Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold302
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: 555664
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 4
Found at i:131876 original size:116 final size:116
Alignment explanation
Indices: 131672--131902 Score: 390
Period size: 116 Copynumber: 2.0 Consensus size: 116
131662 ATCCTTAGTA
131672 GAGGTTTCCTAATTTTCAACCTTAAGGACAAGAATGGTTTTGAGGAAGTAGTGATTGTTGTAAAC
1 GAGGTTTCCTAATTTTCAACCTTAAGGACAAGAATGGTTTTGAGGAAGTAGTGATTGTTGTAAAC
** *
131737 CATTAGGTTTTGGTTACCAATTAAATTTTATTGTTAAGTTTCCATTGACTC
66 CATTAAATTTTGGTTACCAATTAAATTTTATTGTTAAGTTTCCATCGACTC
* * * *
131788 GAGGTTTCTTACTTTTCAACCTTAAGGATAAGAATGGTTTTGAGGAAGTAGTGATTGTTGTAGAC
1 GAGGTTTCCTAATTTTCAACCTTAAGGACAAGAATGGTTTTGAGGAAGTAGTGATTGTTGTAAAC
*
131853 CATTAAATTTTGGTTACCAATTAAATTTTGTTGTTAAGTTTCCATCGACT
66 CATTAAATTTTGGTTACCAATTAAATTTTATTGTTAAGTTTCCATCGACT
131903 TGTTTCAGCA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 107 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (116 bp):
GAGGTTTCCTAATTTTCAACCTTAAGGACAAGAATGGTTTTGAGGAAGTAGTGATTGTTGTAAAC
CATTAAATTTTGGTTACCAATTAAATTTTATTGTTAAGTTTCCATCGACTC
Found at i:139220 original size:15 final size:15
Alignment explanation
Indices: 139202--139233 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
139192 AGAGAGGTAA
139202 AAACAGATAGGAGAG
1 AAACAGATAGGAGAG
*
139217 AAACAGATTGGAGAG
1 AAACAGATAGGAGAG
139232 AA
1 AA
139234 TAGCTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.31, T:0.09
Consensus pattern (15 bp):
AAACAGATAGGAGAG
Found at i:139456 original size:16 final size:16
Alignment explanation
Indices: 139396--139499 Score: 73
Period size: 16 Copynumber: 6.2 Consensus size: 16
139386 ATTCAAGGAT
**
139396 ATCTAGAAAATCAAGAA
1 ATCT-GAAAATCTGGAA
* * *
139413 ATCTCAAAATCAGTAA
1 ATCTGAAAATCTGGAA
* * *
139429 ATTTGCAGATCTGGAA
1 ATCTGAAAATCTGGAA
**
139445 ATGAGAAAATCTGTTAGAA
1 ATCTGAAAATCTG---GAA
*
139464 ATCTGGAAATCTGGAA
1 ATCTGAAAATCTGGAA
139480 ATCTGAAAATCTGGAA
1 ATCTGAAAATCTGGAA
139496 ATCT
1 ATCT
139500 ACACATAAAG
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
16 50 0.75
17 4 0.06
19 13 0.19
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (16 bp):
ATCTGAAAATCTGGAA
Found at i:139472 original size:8 final size:8
Alignment explanation
Indices: 139461--139499 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
139451 AAATCTGTTA
139461 GAAATCTG
1 GAAATCTG
139469 GAAATCTG
1 GAAATCTG
139477 GAAATCTG
1 GAAATCTG
*
139485 AAAATCTG
1 GAAATCTG
139493 GAAATCT
1 GAAATCT
139500 ACACATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (8 bp):
GAAATCTG
Found at i:140972 original size:2 final size:2
Alignment explanation
Indices: 140965--140998 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
140955 ATCTTCGAAC
* *
140965 AT AT AT AT AT AT AT AT AT AT AT GT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140999 TTTTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:144123 original size:2 final size:2
Alignment explanation
Indices: 144116--144152 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
144106 TATTGAGAAA
144116 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
144153 GTGCTTCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:151586 original size:13 final size:13
Alignment explanation
Indices: 151568--151593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
151558 ACATTTCTTC
151568 ATGTATCGATACA
1 ATGTATCGATACA
151581 ATGTATCGATACA
1 ATGTATCGATACA
151594 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:151599 original size:20 final size:20
Alignment explanation
Indices: 151576--151613 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
151566 TCATGTATCG
*
151576 ATACAATGTATCGATACATT
1 ATACAATGTATCAATACATT
*
151596 ATACCATGTATCAATACA
1 ATACAATGTATCAATACA
151614 AATAGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCAATACATT
Found at i:151604 original size:33 final size:32
Alignment explanation
Indices: 151548--151614 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
151538 GTTACAAGCT
*
151548 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTC-TCATGTATCAATACA
151581 ATGTATCGATACATTATAC-CATGTATCAATACA
1 ATGTATCGATACATT-T-CTCATGTATCAATACA
151614 A
1 A
151615 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCAATACA
Found at i:151662 original size:13 final size:13
Alignment explanation
Indices: 151644--151670 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
151634 TACCAGTTTC
151644 ATGTATCGATACA
1 ATGTATCGATACA
151657 ATGTATCGATACA
1 ATGTATCGATACA
151670 A
1 A
151671 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:152234 original size:16 final size:17
Alignment explanation
Indices: 152213--152259 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
152203 ATTTTTCTCT
152213 CCTTAAA-AATTCTCCC
1 CCTTAAACAATTCTCCC
*
152229 CCTTAAACGATTATCTCCC
1 CCTTAAAC-AAT-TCTCCC
152248 CCTTAAACAATT
1 CCTTAAACAATT
152260 ATCTTCTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 4 0.15
19 14 0.54
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (17 bp):
CCTTAAACAATTCTCCC
Found at i:152247 original size:19 final size:19
Alignment explanation
Indices: 152223--152263 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
152213 CCTTAAAAAT
*
152223 TCTCCCCCTTAAACGATTA
1 TCTCCCCCTTAAACAATTA
152242 TCTCCCCCTTAAACAATTA
1 TCTCCCCCTTAAACAATTA
152261 TCT
1 TCT
152264 TCTCCCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.34
Consensus pattern (19 bp):
TCTCCCCCTTAAACAATTA
Found at i:160339 original size:33 final size:32
Alignment explanation
Indices: 160283--160349 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
160273 GTTACAAGCT
160283 ATGTATCGATACATTTCTTCATGTATCAATACA
1 ATGTATCGATACATTTC-TCATGTATCAATACA
*
160316 ATGTATCGATACATTGTAC-CATGTATCGATACA
1 ATGTATCGATACATT-T-CTCATGTATCAATACA
160349 A
1 A
160350 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCAATACA
Found at i:160397 original size:13 final size:13
Alignment explanation
Indices: 160379--160405 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
160369 TGCCAATTTC
160379 ATGTATCGATACA
1 ATGTATCGATACA
160392 ATGTATCGATACA
1 ATGTATCGATACA
160405 A
1 A
160406 AGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:164021 original size:5 final size:5
Alignment explanation
Indices: 164011--164042 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
164001 TTTTACAATA
164011 TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TA
164043 ATTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:166810 original size:20 final size:21
Alignment explanation
Indices: 166764--166810 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
166754 CTCAACAATT
166764 TATATCGATACAATAAGGTAA
1 TATATCGATACAATAAGGTAA
*
166785 TGTATCGATAC-ATAA-GTGAA
1 TATATCGATACAATAAGGT-AA
166805 TATATC
1 TATATC
166811 AATAGATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 10 0.43
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TATATCGATACAATAAGGTAA
Found at i:171398 original size:52 final size:52
Alignment explanation
Indices: 171320--171429 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 52
171310 CAAAATATGA
* *
171320 AAATTTACCTACATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTACCTACATGTATCCATACATTTCATAGTGTATCGATACATCTGGGC
* *
171372 AAATTTACCTATATGTATCCATACATTTCATAGTGTATCTATACATCTGGGC
1 AAATTTACCTACATGTATCCATACATTTCATAGTGTATCGATACATCTGGGC
171424 AAATTT
1 AAATTT
171430 GCTTGCATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (52 bp):
AAATTTACCTACATGTATCCATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:171475 original size:13 final size:13
Alignment explanation
Indices: 171457--171481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171447 AAAAGATCAG
171457 TGTATCGATACAA
1 TGTATCGATACAA
171470 TGTATCGATACA
1 TGTATCGATACA
171482 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:171569 original size:32 final size:32
Alignment explanation
Indices: 171526--171611 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
171516 AGCTTCGTAG
*
171526 CGATACGTTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
171558 CGATACATTGTATCAATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
171590 CAATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
171612 TCATTGAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:172950 original size:13 final size:13
Alignment explanation
Indices: 172932--172957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
172922 CAATTTTTTG
172932 TGTATCGATACAT
1 TGTATCGATACAT
172945 TGTATCGATACAT
1 TGTATCGATACAT
172958 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:172968 original size:32 final size:33
Alignment explanation
Indices: 172912--172975 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
172902 TACAAGCCAA
*
172912 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
172945 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
172976 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:172969 original size:19 final size:19
Alignment explanation
Indices: 172912--172975 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
172902 TACAAGCCAA
*
172912 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
172932 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
172945 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
172964 TGTATCGATACA
1 TGTATCGATACA
172976 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:173052 original size:20 final size:20
Alignment explanation
Indices: 173005--173079 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
172995 AATCCCAATG
* *
173005 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACAT-TGTA
*
173026 TCATGTATCGATACATTGTA
1 ACATGTATCGATACATTGTA
*
173046 ACATGTATCGATACTTTG-A
1 ACATGTATCGATACATTGTA
*
173065 ACTGTGTATCGATAC
1 AC-ATGTATCGATAC
173080 TTTTAAGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.06
20 29 0.62
21 15 0.32
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
ACATGTATCGATACATTGTA
Found at i:175522 original size:13 final size:13
Alignment explanation
Indices: 175504--175541 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
175494 ATAATCCCCC
175504 TGTATCGATACAG
1 TGTATCGATACAG
*
175517 TGTATCGATACAT
1 TGTATCGATACAG
175530 TGTATCGATACA
1 TGTATCGATACA
175542 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:179591 original size:52 final size:51
Alignment explanation
Indices: 179513--179659 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 51
179503 CGAAATATGA
179513 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
179565 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* * **
179617 AAATTTTCCTACATGTATCGATACAAAGATCAGTGTATCGATA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATA
179660 TAATGTATCG
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:179752 original size:33 final size:33
Alignment explanation
Indices: 179715--179781 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
179705 AGTAGCTTAA
179715 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
179748 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
179781 A
1 A
179782 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:179755 original size:13 final size:13
Alignment explanation
Indices: 179737--179761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179727 CAAAAAAATA
179737 TGTATCGATACAT
1 TGTATCGATACAT
179750 TGTATCGATACA
1 TGTATCGATACA
179762 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:180160 original size:15 final size:15
Alignment explanation
Indices: 180140--180170 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
180130 ATTTCGTTTG
*
180140 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
180155 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
180170 G
1 G
180171 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:184266 original size:13 final size:13
Alignment explanation
Indices: 184248--184273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
184238 CAATTTTTTG
184248 TGTATCGATACAT
1 TGTATCGATACAT
184261 TGTATCGATACAT
1 TGTATCGATACAT
184274 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:184284 original size:32 final size:33
Alignment explanation
Indices: 184228--184291 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
184218 TACAAGCCAA
*
184228 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
184261 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
184292 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:184285 original size:19 final size:19
Alignment explanation
Indices: 184228--184291 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
184218 TACAAGCCAA
*
184228 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
184248 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
184261 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
184280 TGTATCGATACA
1 TGTATCGATACA
184292 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:185119 original size:49 final size:48
Alignment explanation
Indices: 184971--185415 Score: 407
Period size: 49 Copynumber: 9.4 Consensus size: 48
184961 CTTAGGAATG
* *
184971 TTAACGATGAAGGTGTCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGAT-AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
185020 TTAAAAGATGACAAAGGCGCTAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGAT----AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
185073 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGAT-AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* ** * * ** *
185122 TTAAAAGACAAAGGTGCTGATATGATGATTCAAGGCCAATGATATTGGAC
1 TT-AAAGA-TAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
185172 TTAAAGCT-A----CCAATGTGCTGATTTAAGGCCAGCGACATTGGTC
1 TTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
185215 TTAAAGACAAAGGTGCCAATATGCTTATTCAAGGCCAGCGATATTGGAC
1 TTAAAGA-TAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
185264 TTAAAGCT-A----CCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
1 TTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
185307 TTAAAGACAAAGGTGCCAATATGTTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGA-TAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
185356 TT----A-AAGGTGCCAACGTGCTGATTTAAGGCCAGCGACATTGGTC
1 TTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
185399 TTAAAGAAAAGATGCCA
1 TTAAAGATAAGGTGCCA
185416 CTGAGTCGTG
Statistics
Matches: 318, Mismatches: 55, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
43 104 0.33
45 3 0.01
47 3 0.01
48 8 0.03
49 112 0.35
50 45 0.14
52 6 0.02
53 37 0.12
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (48 bp):
TTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:185212 original size:43 final size:43
Alignment explanation
Indices: 185147--185404 Score: 255
Period size: 43 Copynumber: 5.7 Consensus size: 43
185137 GCTGATATGA
** * *
185147 TGATTCAAGGCCAATGATATTGGACTTAAAGCTACCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGCTGCCAATGTGC
* * *
185190 TGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAG-C-----TGCCAATGTGC
* * *
185239 TTATTCAAGGCCAGCGATATTGGACTTAAAGCTACCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGCTGCCAATGTGC
* * *
185282 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGT
1 TGATTCAAGGCCAGCGACATTGGACTTAAAG-C-----TGCCAATGTGC
* *
185331 TGATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAACGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGCTGCCAATGTGC
* *
185374 TGATTTAAGGCCAGCGACATTGGTCTTAAAG
1 TGATTCAAGGCCAGCGACATTGGACTTAAAG
185405 AAAAGATGCC
Statistics
Matches: 177, Mismatches: 26, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
43 100 0.56
44 2 0.01
48 1 0.01
49 74 0.42
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
TGATTCAAGGCCAGCGACATTGGACTTAAAGCTGCCAATGTGC
Found at i:185260 original size:92 final size:92
Alignment explanation
Indices: 184987--185415 Score: 581
Period size: 92 Copynumber: 4.6 Consensus size: 92
184977 ATGAAGGTGT
* * *
184987 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGATGACAAAGGCGCTAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AA-A-GACAAAGGTGCCAATATGCTGAT
*
185052 TCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
62 TCAAGGCCAGCGATATTGGACTTAAAGCT--A----C
* ** *
185089 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGACAAAGGTGCTGATATGATGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGACAAAGGTGCCAATATGCTGATTCA
**
185154 AGGCCAATGATATTGGACTTAAAGCTAC
65 AGGCCAGCGATATTGGACTTAAAGCTAC
* *
185182 CAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTTATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAA
185247 GGCCAGCGATATTGGACTTAAAGCTAC
66 GGCCAGCGATATTGGACTTAAAGCTAC
*
185274 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGTTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAA
* * *
185339 GGCCAGCGACATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGCTAC
* * *
185366 CAACGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGA-AAAGATGCCA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCA
185416 CTGAGTCGTG
Statistics
Matches: 304, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
91 9 0.03
92 175 0.58
93 34 0.11
97 1 0.00
99 46 0.15
100 1 0.00
101 3 0.01
102 35 0.12
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGCTAC
Found at i:185445 original size:32 final size:31
Alignment explanation
Indices: 185405--185556 Score: 175
Period size: 32 Copynumber: 4.9 Consensus size: 31
185395 GGTCTTAAAG
*
185405 AAAAGATGCCACTGAGTCGTGGAATTTGAAC
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAC
*
185436 AAAAGGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAAC
* *
185468 AAAAGGATGCCACTTAGTCATGGACTTTGAGAC
1 AAAA-GATGCCACTGAGTCGTGGACTTTGA-AC
* *
185501 -AAA-ATGCCACTGAGTCGTGGGCTTTG-AG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAC
* *
185529 AAGAGATTGCCACTGAGTCATGGACTTT
1 AAAAGA-TGCCACTGAGTCGTGGACTTT
185557 CAGAAGGTAT
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 2 0.02
30 21 0.20
31 23 0.22
32 56 0.54
33 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAC
Found at i:193863 original size:52 final size:52
Alignment explanation
Indices: 193784--193913 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
193774 CCGAAATATG
* *
193784 AAAATTTACCTACATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
1 AAAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGA
* *
193836 CAAATTTACCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGA
1 AAAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGA
* *
193888 AAAATTTGCCTGCATGTCTCGATACA
1 AAAATTTACCTGCATGTATCGATACA
193914 AAGATTAGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (52 bp):
AAAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGA
Found at i:193923 original size:52 final size:52
Alignment explanation
Indices: 193784--193934 Score: 187
Period size: 52 Copynumber: 2.9 Consensus size: 52
193774 CCGAAATATG
* ** *
193784 AAAATTTACCTACATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
1 AAAATTTACCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGA
* * **
193836 CAAATTTACCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGA
1 AAAATTTACCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGA
* * *
193888 AAAATTTGCCTGCATGTCTCGATACA-AAGATTAGTGTATCGATACAT
1 AAAATTTACCTGCATGTATCGATACATAACA-TAGTGTATCGATACAT
193935 TTTCTTGGCA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.01
52 86 0.99
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (52 bp):
AAAATTTACCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGA
Found at i:200385 original size:13 final size:13
Alignment explanation
Indices: 200363--200402 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
200353 ACAATGTTCT
*
200363 TTGTACCGATACA
1 TTGTATCGATACA
200376 TTGTATCGATACA
1 TTGTATCGATACA
*
200389 ATGTATCGATACA
1 TTGTATCGATACA
200402 T
1 T
200403 GGGTTACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:206045 original size:20 final size:20
Alignment explanation
Indices: 206022--206059 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
206012 GCAATGAGAA
206022 ATGTATCGATACAATTTCTT
1 ATGTATCGATACAATTTCTT
206042 ATGTATCGATACAATTTC
1 ATGTATCGATACAATTTC
206060 CTTCCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACAATTTCTT
Found at i:209537 original size:17 final size:17
Alignment explanation
Indices: 209515--209548 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
209505 TATTACAAGC
*
209515 AAACTCCCATCGAAGTT
1 AAACTCCCATCAAAGTT
209532 AAACTCCCATCAAAGTT
1 AAACTCCCATCAAAGTT
209549 TAGTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (17 bp):
AAACTCCCATCAAAGTT
Found at i:214961 original size:13 final size:13
Alignment explanation
Indices: 214943--214967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
214933 TTGCATTCAT
214943 GTTTTTAAAATTG
1 GTTTTTAAAATTG
214956 GTTTTTAAAATT
1 GTTTTTAAAATT
214968 CATAAAGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
GTTTTTAAAATTG
Found at i:217288 original size:2 final size:2
Alignment explanation
Indices: 217277--217305 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
217267 ACATACATGC
217277 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
217306 GTATTGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:220385 original size:3 final size:3
Alignment explanation
Indices: 220377--220429 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
220367 TGCCAGTAAG
* *
220377 AAT AAT AAT AAT AAT AAA AAGT GAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT -AAT AAT AAT AAT AAT AAT AAT
220424 AAT AAT
1 AAT AAT
220430 TAAAATAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:221351 original size:12 final size:12
Alignment explanation
Indices: 221334--221372 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
221324 AAAAATTATG
221334 TATTTATATTTT
1 TATTTATATTTT
*
221346 TATTTATATTAT
1 TATTTATATTTT
*
221358 TATTTTTATTATT
1 TATTTATATT-TT
221371 TA
1 TA
221373 AAATATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:221362 original size:24 final size:25
Alignment explanation
Indices: 221322--221399 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
221312 TAGTATATGA
* *
221322 ATAAAAATTATGTATTTATATTTTT
1 ATAAATATTATATATTTATATTTTT
** *
221347 ATTTATATTAT-TATTTTTATTATTT
1 ATAAATATTATATATTTATATT-TTT
*
221372 A-AAATATTATAAATTTATATATTTT
1 ATAAATATTATATATTTATAT-TTTT
221397 ATA
1 ATA
221400 TTTTTATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
24 16 0.39
25 23 0.56
26 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
ATAAATATTATATATTTATATTTTT
Found at i:221369 original size:21 final size:20
Alignment explanation
Indices: 221337--221382 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
221327 AATTATGTAT
* *
221337 TTATATTTTTATTTATATTA
1 TTATATTTTTATTTAAAATA
*
221357 TTATTTTTATTATTTAAAATA
1 TTATATTT-TTATTTAAAATA
221378 TTATA
1 TTATA
221383 AATTTATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTTATTTAAAATA
Found at i:221445 original size:22 final size:23
Alignment explanation
Indices: 221433--221476 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
221423 TTTTTGTGTT
221433 GTGTTT-TAATTATTTTTATATC
1 GTGTTTATAATTATTTTTATATC
221455 GTGTTTATAA-TATTTTTCATAT
1 GTGTTTATAATTATTTTT-ATAT
221477 ATTTAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (23 bp):
GTGTTTATAATTATTTTTATATC
Found at i:222349 original size:2 final size:2
Alignment explanation
Indices: 222338--222376 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
222328 GTTAATATTA
222338 AT AT -T AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
222377 AAAAATTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:227368 original size:20 final size:21
Alignment explanation
Indices: 227343--227395 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
227333 ATCGATATAT
**
227343 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
227363 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
227384 TGTATCGATACA
1 TGTATCGATACA
227396 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:227474 original size:13 final size:13
Alignment explanation
Indices: 227456--227481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
227446 ACACCCAATA
227456 TGTATCGATACAT
1 TGTATCGATACAT
227469 TGTATCGATACAT
1 TGTATCGATACAT
227482 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:227477 original size:32 final size:33
Alignment explanation
Indices: 227436--227503 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
227426 CCTTAACTGT
*
227436 TTGTATCGATACA-CCCAATATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
227468 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
227501 TTG
1 TTG
227504 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCCCAAAATGTATCGATACA
Found at i:233632 original size:13 final size:13
Alignment explanation
Indices: 233614--233651 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
233604 CAGCATTCTC
*
233614 TGTATCGATACAT
1 TGTATCGATACAG
233627 TGTATCGATACAG
1 TGTATCGATACAG
233640 TGTATCGATACA
1 TGTATCGATACA
233652 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:236102 original size:13 final size:13
Alignment explanation
Indices: 236084--236108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
236074 AGCTTGCACA
236084 GTATCGATACATT
1 GTATCGATACATT
236097 GTATCGATACAT
1 GTATCGATACAT
236109 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:236121 original size:20 final size:21
Alignment explanation
Indices: 236096--236148 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
236086 ATCGATACAT
**
236096 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
236116 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
236137 TGTATCGATACA
1 TGTATCGATACA
236149 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:236216 original size:13 final size:13
Alignment explanation
Indices: 236198--236223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
236188 ACACCCAATA
236198 TGTATCGATACAT
1 TGTATCGATACAT
236211 TGTATCGATACAT
1 TGTATCGATACAT
236224 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:236234 original size:33 final size:32
Alignment explanation
Indices: 236178--236244 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
236168 CCTTAACTGT
* *
236178 TTGTATTGATACACCCAATATGTATCGATACA
1 TTGTATCGATACACCCAAAATGTATCGATACA
236210 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CCCAAAATGTATCGATACA
236243 TT
1 TT
236245 TACACGGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACCCAAAATGTATCGATACA
Found at i:237780 original size:52 final size:52
Alignment explanation
Indices: 237716--238075 Score: 233
Period size: 52 Copynumber: 7.1 Consensus size: 52
237706 ATTGGGCTTA
* * * *
237716 AAGATGTAAAGAATGTCAATGTGCTGATTGACGGTCAGCGACATTAGACTTG
1 AAGATGTAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* * *
237768 AAGATG-AGAAGAATGCCAATGTGTTGTTTCAAGGCCAGCGACATTAGA-TTT
1 AAGATGTA-AAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* * * ** *
237819 AAGAATGTTACAG-ATGCCAATATGCTGATTCAAGGCCAGTGATTTTGGACTT-
1 AAG-ATG-TAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* * * * ** * *
237871 AA-AGGTGAAG-GTGCTAATGTGCTGATTCAAGGCCAATGACATTGGACTTA
1 AAGATGTAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* ** * * * * *
237921 AAGATGACAAAG-GCGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
1 AAGATG-TAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* *
237973 AAGATG--AAG-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT-
1 AAGATGTAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
* * * * * * * *
238021 AA-AGGTGAAG-GTGCTAATGTGCTGATTTAAGGCCAACAACATTGGACTTAG
1 AAGATGTAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTT-G
238072 AAGA
1 AAGA
238076 AGATGCCACT
Statistics
Matches: 252, Mismatches: 43, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 110 0.44
50 4 0.02
51 10 0.04
52 119 0.47
53 4 0.02
54 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (52 bp):
AAGATGTAAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTG
Found at i:237900 original size:49 final size:49
Alignment explanation
Indices: 237732--238075 Score: 303
Period size: 49 Copynumber: 6.8 Consensus size: 49
237722 TAAAGAATGT
* * * * * * *
237732 CAATGTGCTGATTGACGGTCAGCGACATTAGACTTGAAGATGAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGAT--GAAG-GTGC
* * * * * *
237784 CAATGTGTTGTTTCAAGGCCAGCGACATTAGA-TTTAAGAATGTTACAGATGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG-ATG--A-AGGTGC
* ** ** *
237836 CAATATGCTGATTCAAGGCCAGTGATTTTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGC
* * *
237885 TAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG---AAGGTGC
* * *
237937 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGC
* * *
237986 CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGC
* * *
238035 TAATGTGCTGATTTAAGGCCAACAACATTGGACTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTA-AAGA
238076 AGATGCCACT
Statistics
Matches: 244, Mismatches: 39, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
49 122 0.50
50 5 0.02
51 5 0.02
52 105 0.43
53 7 0.03
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGC
Found at i:237939 original size:101 final size:101
Alignment explanation
Indices: 237834--238083 Score: 312
Period size: 101 Copynumber: 2.5 Consensus size: 101
237824 TGTTACAGAT
** * * * *
237834 GCCAATATGCTGATTCAAGGCCAGTGATTTTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTC
**
237899 AAGGCCAATGACATTGGACTTAAAGATGACAAAGGC
66 AAGGCCAACAACATTGGACTTAAAGATGACAAAGGC
237935 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTC
* * *
238000 AAGGCCAGCAACATTGGACTTAAAGGTG---AAGGT
66 AAGGCCAACAACATTGGACTTAAAGATGACAAAGGC
* * * * * *
238033 GCTAATGTGCTGATTTAAGGCCAACAACATTGGACTT--AGAAGAAGATGCCA
1 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCA
238084 CTAACTTGTG
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
96 13 0.10
98 36 0.27
101 83 0.63
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (101 bp):
GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTC
AAGGCCAACAACATTGGACTTAAAGATGACAAAGGC
Found at i:238131 original size:29 final size:29
Alignment explanation
Indices: 238092--238275 Score: 197
Period size: 27 Copynumber: 6.6 Consensus size: 29
238082 CACTAACTTG
*
238092 TGTGGGCTTTTGAAAGGGTTG-CACCGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
238121 TGTGTGCTTTTG-AAGGTTGCCACTGCCT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
238149 TGTGGGC-TTTGAAA-GTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
238176 TGTGGG--TTTGAAAAGG-TGCTACTAACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
* *
238203 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
238232 TGTGGGCTTTTG-AAGGCTGCCATTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
238260 TATGGGC-TTTGAAAGG
1 TGTGGGCTTTTGAAAGG
238276 GGTGTTACCG
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
26 4 0.03
27 49 0.37
28 44 0.33
29 36 0.27
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:238706 original size:37 final size:37
Alignment explanation
Indices: 238658--238748 Score: 168
Period size: 37 Copynumber: 2.5 Consensus size: 37
238648 CAAAGAAAAG
238658 ATGAA-GT-ACAAATGCATCATGCAAAATGAAATGTT
1 ATGAATGTCACAAATGCATCATGCAAAATGAAATGTT
238693 ATGAATGTCACAAATGCATCATGCAAAATGAAATGTT
1 ATGAATGTCACAAATGCATCATGCAAAATGAAATGTT
238730 ATGAATGTCACAAATGCAT
1 ATGAATGTCACAAATGCAT
238749 GATTGTGGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 5 0.09
36 2 0.04
37 47 0.87
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (37 bp):
ATGAATGTCACAAATGCATCATGCAAAATGAAATGTT
Found at i:239814 original size:8 final size:8
Alignment explanation
Indices: 239770--239816 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
239760 CATCCGGACC
239770 TTTTTTGT
1 TTTTTTGT
239778 TGTTTTT-T
1 T-TTTTTGT
239786 TCTTTTTG-
1 T-TTTTTGT
*
239794 TTTTCTGT
1 TTTTTTGT
239802 TTTTTTGT
1 TTTTTTGT
239810 TTTTTTG
1 TTTTTTG
239817 CGGAGGACGC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 5 0.15
8 23 0.70
9 5 0.15
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (8 bp):
TTTTTTGT
Found at i:249468 original size:26 final size:27
Alignment explanation
Indices: 249439--249490 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
249429 TTTTGAAAAT
249439 AAAAT-CGGGGTT-GTAGTATCCCCTCA
1 AAAATACGGGGTTAG-AGTATCCCCTCA
249465 AAAATAACGGGGTTAGAGTATCCCCT
1 AAAAT-ACGGGGTTAGAGTATCCCCT
249491 ATTGTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.22
28 17 0.74
29 1 0.04
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (27 bp):
AAAATACGGGGTTAGAGTATCCCCTCA
Found at i:249487 original size:79 final size:79
Alignment explanation
Indices: 249339--249487 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 79
249329 TCCGATTATG
* * * * *
249339 GAAAATTGGTGTTCTGGAAATAAAATTGGGGTTGGAGTATCCCCACGAAAATAACAAGGTTGGAC
1 GAAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCACAAAAATAACAAGGTTAGAC
249404 TATCCTTGAGTATA
66 TATCCTTGAGTATA
* * * ** *
249418 GAAAATTGGTATTTTGAAAATAAAATCGGGGTTGTAGTATCCCCTCAAAAATAACGGGGTTAGAG
1 GAAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCACAAAAATAACAAGGTTAGAC
249483 TATCC
66 TATCC
249488 CCTATTGTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GAAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCACAAAAATAACAAGGTTAGAC
TATCCTTGAGTATA
Found at i:249502 original size:79 final size:79
Alignment explanation
Indices: 249322--249502 Score: 177
Period size: 79 Copynumber: 2.3 Consensus size: 79
249312 AATAGGGCTG
* * * * * * *
249322 GAGTATCTCCGATTATGGAAAATTGGTGTTCTGGAAATAAAATTGGGGTTGGAGTATCCCCACGA
1 GAGTATCCCCTATTATGAAAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCACAA
*
249387 AAATAACAAGGTTG
66 AAATAACAAGGTTA
* * * * * *
249401 GACTAT-CCTTGAGTAT-AGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGTAGTATCCCCTC
1 GAGTATCCCCT-ATTATGA-AAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCAC
**
249464 AAAAATAACGGGGTTA
64 AAAAATAACAAGGTTA
*
249480 GAGTATCCCCTATTGTGAAAAAT
1 GAGTATCCCCTATTATGAAAAAT
249503 CGATGCTTTA
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
78 1 0.01
79 73 0.94
80 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
GAGTATCCCCTATTATGAAAAATTGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCACAA
AAATAACAAGGTTA
Found at i:249569 original size:51 final size:51
Alignment explanation
Indices: 249474--249588 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
249464 AAAAATAACG
* * * * *
249474 GGGTTAGAGTATCCCCTATTGTGAAAAATCGATGCTTTAGAAAT-AAGGCTA
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAGAAATAAAGTC-A
* * *
249525 GGGTTGGAGTATCCCCAATTGTGAGAAATCAATA-TTTTGAAAATAAAGTCG
1 GGGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAG-AAATAAAGTCA
249576 GGGTTGGAGTATC
1 GGGTTGGAGTATC
249589 TCCTTGGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 4 0.07
51 46 0.85
52 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAGAAATAAAGTCA
Found at i:249610 original size:28 final size:28
Alignment explanation
Indices: 249576--249650 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
249566 AATAAAGTCG
*
249576 GGGTTGGAGTATCTCC-TTGGAAATAAC-
1 GGGTTGGAGTATCTCCGAT-GAAATAACA
*
249603 GAGGTTGGAGTATCCCCGATGAAATAACA
1 G-GGTTGGAGTATCTCCGATGAAATAACA
*
249632 GGGTTGGAGTGTCTCCGAT
1 GGGTTGGAGTATCTCCGAT
249651 TGTAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 38 0.93
29 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (28 bp):
GGGTTGGAGTATCTCCGATGAAATAACA
Found at i:249701 original size:51 final size:49
Alignment explanation
Indices: 249646--249798 Score: 164
Period size: 51 Copynumber: 3.0 Consensus size: 49
249636 TGGAGTGTCT
* *
249646 CCGATTGTAAAAAATTGGTGTATTGGAAATAAAATCAGAGTTGGAGTATCC
1 CCGATTGT-AAAAATTGGTGTTTTGGAAA-AAAATCAGAGTTAGAGTATCC
* * *
249697 CCGATTGTGAAAATTGGTGTTTTAGAAAAAAA-CCGAGGTTAGAGTATCC
1 CCGATTGTAAAAATTGGTGTTTTGGAAAAAAATCAGA-GTTAGAGTATCC
* * * * *
249746 CCAATTGTGAAACATTGGTATTTTGGGAAAAAAATCGGGGTTAGAGTATCC
1 CCGATTGT-AAAAATTGGTGTTTT-GGAAAAAAATCAGAGTTAGAGTATCC
249797 CC
1 CC
249799 TCAGAAATAA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
48 3 0.03
49 22 0.26
50 29 0.34
51 30 0.35
52 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (49 bp):
CCGATTGTAAAAATTGGTGTTTTGGAAAAAAATCAGAGTTAGAGTATCC
Found at i:249763 original size:50 final size:49
Alignment explanation
Indices: 249656--249798 Score: 180
Period size: 50 Copynumber: 2.9 Consensus size: 49
249646 CCGATTGTAA
* * *
249656 AAAATTGGTGTATTGGAAATAAAATC-AGAGTTGGAGTATCCCCGATTGTG
1 AAAATTGGTGTTTTGGAAA-AAAATCGAG-GTTAGAGTATCCCCAATTGTG
* *
249706 AAAATTGGTGTTTTAGAAAAAAACCGAGGTTAGAGTATCCCCAATTGTG
1 AAAATTGGTGTTTTGGAAAAAAATCGAGGTTAGAGTATCCCCAATTGTG
* *
249755 AAACATTGGTATTTTGGGAAAAAAATCGGGGTTAGAGTATCCCC
1 AAA-ATTGGTGTTTT-GGAAAAAAATCGAGGTTAGAGTATCCCC
249799 TCAGAAATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
49 27 0.33
50 29 0.36
51 25 0.31
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (49 bp):
AAAATTGGTGTTTTGGAAAAAAATCGAGGTTAGAGTATCCCCAATTGTG
Found at i:249872 original size:79 final size:79
Alignment explanation
Indices: 249730--249875 Score: 195
Period size: 79 Copynumber: 1.8 Consensus size: 79
249720 AGAAAAAAAC
* * * * * *
249730 CGAGGTTAGAGTATCCCCAATTGTGAAACATTGGTATTTTGGGAAAAAAATCGGGGTTAGAGTAT
1 CGAGATTAGAGTATCCCCAATTATGAAAAATTGATATTTTGGGAAAAAAACCGGGATTAGAGTAT
249795 CCCCTCAGAAATAA
66 CCCCTCAGAAATAA
* * *
249809 CGAGATTAGAGTATCCCCGATTATGAAAAATTGATGTTTT-GGAAATAAAACCGGGATTGGAGTA
1 CGAGATTAGAGTATCCCCAATTATGAAAAATTGATATTTTGGGAAA-AAAACCGGGATTAGAGTA
249873 TCC
65 TCC
249876 TCGAGATAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 5 0.09
79 52 0.91
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (79 bp):
CGAGATTAGAGTATCCCCAATTATGAAAAATTGATATTTTGGGAAAAAAACCGGGATTAGAGTAT
CCCCTCAGAAATAA
Found at i:252294 original size:20 final size:20
Alignment explanation
Indices: 252243--252298 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
252233 ATGTATTGAT
*
252243 ACAATGTATCAATACAATGA
1 ACAATGTATCGATACAATGA
252263 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
252283 ACAATGTTTCGATACA
1 ACAATGTATCGATACA
252299 TTTGGGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:253334 original size:13 final size:13
Alignment explanation
Indices: 253316--253343 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
253306 CCGTTACAAG
253316 CAATGTATCGATA
1 CAATGTATCGATA
253329 CAATGTATCGATA
1 CAATGTATCGATA
253342 CA
1 CA
253344 TTGTCCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:253437 original size:19 final size:19
Alignment explanation
Indices: 253393--253448 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
253383 CTTCCAATCT
*
253393 CATGTATCAATACAATTGTC
1 CATGTATCAATACAA-TGAC
* *
253413 CATGTATCTATACAATGAG
1 CATGTATCAATACAATGAC
*
253432 CATGTATCGATACAATG
1 CATGTATCAATACAATG
253449 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCAATACAATGAC
Found at i:253451 original size:13 final size:13
Alignment explanation
Indices: 253433--253459 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
253423 TACAATGAGC
253433 ATGTATCGATACA
1 ATGTATCGATACA
253446 ATGTATCGATACA
1 ATGTATCGATACA
253459 A
1 A
253460 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:254030 original size:22 final size:22
Alignment explanation
Indices: 254003--254076 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
253993 AGTTTTCATT
254003 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAGAA
** *
254025 TTTCT----CTTTTTTAAAAAA
1 TTTCTCCCCCTTAATTAAAGAA
* * *
254043 ATTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATTAAAGAA
254065 TTTCTCCCCCTT
1 TTTCTCCCCCTT
254077 TGTCAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
18 14 0.37
22 24 0.63
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTCTCCCCCTTAATTAAAGAA
Found at i:254846 original size:13 final size:13
Alignment explanation
Indices: 254828--254856 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
254818 AAATAGTACC
254828 CAATGTATCGATA
1 CAATGTATCGATA
254841 CAATGTATCGATA
1 CAATGTATCGATA
254854 CAA
1 CAA
254857 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:259418 original size:3 final size:3
Alignment explanation
Indices: 259410--259458 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
259400 TCCGAGTCAC
259410 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
259458 C
1 C
259459 TTCCTCTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:261093 original size:13 final size:13
Alignment explanation
Indices: 261052--261100 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
261042 CCGTTACAAG
261052 CAATGTATCGATA
1 CAATGTATCGATA
261065 CAAT-T-TC-AT-
1 CAATGTATCGATA
261074 C-ATGTATCGATA
1 CAATGTATCGATA
261086 CAATGTATCGATA
1 CAATGTATCGATA
261099 CA
1 CA
261101 TTATCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:261194 original size:19 final size:19
Alignment explanation
Indices: 261150--261205 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
261140 CTGCCAATAT
*
261150 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
261170 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
261189 CATGTATCGATACAATG
1 CATGTATCGATACAATG
261206 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:261208 original size:13 final size:13
Alignment explanation
Indices: 261190--261216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
261180 TACAATGAGC
261190 ATGTATCGATACA
1 ATGTATCGATACA
261203 ATGTATCGATACA
1 ATGTATCGATACA
261216 A
1 A
261217 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:263154 original size:5 final size:6
Alignment explanation
Indices: 263126--263155 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
263116 AATAAAAAAG
263126 AAATTA AAATTA AAATTA AAATT- AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA A
263156 TTAATTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:263295 original size:62 final size:62
Alignment explanation
Indices: 263220--263413 Score: 307
Period size: 62 Copynumber: 3.1 Consensus size: 62
263210 AATTTGGTGG
* * **
263220 ATTTCATGCTTAATTTGCTGCCACCTAAGCTTTTTAGACGTCATTGCATTACATTGCATTGC
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
* *
263282 ATTTCATGTTTAATTTGTTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGG
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
** *
263344 ATTTCATGTTTAATTTGCTGCCATATAAGCTTTCTAGGTGTCATTGCATAACATTGCATTGC
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
263406 ATTTCATG
1 ATTTCATG
263414 CATGCTTTCA
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 121 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (62 bp):
ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
Found at i:263806 original size:33 final size:33
Alignment explanation
Indices: 263769--263837 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
263759 ACTGCAAGCA
263769 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
1 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
* * **
263802 AATGAATGTAATCGAAATAGCGGTTCAAAGGAG
1 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
263835 AAT
1 AAT
263838 AAAAGCAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (33 bp):
AATGAATGCAATCAAAATAGCAATTCAAAGGAG
Found at i:264024 original size:24 final size:24
Alignment explanation
Indices: 263997--264056 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
263987 CGAAAGAGAA
263997 GAGAGAAGGAGAAAAAAAGGTAAG
1 GAGAGAAGGAGAAAAAAAGGTAAG
264021 GAGAGAAGGAGAAAAAAAGGTAAG
1 GAGAGAAGGAGAAAAAAAGGTAAG
264045 GAGAGAA-GAGAA
1 GAGAGAAGGAGAA
264057 GAGAGGAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.03
Consensus pattern (24 bp):
GAGAGAAGGAGAAAAAAAGGTAAG
Found at i:267704 original size:21 final size:21
Alignment explanation
Indices: 267672--267716 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
267662 AGGCCAAATT
*
267672 TTTTAAAATTTAAAATTTA-G
1 TTTTAAAATTTAAAAATTACG
267692 TTTTAAAATTTTAAAAATTACG
1 TTTTAAAA-TTTAAAAATTACG
267714 TTT
1 TTT
267717 CGTACCCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 10 0.45
22 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTTAAAAATTACG
Found at i:268995 original size:14 final size:14
Alignment explanation
Indices: 268971--269005 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
268961 CGTCTTGCTA
268971 TTTTGTTTTTTTTTC
1 TTTT-TTTTTTTTTC
268986 TTTTTTTTTTTTTC
1 TTTTTTTTTTTTTC
269000 TGTTTT
1 T-TTTT
269006 GATTATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:274352 original size:2 final size:2
Alignment explanation
Indices: 274345--274379 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
274335 CTTTCTCTTT
274345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
274380 TGATATGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:283921 original size:3 final size:3
Alignment explanation
Indices: 283913--283954 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
283903 TATCTAAATA
*
283913 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
283955 AGTGTGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:284806 original size:26 final size:26
Alignment explanation
Indices: 284777--284835 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
284767 TGATTTTTGT
*
284777 TTTGATTTTCATTTTTTTATTACTTA
1 TTTGATTTTCAGTTTTTTATTACTTA
* *
284803 TTTG-TTCTTCGGTTTTTTATTATTTA
1 TTTGATT-TTCAGTTTTTTATTACTTA
284829 TTT-ATTT
1 TTTGATTT
284836 ATTATTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (26 bp):
TTTGATTTTCAGTTTTTTATTACTTA
Found at i:284864 original size:141 final size:141
Alignment explanation
Indices: 284708--284961 Score: 447
Period size: 141 Copynumber: 1.8 Consensus size: 141
284698 TCCATTAGGC
284708 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAA-CTCAATTTAATTTTGATT
1 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAACCT-AATTTAATTTTGATT
* * *
284772 TTTGTTTTGATTTTCATTTTTTTATTACTTATTTGTTCTTCGGTTTTTTATTATTTATTTATTTA
65 TTTATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTTTATTATTTATTTATTTA
284837 TTATTTTGACTT
130 TTATTTTGACTT
*
284849 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAACCTAATTTAGTTTTGATTT
1 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAACCTAATTTAATTTTGATTT
*
284914 TTATTTTGATTTTCATTTATTTATTATTTATTTGTTCTTCCGTTTTTT
66 TTATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTTT
284962 CTCTTTTGGT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
141 105 0.98
142 2 0.02
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (141 bp):
TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAACCTAATTTAATTTTGATTT
TTATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTTTATTATTTATTTATTTAT
TATTTTGACTT
Found at i:284881 original size:9 final size:8
Alignment explanation
Indices: 284817--284885 Score: 56
Period size: 7 Copynumber: 8.4 Consensus size: 8
284807 TTCTTCGGTT
284817 TTTTATTA
1 TTTTATTA
284825 -TTTATT-
1 TTTTATTA
284831 TATTTATTA
1 T-TTTATTA
284840 TTTTGACTTTCA
1 TTTT-A--TT-A
284852 TTTTATT-
1 TTTTATTA
284859 TTTTATTA
1 TTTTATTA
284867 -TTTATTA
1 TTTTATTA
284874 CTTTTATTA
1 -TTTTATTA
284883 TTT
1 TTT
284886 CTTTTTTAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 20
0.72 0.00 0.28
Matches are distributed among these distances:
7 20 0.39
8 12 0.24
9 11 0.22
11 3 0.06
12 5 0.10
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTTATTA
Found at i:288214 original size:22 final size:20
Alignment explanation
Indices: 288165--288220 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
288155 AAAAACCCAG
288165 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
**
288185 AATGTATCGATACAATTTGA
1 AATGTATCGATACAATGAGA
288205 AGCATGTATCGATACA
1 A--ATGTATCGATACA
288221 TTTATTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.59
22 13 0.41
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:288233 original size:20 final size:20
Alignment explanation
Indices: 288165--288243 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
288155 AAAAACCCAG
* * *
288165 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTTAAA
*
288185 AATGTATCGATACAATTTGAAG
1 AATGTATCGATAC-ATTT-AAA
* **
288207 CATGTATCGATACATTTATT
1 AATGTATCGATACATTTAAA
*
288227 AATGTATTGATACATTT
1 AATGTATCGATACATTT
288244 CCTTGGCAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
20 29 0.60
21 6 0.12
22 13 0.27
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTTAAA
Found at i:288240 original size:133 final size:133
Alignment explanation
Indices: 288002--288281 Score: 488
Period size: 133 Copynumber: 2.1 Consensus size: 133
287992 TATTGAATAA
*
288002 TGTATCGATACATTTGGGTCAAAAACCCAGAATATATCGATACAATGAGAAATGTATCAATATAA
1 TGTATCGATACATTTGGGTCAAAAACCCAGAATATATCGATACAATGAGAAATGTATCAATACAA
* *
288067 TTTGAAGCATGTATCGATACATTTATTAATGTATCGATACATTTCCTGGGCAGTATGCAAGGTGA
66 TTTGAAGCATGTATCGATACATTTATTAATGTATCGATACATTTCCTGGGCAGCATACAAGGTGA
288132 TTT
131 TTT
* *
288135 TGTATCGATACATTTGGGTCAAAAACCCAGAATGTATCGATACAATGAGAAATGTATCGATACAA
1 TGTATCGATACATTTGGGTCAAAAACCCAGAATATATCGATACAATGAGAAATGTATCAATACAA
* * *
288200 TTTGAAGCATGTATCGATACATTTATTAATGTATTGATACATTTCCTTGGCAGCATACAGGGTGA
66 TTTGAAGCATGTATCGATACATTTATTAATGTATCGATACATTTCCTGGGCAGCATACAAGGTGA
288265 TTT
131 TTT
288268 TGTATCGATACATT
1 TGTATCGATACATT
288282 GTATCGATAC
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 139 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (133 bp):
TGTATCGATACATTTGGGTCAAAAACCCAGAATATATCGATACAATGAGAAATGTATCAATACAA
TTTGAAGCATGTATCGATACATTTATTAATGTATCGATACATTTCCTGGGCAGCATACAAGGTGA
TTT
Found at i:288285 original size:13 final size:13
Alignment explanation
Indices: 288267--288294 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
288257 CAGGGTGATT
288267 TTGTATCGATACA
1 TTGTATCGATACA
288280 TTGTATCGATACA
1 TTGTATCGATACA
288293 TT
1 TT
288295 TACTGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:289174 original size:29 final size:30
Alignment explanation
Indices: 289100--289399 Score: 315
Period size: 29 Copynumber: 10.1 Consensus size: 30
289090 GTAAAAGGCA
*
289100 CCTTCTTCAAAGTCCATGACTTAGGGGCATC
1 CCTTC-TCAAAGTCCATGACTTAGTGGCATC
* * *
289131 TCTTCTCAAAATCCATGACTCAGTGGCA-C
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* *
289160 CCTTCTCAAAGTCCACGACTCAGTGGCATC
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* * *
289190 CCTTTTTAAAGTCCATGACTTAGT-GCATG
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* * *
289219 TCTTCTCAAAGTCCACGACTCAGTGGCATC
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
289249 CCTTCTCAAAGTCCATGACTTAGTGGCA-C
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* * *
289278 CTTTCTTAAAGTCCACGACTTAGTGGCATC
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* * * *
289308 TCTTC-CAAAGTCGACGACTTAGTGGCATA
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
* **
289337 TCTTC-CAAAGTCCACAAAC-TAGTGGCATC
1 CCTTCTCAAAGTCCA-TGACTTAGTGGCATC
* * *
289366 TCTTCTTAAAGTCCATGACTCAGTGGCATC
1 CCTTCTCAAAGTCCATGACTTAGTGGCATC
289396 CCTT
1 CCTT
289400 TGTAAAGTCC
Statistics
Matches: 225, Mismatches: 38, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
29 125 0.56
30 96 0.43
31 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (30 bp):
CCTTCTCAAAGTCCATGACTTAGTGGCATC
Found at i:289174 original size:59 final size:60
Alignment explanation
Indices: 289100--289421 Score: 352
Period size: 59 Copynumber: 5.4 Consensus size: 60
289090 GTAAAAGGCA
* * * *
289100 CCTTCTTCAAAGTCCATGACTTAGGGGCATCTCTTCTCAAAATCCATGACTCAGTGGCA-C
1 CCTTC-TCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
* * * * *
289160 CCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTTTTAAAGTCCATGACTTAGT-GCATG
1 CCTTCTCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
* * *
289219 TCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGTCCATGACTTAGTGGCA-C
1 CCTTCTCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
* * * * *
289278 CTTTCTTAAAGTCCACGACTTAGTGGCATCTCTTC-CAAAGTCGACGACTTAGTGGCATA
1 CCTTCTCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
* * * *
289337 TCTTC-CAAAGTCCACAAAC-TAGTGGCATCTCTTCTTAAAGTCCATGACTCAGTGGCATC
1 CCTTCTCAAAGTCCAC-GACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
* * *
289396 CCTT-TGTAAAGTCCACAACTTTGTGG
1 CCTTCT-CAAAGTCCACGACTTAGTGG
289422 TACTCTTTTT
Statistics
Matches: 221, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
58 47 0.21
59 152 0.69
60 22 0.10
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (60 bp):
CCTTCTCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCATGACTTAGTGGCATC
Found at i:289240 original size:88 final size:88
Alignment explanation
Indices: 289108--289395 Score: 352
Period size: 88 Copynumber: 3.2 Consensus size: 88
289098 CACCTTCTTC
* * *
289108 AAAGTCCATGACTTAGGGGCATCTCTTCTCAAAATCCATGACTCAGTGGCA-CCCTTCTCAAAGT
1 AAAGTCCATGACTTA-GTGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGT
289172 CCACGACTCAGTGGCATCCCTTTTT
65 CCACGACT-AGTGGCATCCCTTTTT
*
289197 AAAGTCCATGACTTAGTGCATGTCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGTC
1 AAAGTCCATGACTTAGTGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGTC
*
289262 CATGACTTAGTGGCA--CCTTTCTT
66 CACGAC-TAGTGGCATCCCTTT-TT
* * * **
289285 AAAGTCCACGACTTAGTGGCATCTCTTC-CAAAGTCGACGACTTAGTGGCATATCTTC-CAAAGT
1 AAAGTCCATGACTTAGT-GCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGT
* * *
289348 CCACAAACTAGTGGCATCTCTTCTT
65 CCAC-GACTAGTGGCATCCCTTTTT
*
289373 AAAGTCCATGACTCAGTGGCATC
1 AAAGTCCATGACTTAGT-GCATC
289396 CCTTTGTAAA
Statistics
Matches: 175, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
87 22 0.13
88 99 0.57
89 53 0.30
90 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (88 bp):
AAAGTCCATGACTTAGTGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCCTTCTCAAAGTC
CACGACTAGTGGCATCCCTTTTT
Found at i:289453 original size:32 final size:31
Alignment explanation
Indices: 289402--290069 Score: 415
Period size: 32 Copynumber: 21.5 Consensus size: 31
289392 CATCCCTTTG
* *
289402 TAAAGTCCACAACTTTGTGGTACTCTTTTTTT
1 TAAAGTCCACAACTCTGTGGCAC-CTTTTTTT
* * *
289434 TAATGTCAACAACTCTGTGGCA-CTTCTTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
*
289464 CAAAGTCCACAACT-TCGTGGCACTCTTTTATTTT
1 TAAAGTCCACAACTCT-GTGGCAC-C-TTT-TTTT
*
289498 TAAA-T-CACAACTCTGTGGCACC-TCTTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
* ** *
289526 TAAAGTCCACAACTCTATAACA-CTCCTTTTT
1 TAAAGTCCACAACTCTGTGGCACCT-TTTTTT
**
289557 TAAAGTCCACAACTCCATGGCACCTTTTTCTTT
1 TAAAGTCCACAACTCTGTGGCACC-TTTT-TTT
289590 TAAAGTCCACAACTCTGTGGCACCTTTTTTTT
1 TAAAGTCCACAACTCTGTGGCACC-TTTTTTT
* *
289622 TAAAGTCCACAACTCCGTGGTAACC----TTT
1 TAAAGTCCACAACTCTGTGG-CACCTTTTTTT
* *
289650 T-AAGTTCACAACTCCGTGGCACCCTTTTCTCTTT
1 TAAAGTCCACAACTCTGTGGCA-CC-TTT-T-TTT
** * * *
289684 TAAAGTTTACAACTTTTTGGCACC---CTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
289712 T-AAGTCCACAACT-TCGTGGCACCTTTTTTCT
1 TAAAGTCCACAACTCT-GTGGCACCTTTTTT-T
* *
289743 TATAGTCCACAACTCTGTGGCA-C--ATTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
*
289771 T-AAGTCCACAATCTCAGTGGCACCCTTTTTCTT
1 TAAAGTCCACAA-CTCTGTGGCA-CCTTTTT-TT
* * **
289804 TCAAAGTTCACAACTCTATAACACTCTTTTTCTTT
1 T-AAAGTCCACAACTCTGTGGCAC-C-TTTT-TTT
289839 TAAAGTCCACAACT-TGATGGCACC---TTTT
1 TAAAGTCCACAACTCTG-TGGCACCTTTTTTT
* * * * * *
289867 T-CAGTCCGCAAGTTTGTAGTACTCTTTTTCTTT
1 TAAAGTCCACAACTCTGTGGCAC-C-TTTT-TTT
* *
289900 TAAAGTCAACAACTCTATGGCACCATTTTTTCT
1 TAAAGTCCACAACTCTGTGGCACC-TTTTTT-T
* **
289933 TAAAGTCCATAACTCTGTGGCACC--CCTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
*
289962 TAAAGTCCACAACTCTGTGACACCTATCTTTTT
1 TAAAGTCCACAACTCTGTGGCACCT-T-TTTTT
* *
289995 T-AAGTCCATAACTCTGTGGCACCCTTTCTTT
1 TAAAGTCCACAACTCTGTGGCA-CCTTTTTTT
* * * *
290026 CAGATTCCACAACTCCGTGGCA-CTTTTTTT
1 TAAAGTCCACAACTCTGTGGCACCTTTTTTT
290056 T-AAGTCCACAACTC
1 TAAAGTCCACAACTC
290070 CATGGCATCC
Statistics
Matches: 495, Mismatches: 84, Indels: 117
0.71 0.12 0.17
Matches are distributed among these distances:
26 2 0.00
27 58 0.12
28 34 0.07
29 42 0.08
30 48 0.10
31 31 0.06
32 115 0.23
33 83 0.17
34 49 0.10
35 32 0.06
36 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (31 bp):
TAAAGTCCACAACTCTGTGGCACCTTTTTTT
Found at i:289469 original size:62 final size:62
Alignment explanation
Indices: 289371--290076 Score: 358
Period size: 62 Copynumber: 11.4 Consensus size: 62
289361 GCATCTCTTC
** * * * *
289371 TTAAAGTCCATGACTCAGTGGCA-TCCCTTTGTAAAGTCCACAACTTTGTGGTACTC-TTTTTT
1 TTAAAGTCCACAACTCCGTGGCACT-TCTTT-TAAAGTCCACAACTCTGTGGCACTCTTTTTTT
* * *
289433 TTAATGTCAACAACTCTGTGGCACTTCTTTTCAAAGTCCACAACT-TCGTGGCACTCTTTTATTT
1 TTAAAGTCCACAACTCCGTGGCACTTCTTTT-AAAGTCCACAACTCT-GTGGCACTCTTTT-TTT
* * * ** *
289497 TTAAA-T-CACAACTCTGTGGCACCTCTTTTTAAAGTCCACAACTCTATAACACTC--CTTTT
1 TTAAAGTCCACAACTCCGTGGCACTTC-TTTTAAAGTCCACAACTCTGTGGCACTCTTTTTTT
*
289556 TTAAAGTCCACAACTCCATGGCACCTTTTTCTTTTAAAGTCCACAACTCTGTGGCAC-CTTTTTT
1 TTAAAGTCCACAACTCCGTGGCA-C---TTCTTTTAAAGTCCACAACTCTGTGGCACTCTTTTTT
289620 T
62 T
* * * *
289621 TTAAAGTCCACAACTCCGTGGTAAC--CTTTT-AAGTTCACAACTCCGTGGCACCCTTTTCTCTT
1 TTAAAGTCCACAACTCCGTGG-CACTTCTTTTAAAGTCCACAACTCTGTGGCACTCTTTT-T-TT
** *** * *
289683 TTAAAGTTTACAACTTTTTGGCAC-CCTTTT-AAGTCCACAACT-TCGTGGCAC-CTTTTTTC
1 TTAAAGTCCACAACTCCGTGGCACTTCTTTTAAAGTCCACAACTCT-GTGGCACTCTTTTTTT
* * * * *
289742 TTATAGTCCACAACTCTGTGGCACAT-TTTT-AAGTCCACAATCTCAGTGGCACCCTTTTTCTT
1 TTAAAGTCCACAACTCCGTGGCACTTCTTTTAAAGTCCACAA-CTCTGTGGCACTCTTTTT-TT
* * ** **
289804 TCAAAGTTCACAACTCTATAACACTCTTTTTCTTTTAAAGTCCACAACT-TGATGGCAC-C----
1 TTAAAGTCCACAACTCCGTGGCA--C---TTCTTTTAAAGTCCACAACTCTG-TGGCACTCTTTT
289863 TTT
60 TTT
* * * ** * * * *
289866 TT-CAGTCCGCAAGTTTGTAGTACTCTTTTTCTTTTAAAGTCAACAACTCTATGGCAC-CATTTT
1 TTAAAGTCCACAACTCCGT-G-GCAC---TTCTTTTAAAGTCCACAACTCTGTGGCACTC-TTTT
*
289929 TTC
60 TTT
* * ** * *
289932 TTAAAGTCCATAACTCTGTGGCACCCCTTTTAAAGTCCACAACTCTGTGACAC-CTATCTTTT
1 TTAAAGTCCACAACTCCGTGGCACTTCTTTTAAAGTCCACAACTCTGTGGCACTCT-TTTTTT
* * * * * *
289994 TT-AAGTCCATAACTCTGTGGCACCCTTTCTTTCAGATTCCACAACTCCGTGGCA--C-TTTTTT
1 TTAAAGTCCACAACTCCGTGGCA--C-TTCTTTTAAAGTCCACAACTCTGTGGCACTCTTTTTTT
*
290055 TT-AAGTCCACAACTCCATGGCA
1 TTAAAGTCCACAACTCCGTGGCA
290077 TCCTATCAAA
Statistics
Matches: 510, Mismatches: 87, Indels: 95
0.74 0.13 0.14
Matches are distributed among these distances:
59 61 0.12
60 22 0.04
61 114 0.22
62 174 0.34
63 16 0.03
64 52 0.10
65 29 0.06
66 6 0.01
67 14 0.03
68 12 0.02
69 10 0.02
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (62 bp):
TTAAAGTCCACAACTCCGTGGCACTTCTTTTAAAGTCCACAACTCTGTGGCACTCTTTTTTT
Found at i:289491 original size:29 final size:29
Alignment explanation
Indices: 289096--289492 Score: 245
Period size: 30 Copynumber: 13.4 Consensus size: 29
289086 CACAGTAAAA
* *
289096 GGCAC-CTTCTTCAAAGTCCATGACTTAGG
1 GGCACTCTT-TTCAAAGTCCACGACTTAGT
* * * *
289125 GGCATCTCTTCTCAAAATCCATGACTCAGT
1 GGCA-CTCTTTTCAAAGTCCACGACTTAGT
* * *
289155 GGCACCCTTCTCAAAGTCCACGACTCAGT
1 GGCACTCTTTTCAAAGTCCACGACTTAGT
* * *
289184 GGCATCCCTTTTTAAAGTCCATGACTTAGT
1 GGCA-CTCTTTTCAAAGTCCACGACTTAGT
* * *
289214 -GCATGTCTTCTCAAAGTCCACGACTCAGT
1 GGCA-CTCTTTTCAAAGTCCACGACTTAGT
* * *
289243 GGCATCCCTTCTCAAAGTCCATGACTTAGT
1 GGCA-CTCTTTTCAAAGTCCACGACTTAGT
*
289273 GGCAC-CTTTCTTAAAGTCCACGACTTAGT
1 GGCACTCTTT-TCAAAGTCCACGACTTAGT
* *
289302 GGCA-TCTCTTCCAAAGTCGACGACTTAGT
1 GGCACTCT-TTTCAAAGTCCACGACTTAGT
* * *
289331 GGCA-TATCTTCCAAAGTCCACAAAC-TAGT
1 GGCACTCT-TTTCAAAGTCCAC-GACTTAGT
* *
289360 GGCATCTCTTCTT-AAAGTCCATGACTCAGT
1 GGCA-CTCTT-TTCAAAGTCCACGACTTAGT
* * *
289390 GGCATCCCTTTGT-AAAGTCCACAACTTTGT
1 GGCA-CTCTTT-TCAAAGTCCACGACTTAGT
* * * * *
289420 GGTACTCTTTTTTTTAATGTCAACAACTCT-GT
1 GGCACTC---TTTTCAAAGTCCACGACT-TAGT
* *
289452 GGCACTTCTTTTCAAAGTCCACAACTTCGT
1 GGCAC-TCTTTTCAAAGTCCACGACTTAGT
289482 GGCACTCTTTT
1 GGCACTCTTTT
289493 ATTTTTAAAT
Statistics
Matches: 300, Mismatches: 48, Indels: 40
0.77 0.12 0.10
Matches are distributed among these distances:
28 3 0.01
29 132 0.44
30 135 0.45
31 7 0.02
32 20 0.07
33 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (29 bp):
GGCACTCTTTTCAAAGTCCACGACTTAGT
Found at i:289526 original size:92 final size:92
Alignment explanation
Indices: 289397--289771 Score: 313
Period size: 94 Copynumber: 4.0 Consensus size: 92
289387 AGTGGCATCC
* * * * *
289397 CTTTGTAAAGTCCACAACTTTGTGGTACTCTTTTTTTTAATGTCAACAACTCTGTGGCACTTCTT
1 CTTT-TAAAGT-CACAACTCTGTGGCAC-C-TCTTTTTAAAGTCCACAACTCTGTGGCACTTCTT
*
289462 TTCAAAGTCCACAACTTCGTGGCACTCTTTTAT
62 TTCAAAGTCCACAACTCCGTGGCAC-CTTTT-T
* ** * *
289495 -TTTTAAA-TCACAACTCTGTGGCACCTCTTTTTAAAGTCCACAACTCTATAACACTCCTTTTTT
1 CTTTTAAAGTCACAACTCTGTGGCACCTCTTTTTAAAGTCCACAACTCTGTGGCACTTC-TTTTC
*
289558 AAAGTCCACAACTCCATGGCACCTTTTT
65 AAAGTCCACAACTCCGTGGCACCTTTTT
* * *
289586 CTTTTAAAGTCCACAACTCTGTGGCACCTTTTTTTTTAAAGTCCACAACTCCGTGGTAAC--CTT
1 CTTTTAAAGT-CACAACTCTGTGGCACC--TCTTTTTAAAGTCCACAACTCTGTGG-CACTTCTT
*
289649 TT--AAGTTCACAACTCCGTGGCACCCTTTTCT
62 TTCAAAGTCCACAACTCCGTGGCA-CCTTTT-T
* * *
289680 CTTTTAAAGTTTACAACTTTTTGGCACC-C-TTTT-AAGTCCACAACT-TCGTGGCACCTT-TTT
1 CTTTTAAAG-TCACAACTCTGTGGCACCTCTTTTTAAAGTCCACAACTCT-GTGGCA-CTTCTTT
* * *
289740 TCTTATAGTCCACAACTCTGTGGCACATTTTT
63 TC--AAAGTCCACAACTCCGTGGCACCTTTTT
289772 AAGTCCACAA
Statistics
Matches: 229, Mismatches: 30, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
88 1 0.00
89 17 0.07
90 8 0.03
91 1 0.00
92 56 0.24
93 37 0.16
94 76 0.33
95 3 0.01
96 25 0.11
97 5 0.02
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.39
Consensus pattern (92 bp):
CTTTTAAAGTCACAACTCTGTGGCACCTCTTTTTAAAGTCCACAACTCTGTGGCACTTCTTTTCA
AAGTCCACAACTCCGTGGCACCTTTTT
Found at i:289731 original size:121 final size:122
Alignment explanation
Indices: 289586--289818 Score: 330
Period size: 121 Copynumber: 1.9 Consensus size: 122
289576 GCACCTTTTT
*
289586 CTTTTAAAGTCCACAACTCTGTGGCACCTTTTTTTTTAAAGTCCACAACTCCGTGGTAAC-CTTT
1 CTTTTAAAGTCCACAACTCTGTGGCACCTTTTTTCTTAAAGTCCACAACTCCGTGG-AACACTTT
* * * *
289650 TAAGTTCACAA-CTCCGTGGCACCCTTTTCTCTTTTAAAGTTTACAACTTTTTGGCACC
65 TAAGTCCACAATCTCAGTGGCACCCTTTT-TCTTTCAAAGTTCACAACTTTTTGGCACC
* * * *
289708 CTTTT-AAGTCCACAACT-TCGTGGCACCTTTTTTCTTATAGTCCACAACTCTGTGGCACATTTT
1 CTTTTAAAGTCCACAACTCT-GTGGCACCTTTTTTCTTAAAGTCCACAACTCCGTGGAACACTTT
289771 TAAGTCCACAATCTCAGTGGCACCCTTTTTCTTTCAAAGTTCACAACT
65 TAAGTCCACAATCTCAGTGGCACCCTTTTTCTTTCAAAGTTCACAACT
289819 CTATAACACT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
120 3 0.03
121 75 0.76
122 21 0.21
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (122 bp):
CTTTTAAAGTCCACAACTCTGTGGCACCTTTTTTCTTAAAGTCCACAACTCCGTGGAACACTTTT
AAGTCCACAATCTCAGTGGCACCCTTTTTCTTTCAAAGTTCACAACTTTTTGGCACC
Found at i:290114 original size:30 final size:30
Alignment explanation
Indices: 290078--290157 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
290068 TCCATGGCAT
*
290078 CCTATCAAAGCCTATAAGTCGGTAGCGTCC
1 CCTATCAAAGCCCATAAGTCGGTAGCGTCC
*
290108 CCTATCAAAGCCCATAAGTCGGTGGCGTCC
1 CCTATCAAAGCCCATAAGTCGGTAGCGTCC
*
290138 CCTACCAAAGCCCATAAGTC
1 CCTATCAAAGCCCATAAGTC
290158 AGTGACACCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.20
Consensus pattern (30 bp):
CCTATCAAAGCCCATAAGTCGGTAGCGTCC
Found at i:290177 original size:28 final size:28
Alignment explanation
Indices: 290144--290957 Score: 769
Period size: 28 Copynumber: 28.8 Consensus size: 28
290134 GTCCCCTACC
* * *
290144 AAAGCCCATAAGTCAGTGACACCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290172 AAAGCCCACAAGTCAATGGCA-CATTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290199 CAAAGCCCACAAGTCAATGGCACCCTCTT
1 -AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290228 AAAGCCCACAAGTTAGTGGCACCCCTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
290256 GAAGCCCACAAGTTAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * *
290284 AAAGCCCACAAGTTAATGGCACCATCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290312 AAAGCCCACAAGTCAATGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290340 AAAGCCCACAAGTCAGTGGCATCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290368 AAAGCTCACAAGTTAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290396 GAAGCCCACAAGTTAGTGGCACCCTTTCT
1 AAAGCCCACAAGTCAGTGGCACCCTTT-T
* *
290425 AAAGCCTACAAGTCAGTGGCACCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * ** *
290453 AAAGCTCACAAGTTAGTGGCACCCCCTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290481 AAAGCCCACAAGTCAGTTGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * *
290509 AAAGCCTACAAGTTAGTGACATCCC-TTC
1 AAAGCCCACAAGTCAGTGGCA-CCCTTTT
**
290537 AAAGCCCACAAGTCAGTGGCACCCTTGC
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290565 AAAGCTCACAAGTCAGTGGCACCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
** **
290593 AAAGCCCACAAGTCAGTGGTGCTTTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
290621 AAAGTCCACAAGTTAGTGGCACCTTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
*
290649 AAAGCCCAC-AGATCAATGGCAACCCCTTTT
1 AAAGCCCACAAG-TCAGTGGC-A-CCCTTTT
* * * *
290679 AAAGCCCACAACTCCGTGGCA-TCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * *
290706 AAAGCCCATAAGTTAGTGGGACCATTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
*
290734 AAAGCCCACAAGTCAGTGGTATCCCCTTTT
1 AAAGCCCACAAGTCAGTGGCA--CCCTTTT
* * *
290764 AAAGCCCATAAGTTAGTAGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* *
290792 AAAGCCCACAAGTTAGTGGCACTCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
*
290820 AAAGCCCAC-AGTCAGTGGCACCTTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
*
290847 AAAGCCCACAAGTTAGTGGCA-CCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTT
* * * * *
290874 CAAAGACCACAACTTAGTGACA-CCTTTCA
1 -AAAGCCCACAAGTCAGTGGCACCCTTT-T
** *
290903 AAAGCCCACTCAAGTTGGTGGAAACCCTCTTT
1 AAAGCCCA--CAAGTCAGTGG-CACCCT-TTT
*
290935 AAAGCCCATACAAGTTAGTGGCA
1 AAAGCCC--ACAAGTCAGTGGCA
290958 TCTCCTTCTA
Statistics
Matches: 649, Mismatches: 115, Indels: 41
0.81 0.14 0.05
Matches are distributed among these distances:
27 58 0.09
28 480 0.74
29 33 0.05
30 52 0.08
31 3 0.00
32 20 0.03
33 2 0.00
34 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTT
Found at i:291126 original size:52 final size:51
Alignment explanation
Indices: 291066--291326 Score: 206
Period size: 52 Copynumber: 5.0 Consensus size: 51
291056 CATTCGTATT
* *
291066 CTTTTCATCTTTAAGTCTAATGTTGCTGACCTTGAATCAACATATTGGCAC
1 CTTTTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAACATATTGGCAC
* * * * *
291117 CTTTGTCATCTTTAAATCTATTATCACTGGCCTTGAATCAGCATATTGGCA-
1 CTTT-TCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAACATATTGGCAC
* * *
291168 CTTTATCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCACC
1 CTTT-TCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAACATATTGGCA-C
* * * *
291221 CTTATCAATTTTTTCAAGT-TCAATGTCGTTGGCCTTGAA-CTAGCATATTGGCA-
1 CTTTTC-A-TCTTT-AAGTCT-AATGTCGCTGGCCTTGAATC-AACATATTGGCAC
* * * * * * * *
291274 TTATTCTCATCTTCAAGCCCAATGTCGCTGGCCGTGAATTAGCACATTGGCAC
1 CT-TT-TCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAACATATTGGCAC
291327 TCTTAACATT
Statistics
Matches: 166, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
51 46 0.28
52 71 0.43
53 8 0.05
54 7 0.04
55 34 0.20
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (51 bp):
CTTTTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAACATATTGGCAC
Found at i:291994 original size:20 final size:21
Alignment explanation
Indices: 291955--292001 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
291945 AATTTTTATT
291955 GATACAAACAGTGAATGTATC
1 GATACAAACAGTGAATGTATC
*
291976 GATACAAA-AGT-AGATGTATT
1 GATACAAACAGTGA-ATGTATC
291996 GATACA
1 GATACA
292002 TGTCTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
GATACAAACAGTGAATGTATC
Found at i:294226 original size:181 final size:181
Alignment explanation
Indices: 293916--294278 Score: 636
Period size: 181 Copynumber: 2.0 Consensus size: 181
293906 TTCGAAAAGG
* **
293916 TATTATTATCATTTTAATGATCTTGGATGAATCCGAGATGATTTTTTAAAATTTGGCATACCATT
1 TATTAATATCATTTTAACAATCTTGGATGAATCCGAGATGATTTTTTAAAATTTGGCATACCATT
* * *
293981 TTTCTTATATGCTCTGCTAGCAGTGCCATAAACCCCACTTCAAGAATTTATTCCCCCTAGAAAAT
66 TTTCTCATATGCTCTGCTAGCAGTGCCATAAACCCCACTCCAAGAATTTATTCCCCATAGAAAAT
294046 GATTTTTCAAAATTTTTAAAATATTTTTAGATTGATCCTCATCGAGTCACC
131 GATTTTTCAAAATTTTTAAAATATTTTTAGATTGATCCTCATCGAGTCACC
* *
294097 TATTAATATCATTTTAACAATCTTGGATGAATTCGAGATGATTTTTTAAAGTTTGGCATACCATT
1 TATTAATATCATTTTAACAATCTTGGATGAATCCGAGATGATTTTTTAAAATTTGGCATACCATT
* *
294162 TTTCTCATATGCTCTGCTAGTAGTGTCATAAACCCCACTCCAAGAATTTATTCCCCATAGAAAAT
66 TTTCTCATATGCTCTGCTAGCAGTGCCATAAACCCCACTCCAAGAATTTATTCCCCATAGAAAAT
294227 GATTTTTCAAAATTTTTAAAATATTTTTAGATTGATCCTCATCGAGTCACC
131 GATTTTTCAAAATTTTTAAAATATTTTTAGATTGATCCTCATCGAGTCACC
294278 T
1 T
294279 TTCCAACAGT
Statistics
Matches: 172, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 172 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (181 bp):
TATTAATATCATTTTAACAATCTTGGATGAATCCGAGATGATTTTTTAAAATTTGGCATACCATT
TTTCTCATATGCTCTGCTAGCAGTGCCATAAACCCCACTCCAAGAATTTATTCCCCATAGAAAAT
GATTTTTCAAAATTTTTAAAATATTTTTAGATTGATCCTCATCGAGTCACC
Found at i:297752 original size:50 final size:51
Alignment explanation
Indices: 297676--297812 Score: 186
Period size: 50 Copynumber: 2.7 Consensus size: 51
297666 ATTTAATTGG
* * * *
297676 ATGTATCAATACAATGAAGAATGTATCGATACATTTAGGTCAAAA-CCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATAAAAACCCAAA
* * *
297726 ATGTATCGATATAATGAATAACGTATCGATACATTTAGATAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATAAAAACCCAAA
**
297777 ATGTATCGATACAATGAAAAATGTATTAATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
297813 TCTTTCTAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 39 0.52
51 36 0.48
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATAAAAACCCAAA
Found at i:297916 original size:21 final size:20
Alignment explanation
Indices: 297869--297941 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
297859 CATTTCAAAC
297869 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
297889 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
* *
297909 GTTGTATCGAT--A-TGACTT
1 -ATGTATCGATACATTCACTT
*
297927 ATGCATCGATACATT
1 ATGTATCGATACATT
297942 TCGATCTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.18
18 5 0.11
19 2 0.04
20 21 0.47
21 9 0.20
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:298911 original size:80 final size:78
Alignment explanation
Indices: 298617--298903 Score: 303
Period size: 80 Copynumber: 3.6 Consensus size: 78
298607 GGAGATAGGA
* * *
298617 GGGTTAGAGTATCCC-GA-GATGAAAAAAATTAATATTTTGGAAGTAAAAAAAGGGTTGGAGTAT
1 GGGTTAGAGTATCCCTGATGGTG--AAAAATTAATATTTTGGAAATAAAAATAGGGTTGGAGTAT
*
298680 CCTCTT-AAAGATGATG
64 -CT-TTCAAAAATGATG
* ** *
298696 GGGTTAGAGTAT-CCTAATGGTGAAAAATGGATATTTTGGAAATAAAAATGGGGTTGGAGTATCT
1 GGGTTAGAGTATCCCTGATGGTGAAAAATTAATATTTTGGAAATAAAAATAGGGTTGGAGTATCT
* *
298760 CTTCTAAAATAATG
66 -TTCAAAAATGATG
* * * *
298774 GGGTTAGAGTATCTCTGAGGGTAAAAAATTTAATATTTTGAAAATAAAAATAGGGTTGGAGTATC
1 GGGTTAGAGTATCCCTGATGGTGAAAAA-TTAATATTTTGGAAATAAAAATAGGGTTGGAGTATC
298839 TTATCAAAAATGATG
65 TT-TCAAAAATGATG
* * * * *
298854 GGGTTGGGGTATCCCCGATGGTGAAAAAGTTGATATTTTGGAAGTAAAAA
1 GGGTTAGAGTATCCCTGATGGTGAAAAA-TTAATATTTTGGAAATAAAAA
298904 CGGGGTTGAT
Statistics
Matches: 172, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
77 5 0.03
78 56 0.33
79 25 0.15
80 86 0.50
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (78 bp):
GGGTTAGAGTATCCCTGATGGTGAAAAATTAATATTTTGGAAATAAAAATAGGGTTGGAGTATCT
TTCAAAAATGATG
Found at i:302139 original size:65 final size:65
Alignment explanation
Indices: 301987--302336 Score: 297
Period size: 66 Copynumber: 5.4 Consensus size: 65
301977 GGGATAAAAG
* *
301987 GTACCACCAGCTTGTGTGGGCTTTAAAAGGAA-AAAAGTATCCTACTCTTTGAGGA--AAAAAAA
1 GTACCACCAGCTTGTGTGGGCTTTAAAA--AAGAAAAGCATCCTACTCTTTGAGGACTAAAAAAT
302049 GA
64 GA
* * * * * *
302051 ATACCACCAACTTATGTGGGCTTTAAAAAAGAAAAGCGTCATGCTCTTTGAGGACTAAAAAATGA
1 GTACCACCAGCTTGTGTGGGCTTTAAAAAAGAAAAGCATCCTACTCTTTGAGGACTAAAAAATGA
* * * * * * *
302116 GTGCCACTAGCTTGTGTGGGCTTTTAAAAAAGGAAAGCGTTCTACTCTTTAAAGACTAATAAAAT
1 GTACCACCAGCTTGTGTGGGC-TTTAAAAAAGAAAAGCATCCTACTCTTTGAGGACTAA-AAAAT
302181 -A
64 GA
* * * * *
302182 GTGCCACCAACGTGTGTGCGCTTTTAAAAAGGAAAAGGCATCCTACTCTTTGAGGACT--AAAA-
1 GTACCACCAGCTTGTGTGGGC-TTTAAAAAAGAAAA-GCATCCTACTCTTTGAGGACTAAAAAAT
302244 G-
64 GA
** * * *
302245 GTACCATTAGCTTGTGTGGGCTTTAAAAGAA-AAAAACATCTTGCTCTTTGAGGACTAAAAGGTA
1 GTACCACCAGCTTGTGTGGGCTTTAAAA-AAGAAAAGCATCCTACTCTTTGAGGACTAAAA---A
*
302309 A-AA
62 ATGA
302312 GGTACCACCAGCTTGTGTGGGCTTT
1 -GTACCACCAGCTTGTGTGGGCTTT
302337 GAAAGAAAAA
Statistics
Matches: 229, Mismatches: 42, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
61 18 0.08
62 13 0.06
63 37 0.16
64 29 0.13
65 24 0.10
66 64 0.28
67 22 0.10
68 22 0.10
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (65 bp):
GTACCACCAGCTTGTGTGGGCTTTAAAAAAGAAAAGCATCCTACTCTTTGAGGACTAAAAAATGA
Found at i:302312 original size:68 final size:68
Alignment explanation
Indices: 302239--302458 Score: 217
Period size: 76 Copynumber: 3.1 Consensus size: 68
302229 CTTTGAGGAC
**
302239 TAAAAGGTACCATTAGCTTGTGTGGGCTTTAAAAGAAAAAAACATCTTGCTCTTTGAGGACTAAA
1 TAAAAGGTACCACCAGCTTGTGTGGGCTTTAAAAGAAAAAAACATCTTGCTCTTTGAGGACTAAA
302304 AGG
66 AGG
*
302307 TAAAAGGTACCACCAGCTTGTGTGGGCTTTGAAAGAAAAAGGAAAGCATCTTGCTTGCTCTTTGA
1 TAAAAGGTACCACCAGCTTGTGTGGGCTTTAAAAG-AAAA--AAA-CA---T-CTTGCTCTTTGA
* *
302372 AGTCTAAAAGG
58 GGACTAAAAGG
* * * **** * *
302383 TAAAAGGTGCCACCAGCTTATGTAGGCTTTGAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAA
1 TAAAAGGTACCACCAGCTTGTGTGGGCTTT-AAAAGAAAAAAACATCTTGCTCTTTGAGGACTAA
302448 AA-G
65 AAGG
*
302451 TAACAGGT
1 TAAAAGGT
302459 TTATGTTTAG
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
68 40 0.32
69 21 0.17
70 1 0.01
71 3 0.02
72 2 0.02
74 1 0.01
75 1 0.01
76 52 0.42
77 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (68 bp):
TAAAAGGTACCACCAGCTTGTGTGGGCTTTAAAAGAAAAAAACATCTTGCTCTTTGAGGACTAAA
AGG
Found at i:302320 original size:131 final size:128
Alignment explanation
Indices: 301981--302336 Score: 334
Period size: 129 Copynumber: 2.8 Consensus size: 128
301971 ATAAATGGGA
* * *
301981 TAAAAGGTACCACCAGCTTGTGTGGGCTTTAAAAGGAAAAAAGTATCCTACTCTTTGAGG---AA
1 TAAAAGGTACCACTAGCTTGTGTGGGCTTTAAAA-GAAAAAAGCATCTTACTCTTTGAGGACTAA
* * * *
302043 AA-AAAAGAATACCACCAACTTATGTGGGC-TTTAAAAAAGAAAAGCGTCATGCTCTTTGAGGAC
65 AATAAAAG-GTACCACCAACTTGTGTGGGCTTTTAAAAAAGAAAAGCATCATACTCTTTGAGGAC
* * * * *
302106 TAAAAAATGAGTGCCACTAGCTTGTGTGGGCTTTTAAAA-AAGGAAAGCGT-TCTACTCTTTAAA
1 T--AAAA-G-GTACCACTAGCTTGTGTGGGC-TTTAAAAGAA-AAAAGCATCT-TACTCTTTGAG
* * * * * *
302169 GACT--AATAAAATAGTGCCACCAACGTGTGTGCGCTTTTAAAAAGGAAAAGGCATCCTACTCTT
59 GACTAAAATAAAA-GGTACCACCAACTTGTGTGGGCTTTTAAAAAAGAAAA-GCATCATACTCTT
302232 TGAGGAC
122 TGAGGAC
* * *
302239 TAAAAGGTACCATTAGCTTGTGTGGGCTTTAAAAGAAAAAAACATCTTGCTCTTTGAGGACTAAA
1 TAAAAGGTACCACTAGCTTGTGTGGGCTTTAAAAGAAAAAAGCATCTTACTCTTTGAGGACTAAA
*
302304 AGGTAAAAGGTACCACCAGCTTGTGTGGGCTTT
66 A--TAAAAGGTACCACCAACTTGTGTGGGCTTT
302337 GAAAGAAAAA
Statistics
Matches: 180, Mismatches: 31, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
125 1 0.01
127 4 0.02
128 27 0.15
129 56 0.31
130 12 0.07
131 44 0.24
132 18 0.10
133 18 0.10
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (128 bp):
TAAAAGGTACCACTAGCTTGTGTGGGCTTTAAAAGAAAAAAGCATCTTACTCTTTGAGGACTAAA
ATAAAAGGTACCACCAACTTGTGTGGGCTTTTAAAAAAGAAAAGCATCATACTCTTTGAGGAC
Found at i:302411 original size:76 final size:77
Alignment explanation
Indices: 302284--302425 Score: 232
Period size: 76 Copynumber: 1.9 Consensus size: 77
302274 AAAAAAACAT
* * *
302284 CTTGCTCTTTGAGGACTAAAAGGTAAAAGGTACCACCAGCTTGTGTGGGCTTTG-AAAGAAAAAG
1 CTTGCTCTTTGAAGACTAAAAGGTAAAAGGTACCACCAGCTTATGTAGGCTTTGAAAAGAAAAAG
302348 GAAAGCATCTTG
66 GAAAGCATCTTG
* *
302360 CTTGCTCTTTGAAGTCTAAAAGGTAAAAGGTGCCACCAGCTTATGTAGGCTTTGAAAAGAAAAAG
1 CTTGCTCTTTGAAGACTAAAAGGTAAAAGGTACCACCAGCTTATGTAGGCTTTGAAAAGAAAAAG
302425 G
66 G
302426 TGTCCTACTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
76 49 0.82
77 11 0.18
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (77 bp):
CTTGCTCTTTGAAGACTAAAAGGTAAAAGGTACCACCAGCTTATGTAGGCTTTGAAAAGAAAAAG
GAAAGCATCTTG
Found at i:307038 original size:7 final size:6
Alignment explanation
Indices: 307010--307037 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
307000 GTAAAAATCA
307010 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
307038 AAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:307066 original size:13 final size:14
Alignment explanation
Indices: 307050--307149 Score: 50
Period size: 14 Copynumber: 8.2 Consensus size: 14
307040 AAATAATAAA
307050 AATGA-AGGCATGG
1 AATGATAGGCATGG
*
307063 AATGATGGGCATGG
1 AATGATAGGCATGG
*
307077 AAT-ATA---A--A
1 AATGATAGGCATGG
307085 AATGA-AGGCATGG
1 AATGATAGGCATGG
*
307098 AATGATGGGCATGG
1 AATGATAGGCATGG
*
307112 AAT-ATA---A--A
1 AATGATAGGCATGG
307120 AATGA-AGGCATGG
1 AATGATAGGCATGG
*
307133 AATGATGGGCATGG
1 AATGATAGGCATGG
307147 AAT
1 AAT
307150 ATAAAAATGG
Statistics
Matches: 63, Mismatches: 9, Indels: 29
0.62 0.09 0.29
Matches are distributed among these distances:
8 8 0.13
9 2 0.03
10 2 0.03
11 2 0.03
13 19 0.30
14 30 0.48
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (14 bp):
AATGATAGGCATGG
Found at i:307085 original size:35 final size:35
Alignment explanation
Indices: 307045--307284 Score: 462
Period size: 35 Copynumber: 6.9 Consensus size: 35
307035 AAAAAAAATA
307045 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
307080 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
307115 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
307150 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
307185 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
307220 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
307255 ATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATGAAGGCATGGAATGATGGGCAT
307285 AAAAAAATTA
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 201 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.20
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:308516 original size:79 final size:79
Alignment explanation
Indices: 308378--309413 Score: 1574
Period size: 79 Copynumber: 13.1 Consensus size: 79
308368 TTTAATTTTC
* *
308378 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
308443 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* ** ** * *
308457 TCAATTTTTCATAATTGAAGATACTCCAACCCCGTTATTTTTGAGGGGACACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
308522 TTATTTTTAAAACA
66 TTATTTCTAAAACA
* * *
308536 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGATGGGACACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
308601 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * *
308615 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTAATTTCTGAGGGGACACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
308680 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
308694 TTAATTTTTCATAATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
308759 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * *
308773 TCAATTTTTCGTAATCGGGGATACTCC-ACCCTGTTATTTTCGAGGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
308837 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * *
308851 TTAATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
308916 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* *
308930 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATGCTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
308995 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * *
309009 TCAATTTTTCATAAACGAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
309074 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
309088 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
309153 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * * *
309167 TCAATTTTTCATAATCGAGGATACTCTAACCTCGTTATTTCTGAAGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
309232 TTATTTTTAAAACA
66 TTATTTCTAAAACA
* *
309246 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTTCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
309311 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
309325 TCAATTTCTCACAATCGGGGATACTCCAACCCCGTTATGTT-C-ACGGGGATACTCCAACCCTGG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTAT-TTCCGA-GGGGATACTCCAACCCCGG
** *
309388 CCCTTATTTCTAAAGCA
64 -TTTTATTTCTAAAACA
309405 TCAATTTTT
1 TCAATTTTT
309414 TTATATAATT
Statistics
Matches: 869, Mismatches: 84, Indels: 7
0.91 0.09 0.01
Matches are distributed among these distances:
78 71 0.08
79 775 0.89
80 23 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:320430 original size:11 final size:10
Alignment explanation
Indices: 320416--320444 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
320406 AAAAAAAAAC
320416 AAAAATACAA
1 AAAAATACAA
320426 AAAAATACAA
1 AAAAATACAA
320436 AAAAA-ACAA
1 AAAAATACAA
320445 CGAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAATACAA
Done.