 ATGCTCCTAT
479114 ATAA-ATAAATATA
1 ATAATATAAATATA
479127 ATAATATAACATATA
1 ATAATATAA-ATATA
479142 ATAAT
1 ATAAT
479147 GAACTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAAATATA
Found at i:487047 original size:14 final size:14
Alignment explanation
Indices: 487028--487074 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
487018 AGTTGTGGAT
487028 TAAAAAAGAAACCC
1 TAAAAAAGAAACCC
487042 TAAAAAAGAAA--C
1 TAAAAAAGAAACCC
*
487054 -AAAAACAAAAACCC
1 TAAAAA-AGAAACCC
487068 TAAAAAA
1 TAAAAAA
487075 TAGTAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
11 5 0.18
12 5 0.18
14 13 0.46
15 5 0.18
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.06
Consensus pattern (14 bp):
TAAAAAAGAAACCC
Found at i:491881 original size:84 final size:85
Alignment explanation
Indices: 491765--491930 Score: 280
Period size: 84 Copynumber: 2.0 Consensus size: 85
491755 TGATGTGGAC
** * *
491765 GCGATTTCGCGGTGTTTCCCACGTTAGGTTTTTTAGGGTTTTTTGGATTTTTAGGGCTTCGGAGA
1 GCGATTTCGCGGTGTTTCCCACGTTAGGTTTTTTAGGGTTTTTAAGATTTTTAAGGCTTCAGAGA
491830 GAAATTAATTAATTAATGCT
66 GAAATTAATTAATTAATGCT
*
491850 GCGATTT-GCGGTGTTTCCCACGTTAGGTTTTTTAGGGTTTTTAATATTTTTAAGGCTTCAGAGA
1 GCGATTTCGCGGTGTTTCCCACGTTAGGTTTTTTAGGGTTTTTAAGATTTTTAAGGCTTCAGAGA
491914 GAAATTAATTAATTAAT
66 GAAATTAATTAATTAAT
491931 TAAAATTAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 69 0.91
85 7 0.09
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (85 bp):
GCGATTTCGCGGTGTTTCCCACGTTAGGTTTTTTAGGGTTTTTAAGATTTTTAAGGCTTCAGAGA
GAAATTAATTAATTAATGCT
Found at i:495434 original size:21 final size:21
Alignment explanation
Indices: 495408--495456 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
495398 CTTTGTCTAG
495408 CTTCCGGCGGCGG-TTGCT-GTT
1 CTTCCGGCGG-GGATT-CTGGTT
495429 CTTCCGGCGGGGATTCTGGTT
1 CTTCCGGCGGGGATTCTGGTT
495450 CTTCCGG
1 CTTCCGG
495457 TACGGCATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.02, C:0.29, G:0.37, T:0.33
Consensus pattern (21 bp):
CTTCCGGCGGGGATTCTGGTT
Found at i:495735 original size:18 final size:18
Alignment explanation
Indices: 495712--495751 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
495702 GACTCGGAAA
*
495712 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
495730 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
495748 AGGA
1 AGGA
495752 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:497557 original size:51 final size:50
Alignment explanation
Indices: 497513--497608 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
497503 AATTATTTAA
497513 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATT-AAATT
* * * * *
497564 AAATATGGCTTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATT
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATT
497609 GAGAGGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 3 0.08
51 36 0.92
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTAAATT
Found at i:497608 original size:12 final size:11
Alignment explanation
Indices: 497573--497626 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
497563 TAAATATGGC
497573 TTTGAGAGAAA
1 TTTGAGAGAAA
*
497584 TTTTGA-AGGAA
1 -TTTGAGAGAAA
497595 TTTGAGAGCAAA
1 TTTGAGAG-AAA
497607 -TTGAGAGGAAA
1 TTTGAGA-GAAA
497618 TTTGAGAGA
1 TTTGAGAGA
497627 GGATTAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 5 0.14
11 17 0.47
12 14 0.39
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:497619 original size:23 final size:21
Alignment explanation
Indices: 497573--497626 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 21
497563 TAAATATGGC
497573 TTTGAGAGAAATTTTGAAGGAA
1 TTTGAGAGAAA-TTTGAAGGAA
497595 TTTGAGAGCAAA-TTGAGAGGAAA
1 TTTGAGAG-AAATTTGA-AGG-AA
497618 TTTGAGAGA
1 TTTGAGAGA
497627 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.14
22 12 0.41
23 13 0.45
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (21 bp):
TTTGAGAGAAATTTGAAGGAA
Found at i:513479 original size:42 final size:42
Alignment explanation
Indices: 513366--513510 Score: 175
Period size: 42 Copynumber: 3.5 Consensus size: 42
513356 TTTTACAAGA
*
513366 TGTGTATCAGCGAAGCTCCCTACATGAGCTTAAGTGATAAGC
1 TGTGTATCAGCGAAGCTCCCTACATGAGCTTAAGTGATAAGT
* * ** * * * *
513408 TGT-TATTAGCAAAGCTCTTTACATAAGCTTAAATGTTAAAT
1 TGTGTATCAGCGAAGCTCCCTACATGAGCTTAAGTGATAAGT
**
513449 TGTGTATCAGCGAAGCTCCCTATGTGAGCTTAAGTGATAAGT
1 TGTGTATCAGCGAAGCTCCCTACATGAGCTTAAGTGATAAGT
*
513491 TGTGTATCAGTGAAGCTCCC
1 TGTGTATCAGCGAAGCTCCC
513511 CATGCGAGTT
Statistics
Matches: 82, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 32 0.39
42 50 0.61
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
TGTGTATCAGCGAAGCTCCCTACATGAGCTTAAGTGATAAGT
Found at i:513524 original size:42 final size:42
Alignment explanation
Indices: 513366--513528 Score: 138
Period size: 42 Copynumber: 3.9 Consensus size: 42
513356 TTTTACAAGA
*
513366 TGTGTATCAGCGAAGCTCCCTACAT--GAGCTTAAGTGATAAGC
1 TGTGTATCAGCGAAGCTCCC--CATGCGAGCTTAAGTGATAAGT
* * ** * * * *
513408 TGT-TATTAGCAAAGCTCTTTACAT--AAGCTTAAATGTTAAAT
1 TGTGTATCAGCGAAGCTC--CCCATGCGAGCTTAAGTGATAAGT
* *
513449 TGTGTATCAGCGAAGCTCCCTATGTGAGCTTAAGTGATAAGT
1 TGTGTATCAGCGAAGCTCCCCATGCGAGCTTAAGTGATAAGT
* *
513491 TGTGTATCAGTGAAGCTCCCCATGCGAGTTTAAGTGAT
1 TGTGTATCAGCGAAGCTCCCCATGCGAGCTTAAGTGAT
513529 TGTGCTCCTC
Statistics
Matches: 94, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
40 2 0.02
41 30 0.32
42 62 0.66
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (42 bp):
TGTGTATCAGCGAAGCTCCCCATGCGAGCTTAAGTGATAAGT
Found at i:515693 original size:26 final size:24
Alignment explanation
Indices: 515616--515693 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 24
515606 TTTCTCATCC
*
515616 CAATTTTACCGCAGTAAAATTTTGA
1 CAATTTTACC-CCGTAAAATTTTGA
** *
515641 TGATTTTACCATCCGGTAAAGTTTTGA
1 CAATTTTACC--CC-GTAAAATTTTGA
515668 CAATTTTACCCCTGATAAAATTTTGA
1 CAATTTTACCCC-G-TAAAATTTTGA
515694 GAAAATTCGT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
25 11 0.27
26 11 0.27
27 19 0.46
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (24 bp):
CAATTTTACCCCGTAAAATTTTGA
Found at i:518753 original size:51 final size:50
Alignment explanation
Indices: 518631--518859 Score: 273
Period size: 51 Copynumber: 4.5 Consensus size: 50
518621 TTTATGTAGA
* *
518631 AGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCACGTAGT
1 AGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTTCACATAGT
*
518681 AGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
1 AGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTTCACATAGT
* * * *
518732 AGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTGCACATTGT
1 AGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTTCACATAGT
* * * * * *
518783 AGCCTTCACTTTGTACTACACATGTGACC-ATCATTTATCGATTCACGTAGT
1 AGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCACATAGT
*
518834 AGCCTTCACACAGTACTACACACGTG
1 AGCCTTCACATAGTACTACACACGTG
518860 NNNNNNNNNN
Statistics
Matches: 154, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
49 2 0.01
50 30 0.19
51 118 0.77
52 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (50 bp):
AGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTTCACATAGT
Found at i:523576 original size:17 final size:18
Alignment explanation
Indices: 523554--523589 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
523544 CTATATCGAC
*
523554 AAAAT-AAAATAATTTAA
1 AAAATAAAAAAAATTTAA
523571 AAAATAAAAAAAATTTAA
1 AAAATAAAAAAAATTTAA
523589 A
1 A
523590 TTTAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAAAAAAAATTTAA
Found at i:523806 original size:9 final size:9
Alignment explanation
Indices: 523782--523825 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
523772 CAAACAAAAC
*
523782 TTGAGAAAA
1 TTGAGAGAA
523791 TTGAGAGAA
1 TTGAGAGAA
*
523800 TTGAGAGAG
1 TTGAGAGAA
523809 TTGAGAGAA
1 TTGAGAGAA
*
523818 TAGAGAGA
1 TTGAGAGA
523826 GTTGGATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.20
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:523807 original size:11 final size:9
Alignment explanation
Indices: 523791--523829 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
523781 CTTGAGAAAA
*
523791 TTGAGAGAA
1 TTGAGAGAG
523800 TTGAGAGAG
1 TTGAGAGAG
*
523809 TTGAGAGAA
1 TTGAGAGAG
*
523818 TAGAGAGAG
1 TTGAGAGAG
523827 TTG
1 TTG
523830 GATTTGAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:523824 original size:18 final size:18
Alignment explanation
Indices: 523791--523829 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
523781 CTTGAGAAAA
*
523791 TTGAGAGAATTGAGAGAG
1 TTGAGAGAATAGAGAGAG
523809 TTGAGAGAATAGAGAGAG
1 TTGAGAGAATAGAGAGAG
523827 TTG
1 TTG
523830 GATTTGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (18 bp):
TTGAGAGAATAGAGAGAG
Found at i:524767 original size:7 final size:7
Alignment explanation
Indices: 524755--524786 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
524745 ATTATTTATT
524755 TTTTGAA
1 TTTTGAA
524762 TTTTGAA
1 TTTTGAA
524769 TTTTGAA
1 TTTTGAA
524776 TTTTGAA
1 TTTTGAA
524783 TTTT
1 TTTT
524787 TAAGAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTTGAA
Found at i:525299 original size:21 final size:21
Alignment explanation
Indices: 525274--525316 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
525264 GCATATGCAT
*
525274 TTTAA-CATCGAGGTATCGATA
1 TTTAAGCATCGA-GTATCAATA
*
525295 TTTAAGCCTCGAGTATCAATA
1 TTTAAGCATCGAGTATCAATA
525316 T
1 T
525317 CTCTGCTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
TTTAAGCATCGAGTATCAATA
Found at i:532302 original size:19 final size:19
Alignment explanation
Indices: 532278--532318 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
532268 GACCATGATG
532278 AGGAGTTGGAGAAGGAAGA
1 AGGAGTTGGAGAAGGAAGA
532297 AGGAGTTGGAGAAGGAAGA
1 AGGAGTTGGAGAAGGAAGA
532316 AGG
1 AGG
532319 TGTCTCCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.49, T:0.10
Consensus pattern (19 bp):
AGGAGTTGGAGAAGGAAGA
Found at i:536848 original size:2 final size:2
Alignment explanation
Indices: 536841--536868 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
536831 ATGTTACGGA
536841 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
536869 CTAATTTGAT
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:544774 original size:25 final size:25
Alignment explanation
Indices: 544740--544803 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
544730 TTAGAAAAAA
544740 GTTGCTTGTCCTCTGCTTGTTGGCT
1 GTTGCTTGTCCTCTGCTTGTTGGCT
*
544765 GTTGCTTGTCCTCTGCTTGTTGGTT
1 GTTGCTTGTCCTCTGCTTGTTGGCT
*
544790 GTTGCTTGTTCTCT
1 GTTGCTTGTCCTCT
544804 TTAGCTTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.00, C:0.22, G:0.27, T:0.52
Consensus pattern (25 bp):
GTTGCTTGTCCTCTGCTTGTTGGCT
Found at i:546921 original size:43 final size:43
Alignment explanation
Indices: 546857--547081 Score: 193
Period size: 43 Copynumber: 5.3 Consensus size: 43
546847 AGTTTATTCG
* *
546857 ATGATGCACAGTGTGTGCTAGTATAATTGTTTCGGTATATCCA
1 ATGATGCACTGTGTATGCTAGTATAATTGTTTCGGTATATCCA
* **
546900 ATTATGCACTGTGTATGCTAGTATAATTACTTCGGTATATCCA
1 ATGATGCACTGTGTATGCTAGTATAATTGTTTCGGTATATCCA
* ** * *
546943 ATGATGCACTGTGTATGCTAGTGTAATTGTTTCAATTTATCCG
1 ATGATGCACTGTGTATGCTAGTATAATTGTTTCGGTATATCCA
* * * * * * * **
546986 ATGATGCATTATGTGTGCCAGTATAAATGCTTT-GGTTTGTCTG
1 ATGATGCACTGTGTATGCTAGTATAATTG-TTTCGGTATATCCA
* * * * * * *
547029 ATGATGCACTATGTGTGCCAATAT-ATTTTTTCGGTTTATCCG
1 ATGATGCACTGTGTATGCTAGTATAATTGTTTCGGTATATCCA
547071 ATGATGCACTG
1 ATGATGCACTG
547082 AGGTACCAGA
Statistics
Matches: 150, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
41 3 0.02
42 20 0.13
43 124 0.83
44 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (43 bp):
ATGATGCACTGTGTATGCTAGTATAATTGTTTCGGTATATCCA
Found at i:547033 original size:86 final size:86
Alignment explanation
Indices: 546855--547080 Score: 238
Period size: 86 Copynumber: 2.6 Consensus size: 86
546845 TTAGTTTATT
* * * * * *
546855 CGATGATGCACAGTGTGTGCTAGTATAATTGTTTCGGTATATCCAATTATGCACTGTGTATGCTA
1 CGATGATGCACTGTGTGTGCTAGTATAATTGTTTCGGTTTATCCGATGATGCACTATGTATGCCA
*
546920 GTATAATTACTTCGGTATATC
66 GTATAAATACTTCGGTATATC
* * * ** * *
546941 CAATGATGCACTGTGTATGCTAGTGTAATTGTTTCAATTTATCCGATGATGCATTATGTGTGCCA
1 CGATGATGCACTGTGTGTGCTAGTATAATTGTTTCGGTTTATCCGATGATGCACTATGTATGCCA
* * * *
547006 GTATAAATGCTTTGGTTTGTC
66 GTATAAATACTTCGGTATATC
* * * * *
547027 TGATGATGCACTATGTGTGCCAATAT-ATTTTTTCGGTTTATCCGATGATGCACT
1 CGATGATGCACTGTGTGTGCTAGTATAATTGTTTCGGTTTATCCGATGATGCACT
547081 GAGGTACCAG
Statistics
Matches: 111, Mismatches: 29, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
85 24 0.22
86 87 0.78
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (86 bp):
CGATGATGCACTGTGTGTGCTAGTATAATTGTTTCGGTTTATCCGATGATGCACTATGTATGCCA
GTATAAATACTTCGGTATATC
Found at i:549524 original size:69 final size:69
Alignment explanation
Indices: 549406--549535 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 69
549396 TATACACTGT
* * * * * *
549406 CATGGTCCAACCATGGCCTTACGTCTAAACAACTGTCATAGTCTCGCTATGGTCTTATGTATATA
1 CATGGTCCAACCATGACCTTACATCCAAAAAACTGCCATAGCCTCGCTATGGTCTTATGTATATA
549471 TTTC
66 TTTC
* * * *
549475 CATGGTCCAACCATGATCTTATATCCAAAAAATTGCCATAGCCTTGCTATGGTCTTATGTA
1 CATGGTCCAACCATGACCTTACATCCAAAAAACTGCCATAGCCTCGCTATGGTCTTATGTA
549536 CGAATGCAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (69 bp):
CATGGTCCAACCATGACCTTACATCCAAAAAACTGCCATAGCCTCGCTATGGTCTTATGTATATA
TTTC
Found at i:552440 original size:18 final size:18
Alignment explanation
Indices: 552389--552433 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
552379 ACTTTAAATT
*
552389 TTTTTTTGA-AAATTTTGA
1 TTTTTTT-ATAAATTTTAA
552407 TTTTTTTATAAATTTTAA
1 TTTTTTTATAAATTTTAA
552425 TATTTTTTA
1 T-TTTTTTA
552434 GAATTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.67
19 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTTTATAAATTTTAA
Found at i:554158 original size:13 final size:13
Alignment explanation
Indices: 554142--554181 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
554132 TTTAAACCAA
554142 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * *
554155 ACTTTTCCACATC
1 ACTTTTCAAAAGC
554168 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
554181 A
1 A
554182 ATGAAGAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:557705 original size:24 final size:24
Alignment explanation
Indices: 557678--557748 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
557668 ATTATGCAAG
557678 CTGTATTTGAAGAAATGCTACGAA
1 CTGTATTTGAAGAAATGCTACGAA
* * * *
557702 CTGTA-TTGTAGAATTACTGCGAA
1 CTGTATTTGAAGAAATGCTACGAA
*
557725 CTATATTT-ACAGAAATGCTACGAA
1 CTGTATTTGA-AGAAATGCTACGAA
557749 ATGCATTGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (24 bp):
CTGTATTTGAAGAAATGCTACGAA
Found at i:557724 original size:23 final size:23
Alignment explanation
Indices: 557661--557785 Score: 71
Period size: 23 Copynumber: 5.5 Consensus size: 23
557651 ACAAATCATG
*
557661 TTGTAGAATTA-TGC-AAGCTGTA
1 TTGTAGAAATACTGCGAA-CTGTA
* * *
557683 TTTGAAGAAATGCTACGAACTGTA
1 -TTGTAGAAATACTGCGAACTGTA
* *
557707 TTGTAGAATTACTGCGAACTATA
1 TTGTAGAAATACTGCGAACTGTA
* * * *
557730 TT-TACAGAAATGCTACGAAATGCA
1 TTGT--AGAAATACTGCGAACTGTA
* *
557754 TTGTAG-AATATTGCGAATTGTA
1 TTGTAGAAATACTGCGAACTGTA
557776 TTGTA-AAATA
1 TTGTAGAAATA
557786 TCGTGGGATT
Statistics
Matches: 76, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
22 21 0.28
23 30 0.39
24 22 0.29
25 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (23 bp):
TTGTAGAAATACTGCGAACTGTA
Found at i:557740 original size:47 final size:47
Alignment explanation
Indices: 557661--557770 Score: 138
Period size: 47 Copynumber: 2.4 Consensus size: 47
557651 ACAAATCATG
* * *
557661 TTGTAGAATTATGC-AAGCTGTATTTGAAGAAATGCTACGAACTGTA
1 TTGTAGAATTATGCGAAGCTATATTTGAAGAAATGCTACGAAATGCA
557707 TTGTAGAATTACTGCGAA-CTATATTT-ACAGAAATGCTACGAAATGCA
1 TTGTAGAATTA-TGCGAAGCTATATTTGA-AGAAATGCTACGAAATGCA
557754 TTGTAGAA-TATTGCGAA
1 TTGTAGAATTA-TGCGAA
557771 TTGTATTGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
46 20 0.35
47 35 0.61
48 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (47 bp):
TTGTAGAATTATGCGAAGCTATATTTGAAGAAATGCTACGAAATGCA
Found at i:557770 original size:22 final size:22
Alignment explanation
Indices: 557745--557786 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
557735 AGAAATGCTA
*
557745 CGAAATGCATTGTAGAATATTG
1 CGAAATGCATTGTAAAATATTG
* *
557767 CGAATTGTATTGTAAAATAT
1 CGAAATGCATTGTAAAATAT
557787 CGTGGGATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (22 bp):
CGAAATGCATTGTAAAATATTG
Found at i:557961 original size:75 final size:75
Alignment explanation
Indices: 557824--558397 Score: 510
Period size: 75 Copynumber: 7.7 Consensus size: 75
557814 AAAGGTTGTA
* * * ** * * * * * * *
557824 ATCGTAAATTAGCGAACTGTTAGAAAGCCAAAGGTCATGATCGTAAATTAGTGAACCATAAAAAT
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGAAAATCAGCGGACCGTAAAAAT
* *
557889 GGCAGTCATG
66 GACAGTCGTG
* * * * * *
557899 ATCATAAATCAACGAATTGTTGGAAAATCAAAGGTCGTGATCGAAAATTAGCGGACCGTAAAAAT
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGAAAATCAGCGGACCGTAAAAAT
* *
557964 GACAGTCATA
66 GACAGTCGTG
* * * * * *
557974 ATCGTAAATCAATGAACTATTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGTAAAAAT
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGAAAATCAGCGGACCGTAAAAAT
*
558039 GATAGTCGTG
66 GACAGTCGTG
* ** * *
558049 ATCGTTAATCAGTGAAGTATTAGAAAATCGAAGGTCGTGATC-ATAAATCAGCGGACCGTAAAAG
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGA-AAATCAGCGGACCGTAAAAA
*
558113 TGACAGTTGTG
65 TGACAGTCGTG
* * * * *
558124 ATCGTAAATCAATGAATTGTTAGAAAATCGAAGGTTGTAATC-ACAAATCAGCGGACCGT-AAAA
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGA-AAATCAGCGGACCGTAAAAA
*
558187 TAACAGTCGTG
65 TGACAGTCGTG
* * * * *
558198 ATCGTAAATCAACGAACTATTAGGAAGTCGAAGGTTGTGATC-ATAAATCAACAGACCGTAAAAA
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGA-AAATCAGCGGACCGTAAAAA
* *
558262 TGACATTTGTG
65 TGACAGTCGTG
* * * * * * * *
558273 ATCGTAAATTAGCAAACTGTTAGAAAATCGAAGGTCGTGATAGTAAATCAACAGACCGTAAAAAT
1 ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGAAAATCAGCGGACCGTAAAAAT
* *
558338 GATAATCGTG
66 GACAGTCGTG
* ** * *
558348 ATCGTAAATCAGCGAA-TAGTTAGAAAGCCGAAGATCGTGATCGTAAATCA
1 ATCGTAAATCAACGAACTA-TTAGAAAATCGAAGGTCGTGATCGAAAATCA
558398 ACAAACTCTT
Statistics
Matches: 416, Mismatches: 79, Indels: 8
0.83 0.16 0.02
Matches are distributed among these distances:
74 63 0.15
75 353 0.85
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (75 bp):
ATCGTAAATCAACGAACTATTAGAAAATCGAAGGTCGTGATCGAAAATCAGCGGACCGTAAAAAT
GACAGTCGTG
Found at i:558017 original size:39 final size:39
Alignment explanation
Indices: 557824--558099 Score: 156
Period size: 39 Copynumber: 7.3 Consensus size: 39
557814 AAAGGTTGTA
* * * **
557824 ATCGTAAATTAGCGAACTGTTAGAAAGCCAAAGGTCATG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
* * ***
557863 ATCGTAAATTAGTGAACCA-TA-AAAATGGCA-GTCATG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
* ** * * * *
557899 ATCATAAATCAACGAATTGTTGGAAAATCAAAGGTCGTG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
* * * * ** * * *
557938 ATCGAAAATTAGCGGAC-CGTA-AAAATGACA-GTCATA
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
*
557974 ATCGTAAATCAATGAACTATTAGAAAATCAAAGGTCATG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
** * * *
558013 ATCGTAAATCAGTGAAC-CGTA-AAAATGATA-GTCGTG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
* * * *
558049 ATCGTTAATCAGTGAAGTATTAGAAAATCGAAGGTCGTG
1 ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
*
558088 ATCATAAATCAG
1 ATCGTAAATCAG
558100 CGGACCGTAA
Statistics
Matches: 170, Mismatches: 58, Indels: 18
0.69 0.24 0.07
Matches are distributed among these distances:
36 54 0.32
37 23 0.14
38 24 0.14
39 69 0.41
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCGTAAATCAGTGAACTATTAGAAAATCAAAGGTCATG
Found at i:558102 original size:150 final size:149
Alignment explanation
Indices: 557818--558397 Score: 581
Period size: 150 Copynumber: 3.9 Consensus size: 149
557808 TGAGTAAAAG
* * ** * *
557818 GTTGTAATCGTAAATTAGCGAACTGTTAGAAAGCCAAAGGTCATGATCGTAAATTAGTGAACCAT
1 GTTGTAATCGTAAATCAACGAACTGTTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGT
* * * * * *
557883 AAAAATGGCAGTCATGATCATAAATCAACGAATTGTTGGAAAATCAAAGGTCGTGATCGA-AAAT
66 AAAAATGACAGTCGTGATCGTAAATCAACGAA-TATTAGAAAATCGAAGGTCGTGATC-ATAAAT
*
557947 TAGCGGACCGTAAAAATGACA
129 CAGCGGACCGTAAAAATGACA
** * *
557968 GTCATAATCGTAAATCAATGAACTATTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGT
1 GTTGTAATCGTAAATCAACGAACTGTTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGT
* * **
558033 AAAAATGATAGTCGTGATCGTTAATCAGTGAAGTATTAGAAAATCGAAGGTCGTGATCATAAATC
66 AAAAATGACAGTCGTGATCGTAAATCAACGAA-TATTAGAAAATCGAAGGTCGTGATCATAAATC
*
558098 AGCGGACCGTAAAAGTGACA
130 AGCGGACCGTAAAAATGACA
* * * * ** * ** * *
558118 GTTGTGATCGTAAATCAATGAATTGTTAGAAAATCGAAGGTTGTAATCACAAATCAGCGGACCGT
1 GTTGTAATCGTAAATCAACGAACTGTTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGT
* * * *
558183 -AAAATAACAGTCGTGATCGTAAATCAACGAACTATTAGGAAGTCGAAGGTTGTGATCATAAATC
66 AAAAATGACAGTCGTGATCGTAAATCAACGAA-TATTAGAAAATCGAAGGTCGTGATCATAAATC
* *
558247 AACAGACCGTAAAAATGACA
130 AGCGGACCGTAAAAATGACA
* * * * * * * * **
558267 TTTGTGATCGTAAATTAGCAAACTGTTAGAAAATCGAAGGTCGTGATAGTAAATCA-ACAGACCG
1 GTTGTAATCGTAAATCAACGAACTGTTAGAAAATCAAAGGTCATGATCGTAAATCAGTGA-ACCG
* * * ** * *
558331 TAAAAATGATAATCGTGATCGTAAATCAGCGAATAGTTAGAAAGCCGAAGATCGTGATCGTAAAT
65 TAAAAATGACAGTCGTGATCGTAAATCAACGAATA-TTAGAAAATCGAAGGTCGTGATCATAAAT
558396 CA
129 CA
558398 ACAAACTCTT
Statistics
Matches: 355, Mismatches: 71, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
149 125 0.35
150 230 0.65
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (149 bp):
GTTGTAATCGTAAATCAACGAACTGTTAGAAAATCAAAGGTCATGATCGTAAATCAGTGAACCGT
AAAAATGACAGTCGTGATCGTAAATCAACGAATATTAGAAAATCGAAGGTCGTGATCATAAATCA
GCGGACCGTAAAAATGACA
Found at i:558276 original size:224 final size:225
Alignment explanation
Indices: 557882--558373 Score: 578
Period size: 224 Copynumber: 2.2 Consensus size: 225
557872 TAGTGAACCA
* * * * * *
557882 TAAAAATGGCAGTCATGATCATAAATCAACGAATTGTTGGAAAATCAAAGGTCGTGATCGAAAAT
1 TAAAAATGACAATCGTGATCGTAAATCAACGAATTGTTAGAAAATCAAAGGTCGTAATCGAAAAT
* * *
557947 TAGCGGACCGTAAAAATGACAGTCATAATCGTAAATCAATGAACTATTAGAAAATCAAAGGTCAT
66 CAGCGGACCGTAAAAATAACAGTCATAATCGTAAATCAACGAACTATTAGAAAATCAAAGGTCAT
* ** * * ** *
558012 GATCGTAAATCAGTGAACCGTAAAAATGATAGTCGTGATCGTTAATCAGTGAAGTATTAGAAAAT
131 GATCATAAATCACAGAACCGTAAAAATGACAGTCGTGATCGTAAATCAGCAAACTATTAGAAAAT
* *
558077 CGAAGGTCGTGATCA-TAAATCAGCGGACCG
196 CGAAGGTCGTGAT-AGTAAATCAACAGACCG
* * * * * *
558107 TAAAAGTGACAGTTGTGATCGTAAATCAATGAATTGTTAGAAAATCGAAGGTTGTAATC-ACAAA
1 TAAAAATGACAATCGTGATCGTAAATCAACGAATTGTTAGAAAATCAAAGGTCGTAATCGA-AAA
* * * * * **
558171 TCAGCGGACCGT-AAAATAACAGTCGTGATCGTAAATCAACGAACTATTAGGAAGTCGAAGGTTG
65 TCAGCGGACCGTAAAAATAACAGTCATAATCGTAAATCAACGAACTATTAGAAAATCAAAGGTCA
* * * *
558235 TGATCATAAATCAACAG-ACCGTAAAAATGACATTTGTGATCGTAAATTAGCAAACTGTTAGAAA
130 TGATCATAAATC-ACAGAACCGTAAAAATGACAGTCGTGATCGTAAATCAGCAAACTATTAGAAA
558299 ATCGAAGGTCGTGATAGTAAATCAACAGACCG
194 ATCGAAGGTCGTGATAGTAAATCAACAGACCG
* * *
558331 TAAAAATGATAATCGTGATCGTAAATCAGCGAATAGTTAGAAA
1 TAAAAATGACAATCGTGATCGTAAATCAACGAATTGTTAGAAA
558374 GCCGAAGATC
Statistics
Matches: 223, Mismatches: 41, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
223 1 0.00
224 157 0.70
225 65 0.29
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (225 bp):
TAAAAATGACAATCGTGATCGTAAATCAACGAATTGTTAGAAAATCAAAGGTCGTAATCGAAAAT
CAGCGGACCGTAAAAATAACAGTCATAATCGTAAATCAACGAACTATTAGAAAATCAAAGGTCAT
GATCATAAATCACAGAACCGTAAAAATGACAGTCGTGATCGTAAATCAGCAAACTATTAGAAAAT
CGAAGGTCGTGATAGTAAATCAACAGACCG
Found at i:558313 original size:39 final size:39
Alignment explanation
Indices: 558193--558404 Score: 145
Period size: 39 Copynumber: 5.6 Consensus size: 39
558183 AAAATAACAG
* * * * *
558193 TCGTGATCGTAAATCAACGAACTATTAGGAAGTCGAAGG
1 TCGTGATCGTAAATCAACAAACTGTTAGAAAATCGAAGA
* * * * *
558232 TTGTGATCATAAATCAACAGACCG-TA-AAAAT-GACA-T
1 TCGTGATCGTAAATCAACAAACTGTTAGAAAATCGA-AGA
* * * *
558268 TTGTGATCGTAAATTAGCAAACTGTTAGAAAATCGAAGG
1 TCGTGATCGTAAATCAACAAACTGTTAGAAAATCGAAGA
* * *
558307 TCGTGATAGTAAATCAACAGACCG-TA-AAAAT-GATA-A
1 TCGTGATCGTAAATCAACAAACTGTTAGAAAATCGA-AGA
* * **
558343 TCGTGATCGTAAATCAGCGAA-TAGTTAGAAAGCCGAAGA
1 TCGTGATCGTAAATCAACAAACT-GTTAGAAAATCGAAGA
558382 TCGTGATCGTAAATCAACAAACT
1 TCGTGATCGTAAATCAACAAACT
558405 CTTTATGAAG
Statistics
Matches: 130, Mismatches: 31, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
36 41 0.32
37 14 0.11
38 14 0.11
39 60 0.46
40 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (39 bp):
TCGTGATCGTAAATCAACAAACTGTTAGAAAATCGAAGA
Found at i:558452 original size:27 final size:27
Alignment explanation
Indices: 558421--558488 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
558411 GAAGTGTTCA
558421 TGATCATAAATCAATGAACTGAAGCCG
1 TGATCATAAATCAATGAACTGAAGCCG
558448 TGATCATAAATCAATGAACTGAAGCCG
1 TGATCATAAATCAATGAACTGAAGCCG
*
558475 TGATCGTAAATCAA
1 TGATCATAAATCAA
558489 CGAGCTTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (27 bp):
TGATCATAAATCAATGAACTGAAGCCG
Found at i:558513 original size:36 final size:36
Alignment explanation
Indices: 558473--558671 Score: 107
Period size: 36 Copynumber: 5.4 Consensus size: 36
558463 GAACTGAAGC
558473 CGTGATCGTAAATCAACGAGCTTTAAAAATGACAGT
1 CGTGATCGTAAATCAACGAGCTTTAAAAATGACAGT
** * * * * *
558509 CGTGATAATAAATCAGCAAACTGTTAGAAAATCAAAGGT
1 CGTGATCGTAAATCAACGAGCT-TTA-AAAATGACA-GT
* * ** * *
558548 TGTGATTGTAAATCAACG-GACCGTAAATATGACACT
1 CGTGATCGTAAATCAACGAG-CTTTAAAAATGACAGT
* * *
558584 CGCGATCGTAAATCAACAAACTATTAGAAAATTGA-AGGT
1 CGTGATCGTAAATCAACGAGCT-TTA-AAAA-TGACA-GT
* * * * *
558623 TGTGATTGTAAATCAGCG-GACTGTAAAAATGATAGT
1 CGTGATCGTAAATCAACGAG-CTTTAAAAATGACAGT
558659 CGTGATCGTAAAT
1 CGTGATCGTAAAT
558672 TAGCAAATTG
Statistics
Matches: 115, Mismatches: 37, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
36 49 0.43
37 16 0.14
38 15 0.13
39 35 0.30
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
CGTGATCGTAAATCAACGAGCTTTAAAAATGACAGT
Found at i:558560 original size:39 final size:39
Alignment explanation
Indices: 558507--558718 Score: 139
Period size: 39 Copynumber: 5.6 Consensus size: 39
558497 AAAAATGACA
**
558507 GTCGTGATAATAAATCAGCAAACTGTTAGAAAATCAAAG
1 GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
* * ** * * * *
558546 GTTGTGATTGTAAATCAACGGACCG-TA-AATATGACA-
1 GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
* * * * * **
558582 CTCGCGATCGTAAATCAACAAACTATTAGAAAATTGAAG
1 GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
* ** * *
558621 GTTGTGATTGTAAATCAGCGGACTG-TA-AAAATGATA-
1 GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
* * * *
558657 GTCGTGATCGTAAATTAGCAAATTGTTAGAAAATCGAAG
1 GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
*
558696 GTCATGATTGTAAATCAGCAAAC
1 GTCGTGATTGTAAATCAGCAAAC
558719 CGCGAGATTC
Statistics
Matches: 121, Mismatches: 46, Indels: 12
0.68 0.26 0.07
Matches are distributed among these distances:
36 36 0.30
37 16 0.13
38 15 0.12
39 54 0.45
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (39 bp):
GTCGTGATTGTAAATCAGCAAACTGTTAGAAAATCAAAG
Found at i:558713 original size:75 final size:75
Alignment explanation
Indices: 558496--558714 Score: 294
Period size: 75 Copynumber: 2.9 Consensus size: 75
558486 CAACGAGCTT
** *
558496 TAAAAATGACAGTCGTGATAATAAATCAGCAAACTGTTAGAAAATCAAAGGTTGTGATTGTAAAT
1 TAAAAATGACAGTCGTGATCGTAAATCAGCAAACTGTTAGAAAATCGAAGGTTGTGATTGTAAAT
*
558561 CAACGGACCG
66 CAGCGGACCG
* * * * * *
558571 TAAATATGACACTCGCGATCGTAAATCAACAAACTATTAGAAAATTGAAGGTTGTGATTGTAAAT
1 TAAAAATGACAGTCGTGATCGTAAATCAGCAAACTGTTAGAAAATCGAAGGTTGTGATTGTAAAT
*
558636 CAGCGGACTG
66 CAGCGGACCG
* * * **
558646 TAAAAATGATAGTCGTGATCGTAAATTAGCAAATTGTTAGAAAATCGAAGGTCATGATTGTAAAT
1 TAAAAATGACAGTCGTGATCGTAAATCAGCAAACTGTTAGAAAATCGAAGGTTGTGATTGTAAAT
558711 CAGC
66 CAGC
558715 AAACCGCGAG
Statistics
Matches: 122, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 122 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (75 bp):
TAAAAATGACAGTCGTGATCGTAAATCAGCAAACTGTTAGAAAATCGAAGGTTGTGATTGTAAAT
CAGCGGACCG
Found at i:572741 original size:26 final size:26
Alignment explanation
Indices: 572710--572763 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
572700 TTTTCTATTT
* *
572710 TTTAAGAAAATGAAAAGAAAATTAAC
1 TTTAAGAAAACGAAAACAAAATTAAC
572736 TTTAAGAAAACGAAAACAAAATTAAC
1 TTTAAGAAAACGAAAACAAAATTAAC
572762 TT
1 TT
572764 AGGTTACCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.24
Consensus pattern (26 bp):
TTTAAGAAAACGAAAACAAAATTAAC
Found at i:574329 original size:31 final size:32
Alignment explanation
Indices: 574293--574353 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
574283 AAAATGGTCA
* *
574293 TTGAACTATTCGAAAG-TTTTCATTTAAGTCG
1 TTGAACAAGTCGAAAGTTTTTCATTTAAGTCG
*
574324 TTGAACAAGTCGAAAGTTTTTTATTTAAGT
1 TTGAACAAGTCGAAAGTTTTTCATTTAAGT
574354 AATTGGGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
TTGAACAAGTCGAAAGTTTTTCATTTAAGTCG
Found at i:577579 original size:23 final size:23
Alignment explanation
Indices: 577548--577599 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
577538 TTGGTGGGAG
* *
577548 CATTATGGCACTATGGTGCAACT
1 CATTCTGGCACTACGGTGCAACT
*
577571 CATTCTGGCACTACGGTGCAATT
1 CATTCTGGCACTACGGTGCAACT
577594 CATTCT
1 CATTCT
577600 ACCTCTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (23 bp):
CATTCTGGCACTACGGTGCAACT
Found at i:582234 original size:31 final size:31
Alignment explanation
Indices: 582199--582321 Score: 79
Period size: 31 Copynumber: 3.9 Consensus size: 31
582189 GTCAATACTT
582199 AACAAACCTAAGCAT-TAAAATTTCAACATCC
1 AACAAACCTAA-CATATAAAATTTCAACATCC
* * * **
582230 AACAATCTTAACATATAAAATTTTAGTATCC
1 AACAAACCTAACATATAAAATTTCAACATCC
* * * *
582261 AACAAACTTAAAATAGAAAAAAATTTCAATATCC
1 AACAAACCTAACAT---ATAAAATTTCAACATCC
* **
582295 AATAAATTTAACATA-AAAATATTCAAC
1 AACAAACCTAACATATAAAAT-TTCAAC
582322 CTACGTTCTA
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
30 8 0.11
31 40 0.55
34 25 0.34
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (31 bp):
AACAAACCTAACATATAAAATTTCAACATCC
Found at i:582294 original size:34 final size:33
Alignment explanation
Indices: 582215--582313 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 33
582205 CCTAAGCATT
* * *
582215 AAAATTTCAACATCCAACAATCTTAACAT--AT
1 AAAATTTCAATATCCAACAAACTTAACATAAAA
* * *
582246 AAAATTTTAGTATCCAACAAACTTAAAATAGAAA
1 AAAATTTCAATATCCAACAAACTTAACATA-AAA
* *
582280 AAAATTTCAATATCCAATAAATTTAACATAAAA
1 AAAATTTCAATATCCAACAAACTTAACATAAAA
582313 A
1 A
582314 TATTCAACCT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 24 0.44
33 4 0.07
34 26 0.48
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (33 bp):
AAAATTTCAATATCCAACAAACTTAACATAAAA
Found at i:588990 original size:17 final size:18
Alignment explanation
Indices: 588964--589002 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
588954 AAAATAATAG
* *
588964 TAATAGTAATA-TTAAAA
1 TAATAATAATAGTAAAAA
588981 TAATAATAATAGTAAAAA
1 TAATAATAATAGTAAAAA
588999 TAAT
1 TAAT
589003 GGTAATACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TAATAATAATAGTAAAAA
Found at i:589017 original size:21 final size:21
Alignment explanation
Indices: 588951--589023 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
588941 TAATATTGTG
* *
588951 GTAAAAATAATAGTAATAGTA
1 GTAAAAATAATGGTAATAATA
*
588972 ATATTAAAATAA---TAATAATA
1 GTA--AAAATAATGGTAATAATA
*
588992 GTAAAAATAATGGTAATACTA
1 GTAAAAATAATGGTAATAATA
* *
589013 TTAAAATTAAT
1 GTAAAAATAAT
589024 CAATTTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
18 7 0.17
20 9 0.22
21 18 0.44
23 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (21 bp):
GTAAAAATAATGGTAATAATA
Found at i:590583 original size:45 final size:45
Alignment explanation
Indices: 590431--590898 Score: 314
Period size: 44 Copynumber: 10.5 Consensus size: 45
590421 GTCTGATGTG
* * * ** *
590431 ATCTACTCTACTGCAACTTCAGAGAGATAAGA--T-CCATCATTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTC-TTCA
* * *
590474 ATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
* * *
590518 ATCTGCTCTACTACAACTTCAGGGAGATAAGATTTGCTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
* * * * * ** *
590563 GTCTGCTCCACTGTACCTTCAGGGAGATAGGACTTAC-AACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
* ** * **
590607 ATCCGCTTTACTGCAACTTCAGGGAGATAA-AATTCGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTTTCTTCA
* * * * *
590652 GTCTGCTCCACTGCAACTTCAGAGAGATAAGGC-TGGTTACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
* *
590696 GTTTG-TCCCACTGCAACTTCAGAGG-GATAAGACTTGCTTTCTTCA
1 ATCTGCT-CCACTGCAACTTCAG-GGAGATAAGACTTGCTTTCTTCA
* * ** *
590741 ATCTGCTCTACTGCAACCTCAGGGAGATAAGACTTG-TAACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
* * * * * *
590785 ATCCGCTCCACTACAACTTCAGGGAGATAGGA--TGATTGACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT-TCTTCA
* * *
590829 ATCTGCTCCACTGTAACTTCAAGGATATAAGA-TTCGCCATCTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-C-T-TTCTTCA
***
590877 ATCCATTCCACTGCAACTTCAG
1 ATCTGCTCCACTGCAACTTCAG
590899 TGGTATAGGA
Statistics
Matches: 328, Mismatches: 79, Indels: 31
0.75 0.18 0.07
Matches are distributed among these distances:
42 2 0.01
43 32 0.10
44 158 0.48
45 111 0.34
46 2 0.01
48 22 0.07
49 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTCTTCA
Found at i:590624 original size:89 final size:89
Alignment explanation
Indices: 590478--590813 Score: 317
Period size: 89 Copynumber: 3.8 Consensus size: 89
590468 CATTTAATCC
** * * *
590478 GCTCCACTGCAA-CTTCAGGGAGATAGGA-TTGGTTTCTTCAATCTGCTCTACTACAACTTCAGG
1 GCTCCACTG-AACCTTCAGGGAGATAGGACTT-GTAACTTTAATCCGCTCCACTACAACTTCAGG
590541 GAGATAAGATTTGCTTTCTTCAGTCT
64 GAGATAAGATTTGCTTTCTTCAGTCT
* ** ** *
590567 GCTCCACTGTACCTTCAGGGAGATAGGACTTACAACTTTAATCCGCTTTACTGCAACTTCAGGGA
1 GCTCCACTGAACCTTCAGGGAGATAGGACTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGA
* * **
590632 GATAAAATTCGCCATCTTCAGTCT
66 GATAAGATTTGCTTTCTTCAGTCT
* * * * * ** *
590656 GCTCCACTGCAA-CTTCAGAGAGATAAGG-CTGGTTACTTCAGTTTG-TCCCACTGCAACTTCAG
1 GCTCCACTG-AACCTTCAGGGAGAT-AGGACTTGTAACTTTAATCCGCT-CCACTACAACTTCAG
* *
590718 AGG-GATAAGACTTGCTTTCTTCAATCT
63 -GGAGATAAGATTTGCTTTCTTCAGTCT
* *
590745 GCTCTACTGCAACC-TCAGGGAGATAAGACTTGTAACTTTAATCCGCTCCACTACAACTTCAGGG
1 GCTCCACTG-AACCTTCAGGGAGATAGGACTTGTAACTTTAATCCGCTCCACTACAACTTCAGGG
590809 AGATA
65 AGATA
590814 GGATGATTGA
Statistics
Matches: 196, Mismatches: 41, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
88 6 0.03
89 180 0.92
90 10 0.05
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (89 bp):
GCTCCACTGAACCTTCAGGGAGATAGGACTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGA
GATAAGATTTGCTTTCTTCAGTCT
Done.