Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1516344 original size:10 final size:10
Alignment explanation
Indices: 1516329--1516403 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
1516319 AGGTCTCCAA
1516329 CGTTTATGTT
1 CGTTTATGTT
1516339 CGTTTATGTT
1 CGTTTATGTT
1516349 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
1516360 ATGTTCATGTT
1 -CGTTTATGTT
1516371 CGTTTATGTT
1 CGTTTATGTT
1516381 CG----TGTT
1 CGTTTATGTT
1516387 CGTTTATGTT
1 CGTTTATGTT
1516397 CGTTTAT
1 CGTTTAT
1516404 TTATTAAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.11
10 36 0.68
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1516360 original size:16 final size:16
Alignment explanation
Indices: 1516335--1516399 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1516325 CCAACGTTTA
1516335 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
1516351 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
1516367 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1516383 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1516399 T
1 T
1516400 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1516492 original size:16 final size:16
Alignment explanation
Indices: 1516471--1516501 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1516461 AAAAATTTTA
1516471 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
1516487 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
1516502 CTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:1517958 original size:14 final size:14
Alignment explanation
Indices: 1517939--1517965 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1517929 AAAATTATTT
1517939 TATGTTTATAATTA
1 TATGTTTATAATTA
1517953 TATGTTTATAATT
1 TATGTTTATAATT
1517966 TATAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATGTTTATAATTA
Found at i:1520687 original size:16 final size:16
Alignment explanation
Indices: 1520666--1520697 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1520656 ACATGTATTT
1520666 CTCAAGTATATTCACA
1 CTCAAGTATATTCACA
1520682 CTCAAGTATATTCACA
1 CTCAAGTATATTCACA
1520698 TGTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
CTCAAGTATATTCACA
Found at i:1521292 original size:21 final size:21
Alignment explanation
Indices: 1521266--1521305 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1521256 TTTTTTCTTT
1521266 AGGGGGAATC-GATACCCCCCA
1 AGGGGGAATCTG-TACCCCCCA
1521287 AGGGGGAATCTGTACCCCC
1 AGGGGGAATCTGTACCCCC
1521306 TGTATAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.12
Consensus pattern (21 bp):
AGGGGGAATCTGTACCCCCCA
Found at i:1523437 original size:29 final size:30
Alignment explanation
Indices: 1523391--1523447 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1523381 TTTGGATTCA
* * * *
1523391 AATTTAATCAAAATTTCACTTTGGTCCTCG
1 AATTAAATCAAAAATTCAATTTAGTCCTCG
1523421 AATTAAAT-AAAAATTCAATTTAGTCCT
1 AATTAAATCAAAAATTCAATTTAGTCCT
1523448 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (30 bp):
AATTAAATCAAAAATTCAATTTAGTCCTCG
Found at i:1529379 original size:11 final size:11
Alignment explanation
Indices: 1529363--1529415 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
1529353 TCGAGACTCG
1529363 AGCTCGATTCA
1 AGCTCGATTCA
*
1529374 AGCTCGAACTCA
1 AGCTCG-ATTCA
* **
1529386 AACTCGAATTTG
1 AGCTCG-ATTCA
1529398 AGCTCGATTCA
1 AGCTCGATTCA
1529409 AGCTCGA
1 AGCTCGA
1529416 ACTCAAACTC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1529404 original size:35 final size:35
Alignment explanation
Indices: 1529343--1529453 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
1529333 GCTCGATTGA
* *
1529343 AACTCGAAACTCGAGACTCGAGCTCGATTCAAGCTCG
1 AACTC-AAACTCGA-ATTTGAGCTCGATTCAAGCTCG
1529380 AACTCAAACTCGAATTTGAGCTCGATTCAAGCTCG
1 AACTCAAACTCGAATTTGAGCTCGATTCAAGCTCG
* *
1529415 AACTCAAACTCAAATTTGAGCCCGATTCAAGCTCG
1 AACTCAAACTCGAATTTGAGCTCGATTCAAGCTCG
1529450 AACT
1 AACT
1529454 TGATTCAAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 57 0.81
36 8 0.11
37 5 0.07
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (35 bp):
AACTCAAACTCGAATTTGAGCTCGATTCAAGCTCG
Found at i:1529458 original size:17 final size:17
Alignment explanation
Indices: 1529438--1529470 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1529428 ATTTGAGCCC
1529438 GATTCAAGCTCGAACTT
1 GATTCAAGCTCGAACTT
1529455 GATTCAAGCTCGAACT
1 GATTCAAGCTCGAACT
1529471 CGAACTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (17 bp):
GATTCAAGCTCGAACTT
Found at i:1529873 original size:16 final size:16
Alignment explanation
Indices: 1529848--1529878 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1529838 AAAAAACAGT
*
1529848 AACATGCTGATTGTTA
1 AACATCCTGATTGTTA
1529864 AACATCCTGATTGTT
1 AACATCCTGATTGTT
1529879 TATTTTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (16 bp):
AACATCCTGATTGTTA
Found at i:1531650 original size:7 final size:7
Alignment explanation
Indices: 1531499--1531693 Score: 146
Period size: 7 Copynumber: 27.9 Consensus size: 7
1531489 GTGTATAAAT
1531499 TAAACCA
1 TAAACCA
*
1531506 TAAATCA
1 TAAACCA
1531513 TAAACCA
1 TAAACCA
*
1531520 TGAATCC-
1 T-AAACCA
*
1531527 CAAACCA
1 TAAACCA
1531534 TAAACCA
1 TAAACCA
*
1531541 TAAATCA
1 TAAACCA
1531548 TAAACCA
1 TAAACCA
1531555 TAAACCA
1 TAAACCA
1531562 TAAACCA
1 TAAACCA
*
1531569 TGAATCC-
1 T-AAACCA
*
1531576 CAAACCA
1 TAAACCA
1531583 TAAACCA
1 TAAACCA
*
1531590 TAAACCC
1 TAAACCA
*
1531597 T-AACTTA
1 TAAAC-CA
* *
1531604 TGAATCA
1 TAAACCA
1531611 TAAACCA
1 TAAACCA
* *
1531618 CAAACCC
1 TAAACCA
*
1531625 T-AACTTA
1 TAAAC-CA
*
1531632 TAAATCA
1 TAAACCA
1531639 TAAACCA
1 TAAACCA
*
1531646 TAAACCC
1 TAAACCA
*
1531653 TAAACCC
1 TAAACCA
*
1531660 TAAACCC
1 TAAACCA
*
1531667 TAAACCC
1 TAAACCA
*
1531674 TAAACCC
1 TAAACCA
*
1531681 TAAACCC
1 TAAACCA
1531688 TAAACC
1 TAAACC
1531694 TATTACATAA
Statistics
Matches: 152, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
6 14 0.09
7 126 0.83
8 12 0.08
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:1536557 original size:18 final size:18
Alignment explanation
Indices: 1536514--1536550 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1536504 CATTAACTCT
* *
1536514 ACTTACCTCGACAACTTC
1 ACTTACCACGACAACATC
1536532 ACTTACCACGACAACATC
1 ACTTACCACGACAACATC
1536550 A
1 A
1536551 TTCACCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.38, G:0.05, T:0.22
Consensus pattern (18 bp):
ACTTACCACGACAACATC
Found at i:1536696 original size:35 final size:36
Alignment explanation
Indices: 1536650--1536722 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
1536640 TTCAATTAAG
*
1536650 CTTTAATAAG-AAAATACTCAAATTTCTCATGAAAC
1 CTTTAATAAGAAAAATACCCAAATTTCTCATGAAAC
*
1536685 CTTTAATAAGAAAAATACCCAAATTTCTTATGAAAC
1 CTTTAATAAGAAAAATACCCAAATTTCTCATGAAAC
1536721 CT
1 CT
1536723 AATTGGTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 10 0.29
36 25 0.71
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (36 bp):
CTTTAATAAGAAAAATACCCAAATTTCTCATGAAAC
Found at i:1541903 original size:2 final size:2
Alignment explanation
Indices: 1541890--1541937 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1541880 TTCTACATGC
*
1541890 AT AT AT AC AT AT AT AT AT A- AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1541930 AT AT AT AT
1 AT AT AT AT
1541938 CGGGATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1545147 original size:20 final size:19
Alignment explanation
Indices: 1545122--1545175 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1545112 GCGAAATAAA
1545122 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1545142 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1545162 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1545176 TATGAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1545188 original size:21 final size:21
Alignment explanation
Indices: 1545162--1545294 Score: 64
Period size: 20 Copynumber: 6.5 Consensus size: 21
1545152 CAGTTCCCAG
1545162 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTATGAAT
*
1545183 AATCGCAATGCGA-TA-GTACA-
1 AATCGCAACGCGATTATG-A-AT
** * ** *
1545203 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTATGAAT
*
1545225 AATCGCAACGCGAATATGAA-
1 AATCGCAACGCGATTATGAAT
* **
1545245 AATCACAACGCGAACAT--AT
1 AATCGCAACGCGATTATGAAT
* *
1545264 AAATCGCAACGCGATTCTGACT
1 -AATCGCAACGCGATTATGAAT
1545286 -ATCGCAACG
1 AATCGCAACG
1545295 AGTATCCGTA
Statistics
Matches: 84, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 42 0.50
21 36 0.43
22 4 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTATGAAT
Found at i:1545253 original size:20 final size:20
Alignment explanation
Indices: 1545225--1545277 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1545215 GATTTTCCAG
*
1545225 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
*
1545245 AATCACAACGCGAACATATA
1 AATCGCAACGCGAACATATA
1545265 AATCGCAACGCGA
1 AATCGCAACGCGA
1545278 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1545333 original size:20 final size:20
Alignment explanation
Indices: 1545286--1545458 Score: 163
Period size: 20 Copynumber: 8.6 Consensus size: 20
1545276 GATTCTGACT
* *
1545286 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
1545307 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* *
1545327 ATTGCAACG-ATAATACGTAAA
1 ATCGCAACGCGT-ATACGT-AA
*
1545348 ATCGCAACGAC-AATACGTAA
1 ATCGCAACG-CGTATACGTAA
1545368 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGCGTATAC-GTAA
* *
1545388 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
1545408 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* * *
1545428 ATCGCAATGTGAATACGTAA
1 ATCGCAACGCGTATACGTAA
1545448 ATCGCAACGCG
1 ATCGCAACGCG
1545459 ATTTTTAAAG
Statistics
Matches: 127, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
19 3 0.02
20 90 0.71
21 34 0.27
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:1545403 original size:40 final size:41
Alignment explanation
Indices: 1545286--1545458 Score: 208
Period size: 40 Copynumber: 4.3 Consensus size: 41
1545276 GATTCTGACT
* * * *
1545286 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
* * * *
1545327 ATTGCAACG-ATAATACGTAAAATCGCAACGACAATACGTAA
1 ATCGCAACGCGT-ATCCGTAAAATCGCAACGAGAATACGTAA
*
1545368 ATCGCAACGCGTATCTGT-AAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
* * *
1545408 ATCGCAATGCGTATCCGT-AAATCGCAATGTGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
1545448 ATCGCAACGCG
1 ATCGCAACGCG
1545459 ATTTTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
40 68 0.60
41 44 0.39
42 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
Found at i:1545954 original size:20 final size:20
Alignment explanation
Indices: 1545929--1545969 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1545919 TTCTAAACTT
*
1545929 AAAATCACAACATGAAAATG
1 AAAATCACAACACGAAAATG
**
1545949 AAAATCGTAACACGAAAATG
1 AAAATCACAACACGAAAATG
1545969 A
1 A
1545970 CTATTGCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:1546089 original size:20 final size:19
Alignment explanation
Indices: 1546058--1546114 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
1546048 ATTGCGATTT
1546058 TCATTTCGCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
**
1546077 TCATTTCCGCGTTGCGATTT
1 TCATTT-CGCGTTGCGATAG
*
1546097 TCATTCTCTCGTTGCGAT
1 TCATT-TCGCGTTGCGAT
1546115 TTTCATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.18
20 26 0.79
21 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:1546115 original size:20 final size:19
Alignment explanation
Indices: 1545992--1546123 Score: 123
Period size: 19 Copynumber: 7.1 Consensus size: 19
1545982 GAAACCAAAA
*
1545992 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1546011 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
1546030 TCGC-TACGCGA--TTC---
1 TCGCGT-TGCGATTTTCATT
* *
1546044 TCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1546063 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1546082 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
1546102 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1546122 TC
1 TC
1546124 AACCAAAAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
14 7 0.08
15 1 0.01
16 3 0.03
17 2 0.02
18 1 0.01
19 43 0.47
20 33 0.36
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1548071 original size:41 final size:42
Alignment explanation
Indices: 1548021--1548113 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 42
1548011 TCCACTCTAT
* *
1548021 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGTCCCTCCCAC
* * *
1548062 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
1548104 CATTCAAGAG
1 CGTTCAAGAG
1548114 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.09
41 20 0.45
42 20 0.45
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:1548112 original size:21 final size:21
Alignment explanation
Indices: 1548051--1548113 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1548041 TTCCTCGAGA
1548051 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
** * *
1548072 G-CCACTGTCATCGTTGAAGAG
1 GTCC-CTCCCACCGTTCAAGAG
*
1548093 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
1548114 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCGTTCAAGAG
Found at i:1549446 original size:14 final size:14
Alignment explanation
Indices: 1549424--1549462 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1549414 TTGATTGTTT
1549424 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1549438 AGA-TGATTTGTAAA
1 A-ATTGATTTGTAAA
1549452 AATTGATTTGT
1 AATTGATTTGT
1549463 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1549591 original size:19 final size:19
Alignment explanation
Indices: 1549569--1549627 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1549559 AAAAATGACT
1549569 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1549588 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1549602 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
1549621 ATCGCAA
1 ATCGCAA
1549628 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1549611 original size:33 final size:32
Alignment explanation
Indices: 1549569--1549658 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 32
1549559 AAAAATGACT
* *
1549569 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
1549602 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
*
1549635 ATCGCAACGCGAAACTAAAATCGC
1 ATCGCAATGCGAAA-TAAAATCGC
1549659 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 51 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:1549656 original size:19 final size:18
Alignment explanation
Indices: 1549601--1549658 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
1549591 GCAACGAGAG
*
1549601 AATCGCAATGCGAAATTAA
1 AATCGCAA-GCGAAACTAA
1549620 AATCGCAA-CG--AC-AA
1 AATCGCAAGCGAAACTAA
1549634 AATCGCAACGCGAAACTAA
1 AATCGCAA-GCGAAACTAA
1549653 AATCGC
1 AATCGC
1549659 GTTGCGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 2 0.06
19 16 0.48
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.14
Consensus pattern (18 bp):
AATCGCAAGCGAAACTAA
Found at i:1549675 original size:14 final size:14
Alignment explanation
Indices: 1549658--1549685 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1549648 ACTAAAATCG
1549658 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1549672 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1549686 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:1549779 original size:20 final size:20
Alignment explanation
Indices: 1549706--1549780 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
1549696 CGATTCTCTC
* *
1549706 GTTGCGATAGT-AATTTTCGC
1 GTTGCGATAGTCAA-TTACGT
* *
1549726 GTTGCGATAGAC-ATTAAGAT
1 GTTGCGATAGTCAATTACG-T
1549746 GATTGCGA-ACGTCAATTACGT
1 G-TTGCGATA-GTCAATTACGT
1549767 GTTGCGATAGTCAA
1 GTTGCGATAGTCAA
1549781 ATGAATGCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.07
20 24 0.56
21 11 0.26
22 5 0.12
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAATTACGT
Found at i:1553174 original size:20 final size:19
Alignment explanation
Indices: 1553153--1553406 Score: 155
Period size: 20 Copynumber: 12.9 Consensus size: 19
1553143 GCGATAGTCA
1553153 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
1553172 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
1553192 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
1553212 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
1553232 GGATACACATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
1553252 GTATTCTCGTTGCGATTT-C
1 G-AATCTCGTTGCGATTTAC
*
1553271 ----CGCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
*
1553286 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
1553306 GAATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
*
1553327 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
1553347 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
*
1553368 GGATACTCGTTGCGATAGTTA-
1 GAAT-CTCGTTGCGAT--TTAC
*
1553389 GAATCGCGTTGCGATTTA
1 GAATCTCGTTGCGATTTA
1553407 TATGTTCGCG
Statistics
Matches: 190, Mismatches: 26, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
14 12 0.06
15 1 0.01
18 4 0.02
19 6 0.03
20 123 0.65
21 38 0.20
22 6 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:1553305 original size:74 final size:75
Alignment explanation
Indices: 1553201--1553344 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 75
1553191 CGTATTCGCA
*
1553201 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACACATTGCGA-TTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGAATACACATTGCGATTTTACGTATTCTCGTTGC
1553265 GATTTCCGCG
66 GATTTCCGCG
* * * *
1553275 TTGCGATTTACGTATTCTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGAATACACATTGCGATTTTACGTATTCTCGTTGC
1553340 GATTT
66 GATTT
1553345 ACGGATACGC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 41 0.64
75 23 0.36
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (75 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGAATACACATTGCGATTTTACGTATTCTCGTTGC
GATTTCCGCG
Found at i:1553334 original size:41 final size:40
Alignment explanation
Indices: 1553159--1553425 Score: 273
Period size: 40 Copynumber: 6.8 Consensus size: 40
1553149 GTCAGAATCT
* * * *
1553159 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGAATACG
* * * * *
1553199 CATTGCGATTTACGTATTCGCATTGCGATTTACGGATACA
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
*
1553239 CATTGCGATTTACGTATTCTCGTTGCGATTT-C-----CG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
1553273 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
*
1553313 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGAATACG
* *
1553354 CGTTGCGATTTTACGGATACTCGTTGCGATAGTTA-GAAT-CG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT--TTACGAATACG
** * *
1553395 CGTTGCGATTTATATGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGTATTCTCGTTGCGATTT
1553426 TCATATTCGT
Statistics
Matches: 199, Mismatches: 18, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
34 31 0.16
35 1 0.01
38 2 0.01
39 2 0.01
40 88 0.44
41 69 0.35
42 3 0.02
43 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
Found at i:1553415 original size:20 final size:20
Alignment explanation
Indices: 1553392--1553444 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1553382 ATAGTTAGAA
*
1553392 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1553412 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
1553432 TCGTGTTGCGATT
1 TCGCGTTGCGATT
1553445 ATGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1553417 original size:61 final size:61
Alignment explanation
Indices: 1553271--1553426 Score: 156
Period size: 61 Copynumber: 2.5 Consensus size: 61
1553261 TTGCGATTTC
* * * * *
1553271 CGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGAATACGCGTTGCGATTTTACGTATT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTTACGAATACGCGTTGCGATGTTACGTAAT
* ** * * *
1553332 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTTA-G-AAT
1 CGCGTTGCGATTTAATG-TTCGCGTTGCGATTTTACGAATACGCGTTGCGAT-GTTACGTAAT
1553393 CGCGTTGCGATTTATATGTTCGCGTTGCGATTTT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTT
1553427 CATATTCGTG
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
61 53 0.69
62 21 0.27
63 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTAATGTTCGCGTTGCGATTTTACGAATACGCGTTGCGATGTTACGTAAT
Found at i:1556821 original size:2 final size:2
Alignment explanation
Indices: 1556814--1556873 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1556804 AGAGTCCTGA
1556814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556856 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1556874 GTGTGTGTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1577349 original size:5 final size:5
Alignment explanation
Indices: 1577339--1577376 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
1577329 ACCCTAATTA
* *
1577339 TTATT TTATT TTATT TTATT GTATT TAATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA
1577377 GTGTTTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:1577363 original size:15 final size:15
Alignment explanation
Indices: 1577333--1577373 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1577323 TATCAAACCC
*
1577333 TAATTATTATTTTATT
1 TAATT-TTATTGTATT
*
1577349 TTATTTTATTGTATT
1 TAATTTTATTGTATT
1577364 TAATTTTATT
1 TAATTTTATT
1577374 TTAGTGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TAATTTTATTGTATT
Found at i:1577606 original size:29 final size:29
Alignment explanation
Indices: 1577572--1577665 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 29
1577562 GTTGAGCAAC
*
1577572 AAATTTTCTTAACGGGAACGAGTCGAGTA
1 AAATTTTCTTAACGGGAACGAGTCGAGAA
*
1577601 AAA--TT-TTAACGAGCAACGAGTCGAGCAA
1 AAATTTTCTTAACG-GGAACGAGTCGAG-AA
* * * *
1577629 CAAATTTTCTTAATGAGCACGAGTCGAGCA
1 -AAATTTTCTTAACGGGAACGAGTCGAGAA
1577659 AAATTTT
1 AAATTTT
1577666 AACGAAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
26 6 0.12
27 14 0.27
28 1 0.02
29 13 0.25
30 1 0.02
31 12 0.23
32 5 0.10
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (29 bp):
AAATTTTCTTAACGGGAACGAGTCGAGAA
Found at i:1577612 original size:58 final size:58
Alignment explanation
Indices: 1577547--1577670 Score: 176
Period size: 58 Copynumber: 2.1 Consensus size: 58
1577537 ACTTAATGAG
** * * * *
1577547 TTTAACGAGTGACGGGTTGAGCAACAAATTTTCTTAACGGGAACGAGTCGAGTAAAAT
1 TTTAACGAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGAACGAGTCGAGCAAAAT
* *
1577605 TTTAACGAGCAACGAGTCGAGCAACAAATTTTCTTAATGAGCACGAGTCGAGCAAAAT
1 TTTAACGAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGAACGAGTCGAGCAAAAT
1577663 TTTAACGA
1 TTTAACGA
1577671 AATTAACGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (58 bp):
TTTAACGAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGAACGAGTCGAGCAAAAT
Found at i:1577653 original size:31 final size:31
Alignment explanation
Indices: 1577565--1577659 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
1577555 GTGACGGGTT
* *
1577565 GAGCAACAAATTTTCTTAACGGGAACGAGTC
1 GAGCAACAAATTTTCTTAACGAGCACGAGTC
*
1577596 GAG-TA-AAA--TT-TTAACGAGCAACGAGTC
1 GAGCAACAAATTTTCTTAACGAGC-ACGAGTC
*
1577623 GAGCAACAAATTTTCTTAATGAGCACGAGTC
1 GAGCAACAAATTTTCTTAACGAGCACGAGTC
1577654 GAGCAA
1 GAGCAA
1577660 AATTTTAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 7 0.13
27 12 0.23
28 1 0.02
29 6 0.11
30 1 0.02
31 18 0.34
32 8 0.15
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (31 bp):
GAGCAACAAATTTTCTTAACGAGCACGAGTC
Found at i:1577679 original size:29 final size:28
Alignment explanation
Indices: 1577588--1577680 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 28
1577578 TCTTAACGGG
* *
1577588 AACGAGTCGAGTAAAATTTTAACG-AGC
1 AACGAGTCGAGCAAAATTTTAACGAATC
* *
1577615 AACGAGTCGAGCAACAAATTTT--CTTAATG
1 AACGAGTCGAGC-A-AAATTTTAAC-GAATC
*
1577644 AGCACGAGTCGAGCAAAATTTTAACGAAATT
1 A--ACGAGTCGAGCAAAATTTTAACG-AATC
1577675 AACGAG
1 AACGAG
1577681 CAACGAGTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
27 12 0.24
28 1 0.02
29 21 0.41
30 1 0.02
31 16 0.31
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (28 bp):
AACGAGTCGAGCAAAATTTTAACGAATC
Found at i:1579619 original size:13 final size:13
Alignment explanation
Indices: 1579601--1579626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1579591 ATCTTTTTTG
1579601 TAAACCGTGAAAT
1 TAAACCGTGAAAT
1579614 TAAACCGTGAAAT
1 TAAACCGTGAAAT
1579627 GATCCACATG
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TAAACCGTGAAAT
Found at i:1582153 original size:419 final size:418
Alignment explanation
Indices: 1581376--1582219 Score: 1480
Period size: 419 Copynumber: 2.0 Consensus size: 418
1581366 GAGATAATTA
*
1581376 TCATTGTTTTCTCATTGGTAGATCGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTTTT
1 TCATTGTTTTCTCATTGGTAGATCGAGAAAAGTTGTAATTCCTATTTTCTCATAGTGAAATTTTT
1581441 CTACCGTTGCTTGTGGTTTTTACCCTATATTATTTAGGGGTTTCCACGTAAAATTTGTGTCTTCT
66 CTACCGTTGCTTGTGGTTTTTACCCTATATTATTTAGGGGTTTCCACGTAAAATTTGTGTCTTCT
*
1581506 TTATTTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTTGCTCTATTCGATAGCCGTATTCC
131 TTATTTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTTGCTCTATCCGATAGCCGTATTCC
*
1581571 GCAACAATTGGTATCCGAGCCAGATTTGAGTGTGTAAAATCTGCTTATTGCCTTTGTGGTTGACA
196 ACAACAATTGGTATCCGAGCCAGATTTGAGTGTGTAAAATCTGCTTATTGCCTTTGTGGTTGACA
* *
1581636 CCAAAAGGTGAATCCTCCAACATAAGAAAGTAAGAAGGTATTACTCATTCTTTGAAGGTTTCAGA
261 CCAAAAGGTGAATCCTCCAACATAAGAAAGTAAGAAGGTAATACTCATTCTTTGAAGGTTCCAGA
* *
1581701 GAACTATTTACGATAGTGAAATAGTGGGAGCTATCCGTAATAGAAGTTATGACAACTAAATTTGA
326 GAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAATAGAAGTTATGACAACGAAATTTGA
1581766 TATTGAAAAATTCAATGGGAGAAATTTC
391 TATTGAAAAATTCAATGGGAGAAATTTC
*
1581794 TCATTGTTTTCTCCTTGGTAGATCGAGAAAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTT
1 TCATTGTTTTCTCATTGGTAGATCGAGAAAAGTTGTAATTCCTATTTTCTCATAGTGAAATT-TT
*
1581859 T-TACTGTTGCCTT-TGGTTTTTACCCTATATTATTTAGGGGTTTTCCACGTAAAATTTGTGTCT
65 TCTACCGTTG-CTTGTGGTTTTTACCCTATATTATTTAGGGG-TTTCCACGTAAAATTTGTGTCT
1581922 TCTTTATTTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTTGCTCTATCCGATAGCCGTAT
128 TCTTTATTTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTTGCTCTATCCGATAGCCGTAT
* * *
1581987 TCCATAACAATTGGTATCCGAGCCAGATTTGAGTGTGTAATATCTGCTTATTGTCTTTGTGGTT-
193 TCCACAACAATTGGTATCCGAGCCAGATTTGAGTGTGTAAAATCTGCTTATTGCCTTTGTGGTTG
*
1582051 ACAACCAAAAGGTGGATCCTCCAACATAAGAAAGTAAGAAGGTAATA-TCCATTCTTTGAAGGTT
258 AC-ACCAAAAGGTGAATCCTCCAACATAAGAAAGTAAGAAGGTAATACT-CATTCTTTGAAGGTT
*
1582115 CCAGAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAATAGAAGTTATGGCAACGAAA
321 CCAGAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAATAGAAGTTATGACAACGAAA
1582180 TTTGATATTGAAAAATTCAATGGGAGAAATTTC
386 TTTGATATTGAAAAATTCAATGGGAGAAATTTC
*
1582213 ACATTGT
1 TCATTGT
1582220 GGAAATTGAA
Statistics
Matches: 406, Mismatches: 15, Indels: 9
0.94 0.03 0.02
Matches are distributed among these distances:
418 97 0.24
419 309 0.76
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (418 bp):
TCATTGTTTTCTCATTGGTAGATCGAGAAAAGTTGTAATTCCTATTTTCTCATAGTGAAATTTTT
CTACCGTTGCTTGTGGTTTTTACCCTATATTATTTAGGGGTTTCCACGTAAAATTTGTGTCTTCT
TTATTTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTTGCTCTATCCGATAGCCGTATTCC
ACAACAATTGGTATCCGAGCCAGATTTGAGTGTGTAAAATCTGCTTATTGCCTTTGTGGTTGACA
CCAAAAGGTGAATCCTCCAACATAAGAAAGTAAGAAGGTAATACTCATTCTTTGAAGGTTCCAGA
GAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAATAGAAGTTATGACAACGAAATTTGA
TATTGAAAAATTCAATGGGAGAAATTTC
Found at i:1584932 original size:20 final size:20
Alignment explanation
Indices: 1584907--1584949 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1584897 CCATTATTCC
* * *
1584907 ATAACCATATACTATAGATA
1 ATAACCATAAACAATAGACA
1584927 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
1584947 ATA
1 ATA
1584950 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:1585108 original size:60 final size:60
Alignment explanation
Indices: 1585015--1585200 Score: 266
Period size: 60 Copynumber: 3.1 Consensus size: 60
1585005 GTGCAATCTT
1585015 GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATATCTCCC
1 GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATATCTCCC
* * * *
1585075 GAATATGACATATAAGGTCGTGTTCACCATCTGTACTAGGTATCCTTAAGTACATCTCTC
1 GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATATCTCCC
* * * * * * *
1585135 GAATATGACACATAAGGTTGTGCCCACCATATATACTAGGTATCATTTAGTGTAT-TCCC
1 GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATATCTCCC
1585194 GAATATG
1 GAATATG
1585201 CAGCCTGCTG
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 10 0.09
60 101 0.91
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (60 bp):
GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATATCTCCC
Found at i:1585377 original size:22 final size:21
Alignment explanation
Indices: 1585346--1585386 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1585336 CTAAATAACA
*
1585346 TTCATGATAAAAATCATATGTG
1 TTCATAAT-AAAATCATATGTG
*
1585368 TTCATAATAACATCATATG
1 TTCATAATAAAATCATATG
1585387 CAAAAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (21 bp):
TTCATAATAAAATCATATGTG
Found at i:1590771 original size:2 final size:2
Alignment explanation
Indices: 1590764--1590808 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1590754 TTGATGTTAC
1590764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1590805 AT AT
1 AT AT
1590809 GAGTTGTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1591450 original size:30 final size:30
Alignment explanation
Indices: 1591416--1591518 Score: 197
Period size: 30 Copynumber: 3.4 Consensus size: 30
1591406 GGTTCTTCGG
*
1591416 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1591446 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1591476 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1591506 GACCTCTGGATAG
1 GACCTCTGGATAG
1591519 GTCCTTCGGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1592616 original size:19 final size:19
Alignment explanation
Indices: 1592592--1592630 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1592582 AGTTACGATT
1592592 TTGCTCTATCCGATAACCG
1 TTGCTCTATCCGATAACCG
*
1592611 TTGCTCTATCCGATAGCCG
1 TTGCTCTATCCGATAACCG
1592630 T
1 T
1592631 ATTCCGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (19 bp):
TTGCTCTATCCGATAACCG
Found at i:1597895 original size:212 final size:204
Alignment explanation
Indices: 1597512--1597933 Score: 763
Period size: 212 Copynumber: 2.0 Consensus size: 204
1597502 AAGCCTGTTA
1597512 TCATTGTATTTCTTCATTGTTATTAAAGAATTTGGCATTGTATTTATTTCATATTTATTTGAGGT
1 TCATTGTATTTCTTCATTGTTATTAAAGAATTTGGCATTGTATTTATTTCATATTTATTTGAGGT
1597577 TAAAAAGACGGGAGATGGTGATTGGAAGCATAGGTGGCAACATCATTATGGCAATTGACCGGGCT
66 TAAAAAGACGGGAGATGGTGATTGGAAGCATAGGTGGCAACATCATTATGGCAATTGACCGGGCT
1597642 ATTGATAGTCTCAAAGTGGAGAATTACAAGCAAAAGCTACCAATTAATTTCCCAAAACCTGGAGG
131 ATTGATAGTCTCAAAGTGGAGAATTACAAGCAAAAGCTACCAATTAATTTCCCAAAACCTGGAGG
1597707 AATAATAAC
196 AATAATAAC
*
1597716 TCATTTTATTTCTTCATTGTTATTAAAGAATTTGGCATTGTATTATTTATGTTCATATTTATTTG
1 TCATTGTATTTCTTCATTGTTATTAAAGAATTTGGCATTG---TATTTAT-TTCATATTTATTTG
1597781 AGGTTAAAAAAGACTGGGAGATGGTGATTGGAAGCATAGGTGGCAACATCATTATGGCAATTGAG
62 AGGTT-AAAAAGAC-GGGAGATGGTGATTGGAAGCATAGGTGGCAACATCATTATGGCAATTGA-
1597846 GCCGGGCTATTGATAGTCTCAAAGTGGAGAATTACAAGCAAAAGCTACCAATTAATTTCCCAAAA
124 -CCGGGCTATTGATAGTCTCAAAGTGGAGAATTACAAGCAAAAGCTACCAATTAATTTCCCAAAA
1597911 CCTGGAGGAATAATAAC
188 CCTGGAGGAATAATAAC
1597928 TCATTG
1 TCATTG
1597934 CTTTTGGATT
Statistics
Matches: 208, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
204 39 0.19
207 7 0.03
208 19 0.09
209 8 0.04
210 49 0.24
212 86 0.41
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (204 bp):
TCATTGTATTTCTTCATTGTTATTAAAGAATTTGGCATTGTATTTATTTCATATTTATTTGAGGT
TAAAAAGACGGGAGATGGTGATTGGAAGCATAGGTGGCAACATCATTATGGCAATTGACCGGGCT
ATTGATAGTCTCAAAGTGGAGAATTACAAGCAAAAGCTACCAATTAATTTCCCAAAACCTGGAGG
AATAATAAC
Found at i:1602248 original size:126 final size:126
Alignment explanation
Indices: 1602093--1602331 Score: 451
Period size: 126 Copynumber: 1.9 Consensus size: 126
1602083 TACTGAAAAC
* *
1602093 CATGAAACAGTTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAATCAAATATCAAATT
1 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
1602158 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
66 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
1602219 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
1 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
*
1602284 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTATCTACAGT
66 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGT
1602332 TTCTACACAC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (126 bp):
CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
Found at i:1603379 original size:15 final size:15
Alignment explanation
Indices: 1603354--1603388 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1603344 ACGTGTATAT
1603354 CGCGC-CCCCTGATC
1 CGCGCTCCCCTGATC
1603368 CGCGCTCCCCTGATC
1 CGCGCTCCCCTGATC
1603383 CGCGCT
1 CGCGCT
1603389 ATACGCCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.06, C:0.54, G:0.23, T:0.17
Consensus pattern (15 bp):
CGCGCTCCCCTGATC
Found at i:1606974 original size:16 final size:17
Alignment explanation
Indices: 1606963--1607003 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
1606953 AAATTATATT
1606963 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
1606980 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
1606998 ATTAAA
1 AGTAAA
1607004 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:1606995 original size:18 final size:18
Alignment explanation
Indices: 1606963--1607016 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
1606953 AAATTATATT
1606963 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1606980 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
* *
1606998 A-TTAAATACATAATATAA
1 AGTAAAATACTTAA-ATAA
1607016 A
1 A
1607017 ATATATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1608429 original size:104 final size:107
Alignment explanation
Indices: 1608201--1608464 Score: 304
Period size: 104 Copynumber: 2.5 Consensus size: 107
1608191 TTAGAAATCA
* * * *
1608201 ACAATAACAAAATAGGTTAATTAATTAATTTGTTATCAATAATATCAACATATTAAATAGCACCT
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAAATAGCACCT
* * *
1608266 AAAATACTATCAAAATTTAAGCTGACATGGCCTTAAAAATCTG
66 AAAATACTACCAAAATTTAAGCTGA-ATGGCATTAAAAATCTC
* * * * ** *
1608309 ACCATAA-GAAATATGTTAATTACTTATTTTGTTATTAATATTATC-ACATATTAGGTAGCATCT
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAAATAGCACCT
* *
1608372 AAAAT-GTACCAAAATTTAAGCTG-GTGGGCATT-AAAATCTC
66 AAAATACTACCAAAATTTAAGCTGAAT-GGCATTAAAAATCTC
* *
1608412 ACAATAACAAAATATGTTAATTTCTTATTTTGTTATAAATAAATATTAACATA
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAAT-AATATCAACATA
1608465 CTAGGTTGCA
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
103 14 0.11
104 34 0.26
105 20 0.15
106 25 0.19
107 32 0.24
108 6 0.05
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (107 bp):
ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAAATAGCACCT
AAAATACTACCAAAATTTAAGCTGAATGGCATTAAAAATCTC
Found at i:1608679 original size:16 final size:17
Alignment explanation
Indices: 1608658--1608692 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1608648 TTAGAGTAAG
1608658 TATGGATAC-TTATTAT
1 TATGGATACATTATTAT
1608674 TATGGATACATTATTAT
1 TATGGATACATTATTAT
1608691 TA
1 TA
1608693 ACATTTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
TATGGATACATTATTAT
Found at i:1609041 original size:23 final size:23
Alignment explanation
Indices: 1608996--1609044 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1608986 GTAACACTTA
* * * *
1608996 TTAACGTAATAGGTAGTGTCTAT
1 TTAACATAATAGGCAGCGCCTAT
1609019 TTAACATAATAGGCAGCGCCTAT
1 TTAACATAATAGGCAGCGCCTAT
1609042 TTA
1 TTA
1609045 TTTTATCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TTAACATAATAGGCAGCGCCTAT
Found at i:1609173 original size:74 final size:71
Alignment explanation
Indices: 1609037--1609342 Score: 260
Period size: 74 Copynumber: 4.2 Consensus size: 71
1609027 ATAGGCAGCG
* * *
1609037 CCTA-TTTATTTTATCG-TACATATTAATAGCCTTTAAAAAAAACCGGTAGATATTTAACGTAAT
1 CCTATTTTATTTTA-CGTTACATATTAGTAACCTTT-AAAAAAACCGATAGATATTTAACGTAAT
1609100 AGATAACA
64 AGATAACA
* * * *
1609108 CCTATTTT-TTTTACTGTTTACATTATTATTAACCTTTAAAAAAACAGATAGCTAGTTTAATGTA
1 CCTATTTTATTTTAC-G-TTACA-TATTAGTAACCTTTAAAAAAACCGATAGATA-TTTAACGTA
* *
1609172 ATAGATAGCG
62 ATAGATAACA
* * * * *
1609182 CTTATTTTATTTTACCATTACATATTAGTAACCTTTAAACAAACCTATAGGTATTTTAACGTAAT
1 CCTATTTTATTTTA-CGTTACATATTAGTAACCTTTAAAAAAACCGATAGATA-TTTAACGTAAT
* *
1609247 AGGTATCA
64 AGATAACA
* * ** * *
1609255 CCTATTTTATTTTACCGTTACATTATTAGTAAACTTCAAAAAAATTGGTAGGCA-ATTTAACATA
1 CCTATTTTATTTTA-CGTTACA-TATTAGTAACCTTTAAAAAAACCGATA-G-ATATTTAACGTA
*
1609319 ATATATAACA
62 ATAGATAACA
*
1609329 TCTATTTTATTTTA
1 CCTATTTTATTTTA
1609343 ACGGTTAAGT
Statistics
Matches: 189, Mismatches: 35, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
70 1 0.01
71 10 0.05
72 3 0.02
73 79 0.42
74 88 0.47
75 7 0.04
76 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (71 bp):
CCTATTTTATTTTACGTTACATATTAGTAACCTTTAAAAAAACCGATAGATATTTAACGTAATAG
ATAACA
Found at i:1609321 original size:147 final size:145
Alignment explanation
Indices: 1609017--1609321 Score: 337
Period size: 147 Copynumber: 2.1 Consensus size: 145
1609007 GGTAGTGTCT
* * *
1609017 ATTTAACATAATAGGCAGCGCCTATTTATTTTATCGTACATATTAATAGCCTTTAAAAAAAACCG
1 ATTTAACATAATAGACAGCGCCTATTTATTTTACCGTACATATTAATAACCTTTAAAAAAAACCG
* * * * *
1609082 GTAGATATTTAACGTAATAGATAACACCTATTTTTTTTACTGTTTACATTATTATTAACCTTTAA
66 ATAGATATTTAACGTAATAGATAACACCTATTTTTTTTACCGTTTACATTATTAGTAAACTTCAA
1609147 AAAAACAGATAGCTA
131 AAAAACAGATAGCTA
* ** * * * * *
1609162 GTTTAATGTAATAGATAGCGCTTATTTTATTTTACCATTACATATTAGTAACCTTT-AAACAAAC
1 ATTTAACATAATAGACAGCGCCTA-TTTATTTTACC-GTACATATTAATAACCTTTAAAAAAAAC
* * * *
1609226 CTATAGGTATTTTAACGTAATAGGTATCACCTATTTTATTTTACCG-TTACATTATTAGTAAACT
64 CGATAGATA-TTTAACGTAATAGATAACACCTATTTT-TTTTACCGTTTACATTATTAGTAAACT
** *
1609290 TCAAAAAAATTGGTAGGC-A
127 TCAAAAAAACAGATA-GCTA
1609309 ATTTAACATAATA
1 ATTTAACATAATA
1609322 TATAACATCT
Statistics
Matches: 129, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
145 18 0.14
146 23 0.18
147 79 0.61
148 9 0.07
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (145 bp):
ATTTAACATAATAGACAGCGCCTATTTATTTTACCGTACATATTAATAACCTTTAAAAAAAACCG
ATAGATATTTAACGTAATAGATAACACCTATTTTTTTTACCGTTTACATTATTAGTAAACTTCAA
AAAAACAGATAGCTA
Found at i:1620405 original size:126 final size:126
Alignment explanation
Indices: 1620180--1620418 Score: 451
Period size: 126 Copynumber: 1.9 Consensus size: 126
1620170 TACTGAAAAC
* *
1620180 CATGAAACAGTTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAATCAAATATCAAATT
1 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
1620245 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
66 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
1620306 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
1 CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
*
1620371 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTATCTACAGT
66 ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGT
1620419 TTCTACACAC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (126 bp):
CATGAAACAATTATCACCTTAAGTCTAAAGAACATCAAACCATATACCAAACCAAATATCAAATT
ACAAATATTCATCTTAAGTGGCCAATTACACATATTTCTAACTACAGTCACAGTTTTTGCA
Found at i:1621476 original size:15 final size:15
Alignment explanation
Indices: 1621450--1621485 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1621440 CGTGTGTATA
1621450 TCGCGC-CCCCTGAT
1 TCGCGCTCCCCTGAT
1621464 TCGCGCTCCCCTGAT
1 TCGCGCTCCCCTGAT
*
1621479 CCGCGCT
1 TCGCGCT
1621486 ATACGCCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.06, C:0.50, G:0.22, T:0.22
Consensus pattern (15 bp):
TCGCGCTCCCCTGAT
Found at i:1625312 original size:19 final size:19
Alignment explanation
Indices: 1625240--1625313 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 19
1625230 AAAAAATTAT
1625240 ATTAGTAAAATATTAAATAA
1 ATTA-TAAAATATTAAATAA
*
1625260 AGTA-AAAATACTTAAATAA
1 ATTATAAAATA-TTAAATAA
1625279 ATTAAATACATAATATTAAA-AA
1 ATT--ATA-A-AATATTAAATAA
1625301 TATTATAAAATAT
1 -ATTATAAAATAT
1625314 ACCTTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
18 6 0.13
19 15 0.33
20 4 0.09
21 4 0.09
22 3 0.07
23 9 0.20
24 4 0.09
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTATAAAATATTAAATAA
Found at i:1626548 original size:217 final size:218
Alignment explanation
Indices: 1626106--1626549 Score: 569
Period size: 218 Copynumber: 2.0 Consensus size: 218
1626096 GTTATTTATA
* * * * **
1626106 TTATCAACATATTAGGTAGCACCTAAAATATTATCAAAGTTTAAGCTGATAGAGCCTTAGAAATT
1 TTATCAATATATTAGGTAGCACCTAAAATATTACCAAAGTTTAAACTGATAGAACAATAGAAATT
* * * *
1626171 CGACGATAACGAAATAGGTTAACTACTAGAAACATAATCAACTATAAATAACATAACAATTAGCG
66 CGACGATAACAAAATAGGTTAACTACTAGAAACATAATCAACCATAAATAACATAACAAGTAACG
* * * *
1626236 TTAATTTAAAGTAATAAGTAGCTCATTTTAAAGGCTGATGGGGTCTTAGAAATCATACTATAACA
131 TTAATTTAAACTAATAAGTAGCGCATTTTAAAGGCTGATGGGCTCTTAGAAATCATACAATAACA
* * *
1626301 AAATTGGTTAATTACTTGATTTG
196 AAATAGGTTAATTAATTAATTTG
* *
1626324 TTATCAATATATTAGGTAGCACGTAAAATGTTACCAAAGTTTAAACTGAT-GAAACAATAGAAA-
1 TTATCAATATATTAGGTAGCACCTAAAATATTACCAAAGTTTAAACTGATAG-AACAATAGAAAT
* * *
1626387 TCTGACGATAACAAAATATGTTAATTACTAGAAACATTATCAACCAT-AATAACATAACAAGTAA
65 TC-GACGATAACAAAATAGGTTAACTACTAGAAACATAATCAACCATAAATAACATAACAAGTAA
* *
1626451 CGCTT-ATTTAATCTAATATGTAGCGCATTTTTAAA-GCTGATGGGACT-TTAGAAATCCA-ACA
129 CG-TTAATTTAAACTAATAAGTAGCGCA-TTTTAAAGGCTGATGGG-CTCTTAGAAAT-CATACA
1626512 ATAACAAAATAGGTTAATTAATTAATTTG
190 ATAACAAAATAGGTTAATTAATTAATTTG
1626541 TTATCAATA
1 TTATCAATA
1626550 ATATCAACAT
Statistics
Matches: 196, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
217 92 0.47
218 104 0.53
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (218 bp):
TTATCAATATATTAGGTAGCACCTAAAATATTACCAAAGTTTAAACTGATAGAACAATAGAAATT
CGACGATAACAAAATAGGTTAACTACTAGAAACATAATCAACCATAAATAACATAACAAGTAACG
TTAATTTAAACTAATAAGTAGCGCATTTTAAAGGCTGATGGGCTCTTAGAAATCATACAATAACA
AAATAGGTTAATTAATTAATTTG
Found at i:1626678 original size:108 final size:107
Alignment explanation
Indices: 1626509--1626788 Score: 326
Period size: 108 Copynumber: 2.6 Consensus size: 107
1626499 TAGAAATCCA
* * * * **
1626509 ACAATAACAAAATAGGTTAATTAATTAATTTGTTATCAATAATATCAACATATTAAATAGCACCT
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAGGTAGCACCT
* * * *
1626574 AAAATACTATCAAAATTTAAGCTGACATGGCCTTAAAAATCTG
66 AAAATACTACCAAAATTTAAGCTGACAGGGCATT-AAAATCTC
* * * * *
1626617 ACCATAAGAAAATATGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAGCATCT
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAGGTAGCACCT
** ***
1626682 AAAATGTTACCAAAATTTAAGCTGGTGGGGCATTAAAATCTC
66 AAAATACTACCAAAATTTAAGCTGACAGGGCATTAAAATCTC
* * * *
1626724 ACAATAACAAAATATGTTAATTTCTTATTTTGTTATAAATAAATATTAACATACTAGGTTGCACC
1 ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAAT-AATATCAACATATTAGGTAGCACC
1626789 CAATAATGTT
Statistics
Matches: 143, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
107 43 0.30
108 100 0.70
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (107 bp):
ACAATAACAAAATATGTTAATTACTTATTTTGTTATAAATAATATCAACATATTAGGTAGCACCT
AAAATACTACCAAAATTTAAGCTGACAGGGCATTAAAATCTC
Found at i:1626994 original size:17 final size:17
Alignment explanation
Indices: 1626972--1627007 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1626962 TTAGAGTAAG
1626972 TATGGATACATTATTAT
1 TATGGATACATTATTAT
1626989 TATGGATACATTATTAT
1 TATGGATACATTATTAT
1627006 TA
1 TA
1627008 ACATTTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (17 bp):
TATGGATACATTATTAT
Found at i:1627183 original size:155 final size:156
Alignment explanation
Indices: 1626989--1627268 Score: 429
Period size: 155 Copynumber: 1.8 Consensus size: 156
1626979 ACATTATTAT
* * *
1626989 TATGGATACATTATTATTAACATTTAGAGTATACTTACTTTTAGAGGAAGTA-TCTATACTTTCG
1 TATGGATACATTATTATTAACATTTAGAGTATACATACTTTTAGAGGAAGTATTC-ATAATTTCA
**** *
1627053 AATTTTTTTAAAAAATATTTCAAACGGTTAAGTTGTATATA-TTTTACCGTTTATATTATTGACG
65 AATTTAAAAAAAAAATATTTCAAACGGTTAAGTTGTATATATTTTTACCGTTTACATTATTGACG
1627117 AAACAATATCCATACTTGTAGAGTAAG
130 AAACAATATCCATACTTGTAGAGTAAG
* * *
1627144 TATGGATACATTATTATTAACCTTTAGAGTATCCATACTTTTAGAGTAAGTATTCATAATTTCAA
1 TATGGATACATTATTATTAACATTTAGAGTATACATACTTTTAGAGGAAGTATTCATAATTTCAA
*
1627209 ATTTAAAAAAAAAATATTTCAAATGGTTAAGTTGTATATATTTTTACCGTTTACATTATT
66 ATTTAAAAAAAAAATATTTCAAACGGTTAAGTTGTATATATTTTTACCGTTTACATTATT
1627269 ATTAACATTT
Statistics
Matches: 111, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
155 91 0.82
156 20 0.18
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (156 bp):
TATGGATACATTATTATTAACATTTAGAGTATACATACTTTTAGAGGAAGTATTCATAATTTCAA
ATTTAAAAAAAAAATATTTCAAACGGTTAAGTTGTATATATTTTTACCGTTTACATTATTGACGA
AACAATATCCATACTTGTAGAGTAAG
Found at i:1627366 original size:23 final size:23
Alignment explanation
Indices: 1627318--1627368 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1627308 ATGTAACACT
* * * *
1627318 TATTTAACGTAATAGGTAGTGTC
1 TATTTAACATAATAGGCAGCGCC
1627341 TATTTAACATAATAGGCAGCGCC
1 TATTTAACATAATAGGCAGCGCC
1627364 TATTT
1 TATTT
1627369 TATTTTATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (23 bp):
TATTTAACATAATAGGCAGCGCC
Found at i:1627445 original size:75 final size:75
Alignment explanation
Indices: 1627362--1627675 Score: 358
Period size: 75 Copynumber: 4.2 Consensus size: 75
1627352 ATAGGCAGCG
* * * * *
1627362 CCTATTTTATTTTATCGTTTACATTATTAATAGCCTTTAAAAAAACCGGTAGATATTTTAACGTA
1 CCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAAAAAACCGATAGGTATTTTAACGTA
1627427 ATAGATAACA
66 ATAGATAACA
* * * * * * *
1627437 CCTATTTTATTTTACTGTTTACATTATTATTAACCTTTAAACAAACAGATAGCTAGTTTAATGTA
1 CCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAAAAAACCGATAGGTATTTTAACGTA
* *
1627502 ATAGATAGCG
66 ATAGATAACA
* * * *
1627512 CTTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCTATAGGTATTTTAACGTA
1 CCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAAAAAACCGATAGGTATTTTAACGTA
* *
1627577 ATAGGTATCA
66 ATAGATAACA
* * ** * * * *
1627587 CCTATTTTATTTTACCGTTTACATTATTAGTAAACTTCAAAAAAATTGGTAGGCAATTTAACATA
1 CCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAAAAAACCGATAGGTATTTTAACGTA
*
1627652 ATATATAACA
66 ATAGATAACA
*
1627662 TCTATTTTATTTTA
1 CCTATTTTATTTTA
1627676 ACCGGTTAAG
Statistics
Matches: 199, Mismatches: 40, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 199 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (75 bp):
CCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAAAAAACCGATAGGTATTTTAACGTA
ATAGATAACA
Found at i:1627647 original size:150 final size:150
Alignment explanation
Indices: 1627358--1627631 Score: 395
Period size: 150 Copynumber: 1.8 Consensus size: 150
1627348 CATAATAGGC
* * * *
1627358 AGCGCCTATTTTATTTTATCGTTTACATTATTAATAGCCTTTAAAAAAACCGGTAGATATTTTAA
1 AGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAACCGATAGATATTTTAA
* * * * *
1627423 CGTAATAGATAACACCTATTTTATTTTACTGTTTACATTATTATTAACCTTTAAACAAACAGATA
66 CGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAACTTCAAAAAAACAGATA
*
1627488 GCTAGTTTAATGTAATAGAT
131 GCTAATTTAATGTAATAGAT
* * * * *
1627508 AGCGCTTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCTATAGGTATTTTAA
1 AGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAACCGATAGATATTTTAA
* *
1627573 CGTAATAGGTATCACCTATTTTATTTTACCGTTTACATTATTAGTAAACTTCAAAAAAA
66 CGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAACTTCAAAAAAA
1627632 TTGGTAGGCA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
150 108 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (150 bp):
AGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAACCGATAGATATTTTAA
CGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAACTTCAAAAAAACAGATA
GCTAATTTAATGTAATAGAT
Found at i:1627654 original size:150 final size:150
Alignment explanation
Indices: 1627342--1627654 Score: 394
Period size: 150 Copynumber: 2.1 Consensus size: 150
1627332 GGTAGTGTCT
* * * *
1627342 ATTTAACATAATAGGCAGCGCCTATTTTATTTTATCGTTTACATTATTAATAGCCTTTAAAAAAA
1 ATTTAACATAATAGACAGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAA
* * * *
1627407 CCGGTAGATATTTTAACGTAATAGATAACACCTATTTTATTTTACTGTTTACATTATTATTAACC
66 CCGATAGATATTTTAACGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAAC
* *
1627472 TTTAAACAAACAGATAGCTA
131 TTCAAAAAAACAGATAGCTA
* ** * * * *
1627492 GTTTAATGTAATAGATAGCGCTTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAA
1 ATTTAACATAATAGACAGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAA
* * * *
1627557 CCTATAGGTATTTTAACGTAATAGGTATCACCTATTTTATTTTACCGTTTACATTATTAGTAAAC
66 CCGATAGATATTTTAACGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAAC
** *
1627622 TTCAAAAAAATTGGTAGGC-A
131 TTCAAAAAAACAGATA-GCTA
1627642 ATTTAACATAATA
1 ATTTAACATAATA
1627655 TATAACATCT
Statistics
Matches: 135, Mismatches: 27, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
150 133 0.99
151 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (150 bp):
ATTTAACATAATAGACAGCGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAAAAAA
CCGATAGATATTTTAACGTAATAGATAACACCTATTTTATTTTACCGTTTACATTATTAGTAAAC
TTCAAAAAAACAGATAGCTA
Found at i:1633921 original size:20 final size:20
Alignment explanation
Indices: 1633896--1633956 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1633886 TTTTGGTGCA
*
1633896 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
1633916 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
1633937 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
1633957 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1641816 original size:21 final size:23
Alignment explanation
Indices: 1641781--1641841 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1641771 TTGGTGCAGA
*
1641781 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
1641801 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
1641824 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
1641842 CAGGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:1641848 original size:21 final size:21
Alignment explanation
Indices: 1641822--1641861 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1641812 CCCCCTTTGA
*
1641822 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1641843 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1641862 TGGGGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1644094 original size:16 final size:16
Alignment explanation
Indices: 1644073--1644105 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1644063 AGAAGTGTTT
1644073 TAAGTGTGTTTAAAAA
1 TAAGTGTGTTTAAAAA
*
1644089 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTAAAAA
1644105 T
1 T
1644106 GATAAATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
TAAGTGTGTTTAAAAA
Found at i:1648057 original size:52 final size:52
Alignment explanation
Indices: 1647987--1648092 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
1647977 TTACTTGATA
* *
1647987 ATTTAATCATTTTTGTAATGTTGTGTTTAAAATAGACAGATTATATGCTAGT
1 ATTTAATCATTTTCGTAATGTTGTGTTTAAAATAGACAAATTATATGCTAGT
* *
1648039 ATTTAATCGTTTTCGTAATGTTGTGTTTAAAATAGACAAATTATATGCTTGT
1 ATTTAATCATTTTCGTAATGTTGTGTTTAAAATAGACAAATTATATGCTAGT
1648091 AT
1 AT
1648093 ACAAGTCACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (52 bp):
ATTTAATCATTTTCGTAATGTTGTGTTTAAAATAGACAAATTATATGCTAGT
Found at i:1649121 original size:13 final size:13
Alignment explanation
Indices: 1649103--1649128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1649093 TTGTACTTGG
1649103 ATTCTTTACAAGT
1 ATTCTTTACAAGT
1649116 ATTCTTTACAAGT
1 ATTCTTTACAAGT
1649129 TCCTTAACTT
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:0.08, T:0.46
Consensus pattern (13 bp):
ATTCTTTACAAGT
Found at i:1657032 original size:156 final size:157
Alignment explanation
Indices: 1656747--1657059 Score: 610
Period size: 156 Copynumber: 2.0 Consensus size: 157
1656737 ATTCTATGTA
*
1656747 GCCTCAGCCTGTCAAGAAAAGTCTGTCACTAAATTAGGTTTATGCAATACAATCTGGTTATGTCA
1 GCCTCAGCCTGTCAAGAAAAGTCTGTCACTAAATTAGGTTTATGCAATACAATCCGGTTATGTCA
1656812 ATGCGAGGCCAATACCCTAGCAACCAGAAGCATCCCACGAGCTACTGTGGATGGTAAGATGGATG
66 ATGCGAGGCCAATACCCTAGCAACCAGAAGCATCCCACGAGCTACTGTGGATGGTAAGATGGATG
1656877 GTATTGTGGCGATAAACCATATGCACC
131 GTATTGTGGCGATAAACCATATGCACC
1656904 GCCTCAGCCTGTCAAGAAAAGTC-GTCACTAAATTAGGTTTATGCAATACAATCCGGTTATGTCA
1 GCCTCAGCCTGTCAAGAAAAGTCTGTCACTAAATTAGGTTTATGCAATACAATCCGGTTATGTCA
1656968 ATGCGAGGCCAATACCCTAGCAACCAGAAGCATCCCACGAGCTACTGTGGATGGTAAGATGGATG
66 ATGCGAGGCCAATACCCTAGCAACCAGAAGCATCCCACGAGCTACTGTGGATGGTAAGATGGATG
1657033 GTATTGTGGCGATAAACCATATGCACC
131 GTATTGTGGCGATAAACCATATGCACC
1657060 ATAAGGAGGT
Statistics
Matches: 155, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
156 132 0.85
157 23 0.15
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (157 bp):
GCCTCAGCCTGTCAAGAAAAGTCTGTCACTAAATTAGGTTTATGCAATACAATCCGGTTATGTCA
ATGCGAGGCCAATACCCTAGCAACCAGAAGCATCCCACGAGCTACTGTGGATGGTAAGATGGATG
GTATTGTGGCGATAAACCATATGCACC
Found at i:1658763 original size:12 final size:12
Alignment explanation
Indices: 1658738--1658771 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1658728 AAAAAATTCC
*
1658738 TTTGAATTGGTT
1 TTTGAATTGTTT
*
1658750 TTTGAGTTGTTT
1 TTTGAATTGTTT
1658762 TTTGAATTGT
1 TTTGAATTGT
1658772 ATTAACCTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.62
Consensus pattern (12 bp):
TTTGAATTGTTT
Found at i:1660872 original size:58 final size:57
Alignment explanation
Indices: 1660675--1660917 Score: 208
Period size: 58 Copynumber: 4.2 Consensus size: 57
1660665 TGACCAATTA
* * * * *
1660675 ATTTTCCTTACCAAA-TTAAAATCATTTAAGATT-TCCAAGGAAAGAAATTCAATAATTT
1 ATTTTCCTTA-CAAAGTTATAATCATTAAAGATTCT-CAAGAAAAAAAATTCAA-CATTT
* *
1660733 ATTTTCCTTACAAAGTTATAATCATTTAAGATTCTCAAGAAAATAAATTCAACATTCT
1 ATTTTCCTTACAAAGTTATAATCATTAAAGATTCTCAAGAAAAAAAATTCAACATT-T
* *
1660791 ATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTTAAGAAAAAAAA-TCTAACTATTT
1 ATTTTCCTTACAAAGTTATAATCATTAAAGATTCTCAAGAAAAAAAATTC-AAC-ATTT
* * ** * * *
1660849 GTTTTCCTTA-AGAAGCTATAATCAACACAAGATTCTAACAATAAAATAAATTCAATGATTT
1 ATTTTCCTTACA-AAGTTATAATCATTA-AAGATTCT--CAAGAAAAAAAATTCAA-CATTT
1660910 A-TTTCCTT
1 ATTTTCCTT
1660918 TATATTATGT
Statistics
Matches: 156, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
57 10 0.06
58 110 0.71
59 12 0.08
60 7 0.04
61 15 0.10
62 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (57 bp):
ATTTTCCTTACAAAGTTATAATCATTAAAGATTCTCAAGAAAAAAAATTCAACATTT
Found at i:1661093 original size:45 final size:45
Alignment explanation
Indices: 1661020--1661182 Score: 163
Period size: 45 Copynumber: 3.6 Consensus size: 45
1661010 GAATTAATCA
* * *
1661020 TTTAATTTAC-CAATCCAATAATCAAAAGGAATTAATCCTTTGAT
1 TTTAATTTTCACACTCCAATAATCAAAAGGAACTAATCCTTTGAT
* * * *
1661064 TTTAATTTTCACACTCCTATAATCGAAAGGAACTGATCCTTTTAT
1 TTTAATTTTCACACTCCAATAATCAAAAGGAACTAATCCTTTGAT
* * *
1661109 TTTACTTTTTGCA-AC-ACAATAATCAAAAGGAACTAATCATTTGAT
1 TTTA-ATTTT-CACACTCCAATAATCAAAAGGAACTAATCCTTTGAT
* *
1661154 TTTACTTTTGACAAC-CCAATAATCAAAAG
1 TTTAATTTTCAC-ACTCCAATAATCAAAAG
1661183 CCTTAGATTA
Statistics
Matches: 97, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 13 0.13
45 75 0.77
46 6 0.06
47 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (45 bp):
TTTAATTTTCACACTCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:1662629 original size:18 final size:20
Alignment explanation
Indices: 1662595--1662638 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1662585 AAAAATAGAT
*
1662595 TTTAAAAATATATTCTC-TA
1 TTTAAAAAAATATTCTCATA
1662614 TTTAAAAAAATA-TCTCATA
1 TTTAAAAAAATATTCTCATA
1662633 TTTAAA
1 TTTAAA
1662639 TTAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAAAAAATATTCTCATA
Found at i:1665407 original size:24 final size:24
Alignment explanation
Indices: 1665363--1665413 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1665353 TATATAAACA
*
1665363 AAGAAACATAGGCAATGTTCAGTG
1 AAGAAACATAGGCAATGTTCAATG
1665387 AAGAAACATAGGCAA-GTTTCAATG
1 AAGAAACATAGGCAATG-TTCAATG
1665411 AAG
1 AAG
1665414 GCATTGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (24 bp):
AAGAAACATAGGCAATGTTCAATG
Found at i:1666214 original size:25 final size:25
Alignment explanation
Indices: 1666186--1666245 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 25
1666176 AGTTCCCAAC
1666186 TTTTTTAGTACAATAAGGTATCTAAT
1 TTTTTTAGTACAATAAGGTA-CTAAT
* *
1666212 TTTTTAATAGTACAATTAGGTACTTAT
1 TTTTT--TAGTACAATAAGGTACTAAT
1666239 TTTTTTA
1 TTTTTTA
1666246 ATTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.07
26 5 0.17
27 9 0.30
28 14 0.47
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.52
Consensus pattern (25 bp):
TTTTTTAGTACAATAAGGTACTAAT
Found at i:1666247 original size:28 final size:28
Alignment explanation
Indices: 1666191--1666243 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1666181 CCAACTTTTT
1666191 TAGTACAATAAGGTATCTAATTTTTTAA
1 TAGTACAATAAGGTATCTAATTTTTTAA
* *
1666219 TAGTACAATTAGGTA-CTTATTTTTT
1 TAGTACAATAAGGTATCTAATTTTTT
1666244 TAATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (28 bp):
TAGTACAATAAGGTATCTAATTTTTTAA
Found at i:1668993 original size:28 final size:28
Alignment explanation
Indices: 1668939--1668993 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1668929 TGCTATTTAA
*
1668939 TCGTATCGTATTGTATTTTAATTATTTT
1 TCGTATCGTATTGTATTTTAATAATTTT
* *
1668967 TCGTATGGTATTGTGTTTTTAA-AATTT
1 TCGTATCGTATTGT-ATTTTAATAATTT
1668994 GCTCAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.58
Consensus pattern (28 bp):
TCGTATCGTATTGTATTTTAATAATTTT
Found at i:1676154 original size:16 final size:16
Alignment explanation
Indices: 1676130--1676163 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1676120 TATCGCCGAC
*
1676130 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1676146 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1676162 CG
1 CG
1676164 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1683979 original size:17 final size:17
Alignment explanation
Indices: 1683954--1684016 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
1683944 ATGAAAACAT
*
1683954 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
1683971 TTAATGAACCAGTTTAAA
1 TTAATGAACTAGTTT-AA
*
1683989 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
1684006 TTAGTGAACTA
1 TTAATGAACTA
1684017 TCTTTATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:1683996 original size:18 final size:18
Alignment explanation
Indices: 1683959--1684005 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1683949 AACATTTAAA
*
1683959 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
1683976 GAACCAGTTTAAATGAAT
1 GAACTAGTTTAAATGAAT
1683994 GAACTAGTTTAA
1 GAACTAGTTTAA
1684006 TTAGTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:1693863 original size:2 final size:2
Alignment explanation
Indices: 1693856--1693881 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1693846 CAAATCTTTC
1693856 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1693882 TAATATGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1693966 original size:20 final size:20
Alignment explanation
Indices: 1693941--1693978 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1693931 TACTAAAATA
*
1693941 ACAATATTAAAAAATAAAGG
1 ACAATAATAAAAAATAAAGG
*
1693961 ACAATAATAAAAATTAAA
1 ACAATAATAAAAAATAAA
1693979 ATAAAATTAT
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:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
ACAATAATAAAAAATAAAGG
Found at i:1695153 original size:11 final size:11
Alignment explanation
Indices: 1695127--1695161 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
1695117 ATTATTTGTA
1695127 ATAATAATATAT
1 ATAATAATA-AT
1695139 ATAATAATAAT
1 ATAATAATAAT
1695150 ATAATAATAAT
1 ATAATAATAAT
1695161 A
1 A
1695162 ATTTCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:1695181 original size:3 final size:3
Alignment explanation
Indices: 1695125--1695163 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1695115 GTATTATTTG
1695125 TAA TAA TAA T-A TATA TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA T
1695164 TTCTTATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1695399 original size:21 final size:21
Alignment explanation
Indices: 1695284--1695399 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
1695274 GCGAAATAAA
**
1695284 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1695304 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
1695324 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
1695345 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
1695365 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1695387 AATCGCAACGCGA
1 AATCGCAACGCGA
1695400 AATATGAAAA
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1695411 original size:21 final size:20
Alignment explanation
Indices: 1695387--1695581 Score: 82
Period size: 20 Copynumber: 9.7 Consensus size: 20
1695377 GATTTTCCAG
*
1695387 AATCGCAACGCGAA-ATATGAA
1 AATCGCAACGCGAACACAT--A
1695408 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1695428 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1695448 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1695468 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1695488 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1695508 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1695528 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAACACAT-A
* *
1695549 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1695569 AATCGCAACGCGA
1 AATCGCAACGCGA
1695582 TTTTTAAAGC
Statistics
Matches: 154, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.01
20 117 0.76
21 31 0.20
22 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1695432 original size:20 final size:20
Alignment explanation
Indices: 1695407--1695580 Score: 244
Period size: 20 Copynumber: 8.7 Consensus size: 20
1695397 CGAAATATGA
* *
1695407 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1695427 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1695447 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
1695467 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1695487 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1695507 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1695527 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
1695547 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1695568 AAATCGCAACGCG
1 AAATCGCAACGCG
1695581 ATTTTTAAAG
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
20 119 0.86
21 19 0.14
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1695995 original size:33 final size:33
Alignment explanation
Indices: 1695956--1696026 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1695946 TTCACTTAGA
1695956 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1695989 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1696022 TTTCA
1 TTTCA
1696027 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1696143 original size:20 final size:20
Alignment explanation
Indices: 1696106--1696178 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 20
1696096 TGCAGAAGAG
1696106 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1696127 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1696147 TCTGCAACGAGAAAATGAAAA
1 TC-GCAACGAGAAAATGAAAA
1696168 TCGCAACGAGA
1 TCGCAACGAGA
1696179 GAATTGCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1696204 original size:14 final size:14
Alignment explanation
Indices: 1696166--1696204 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
1696156 AGAAAATGAA
1696166 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1696180 AATTGCAAACGAGAG
1 AATCGC-AACGAGAG
1696195 AATCGCAACG
1 AATCGCAACG
1696205 CGAAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1696257 original size:14 final size:14
Alignment explanation
Indices: 1696238--1696294 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1696228 TTTCATTTCG
1696238 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1696252 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1696271 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1696285 CGTTGCGATT
1 CGTTGCGATT
1696295 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1696263 original size:33 final size:33
Alignment explanation
Indices: 1696221--1696343 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1696211 CAAAATCGCA
1696221 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1696254 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1696287 TTGCGATTTTCATTTCTCTAGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGC--GTT--G-C-G--ATTCTCTCG
1696328 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1696344 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 3 0.04
37 1 0.01
38 1 0.01
39 1 0.01
41 25 0.31
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1696305 original size:21 final size:21
Alignment explanation
Indices: 1696279--1696343 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1696269 CGCGTTGCGA
1696279 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
1696300 TTCTCTAGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1696320 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1696341 TTC
1 TTC
1696344 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1698236 original size:92 final size:93
Alignment explanation
Indices: 1698025--1698326 Score: 558
Period size: 91 Copynumber: 3.3 Consensus size: 93
1698015 AGTAAATTAT
1698025 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTT
1698090 TTGTC-TTTGGTTGAAAGTAAATTTGT-
66 TTGTCTTTTGGTTGAAAGTAAATTTGTC
1698116 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGT
1698181 TTTGTCTTTTGGTTGAAAGTAAATTTGTC
65 TTTGTCTTTTGGTTGAAAGTAAATTTGTC
1698210 T-GGTTG-TGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTT
*
1698273 TTGTCTTTTGGTTGAAAGTAAATTTGTT
66 TTGTCTTTTGGTTGAAAGTAAATTTGTC
1698301 TCGGTTGCTGCCAATTCTGCTAAACT
1 TCGGTTGCTGCCAATTCTGCTAAACT
1698327 AATACCCTGA
Statistics
Matches: 205, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
91 93 0.45
92 67 0.33
93 44 0.21
94 1 0.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (93 bp):
TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTT
TTGTCTTTTGGTTGAAAGTAAATTTGTC
Found at i:1698508 original size:19 final size:19
Alignment explanation
Indices: 1698484--1698541 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1698474 ATCGCGACAG
1698484 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1698503 AATCGCAA--CG--A-C-A
1 AATCGCAACGCGAAACCAA
1698516 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1698535 AATCGCA
1 AATCGCA
1698542 TTGCGATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 3 0.09
17 3 0.09
18 1 0.03
19 16 0.48
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1698527 original size:32 final size:33
Alignment explanation
Indices: 1698423--1698541 Score: 140
Period size: 32 Copynumber: 3.7 Consensus size: 33
1698413 TAGTTTACTT
* * *
1698423 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
***
1698457 TCGCAACGC-AAAATGAAATCG---CGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
1698486 TCGCAACGCGAAACCAAAATCGCAACGACA-AA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
1698518 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1698542 TTGCGATTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
29 16 0.22
30 9 0.12
32 33 0.45
33 8 0.11
34 8 0.11
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:1698538 original size:62 final size:63
Alignment explanation
Indices: 1698423--1698540 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 63
1698413 TAGTTTACTT
* * **
1698423 TCGCAACACGAAACTTAAAATCGCAACGAGAGAATCGCAACGCAAAATGAAATCGCGACAGAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAGAATCGCAACGCAAAACAAAATCGCGACAGAA
* *
1698486 TCGCAACGCGAAAC-CAAAATCGCAACGACA-AATCGCAACGCGAAACCAAAATCGC
1 TCGCAACACGAAACTCAAAATCGCAACGACAGAATCGCAACGC-AAAACAAAATCGC
1698541 ATTGCGATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 11 0.23
62 24 0.50
63 13 0.27
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (63 bp):
TCGCAACACGAAACTCAAAATCGCAACGACAGAATCGCAACGCAAAACAAAATCGCGACAGAA
Found at i:1698563 original size:18 final size:18
Alignment explanation
Indices: 1698537--1698689 Score: 110
Period size: 18 Copynumber: 8.8 Consensus size: 18
1698527 GAAACCAAAA
*
1698537 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
1698555 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
1698569 TCTCGTTGCGATTTTCA-T
1 TCGCGTTGCGA-TTTCATT
* *
1698587 TCGCATTGCGA-TTC-TG
1 TCGCGTTGCGATTTCATT
1698603 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
**
1698620 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGA-TTTCATT
**
1698639 T-GCGTTGCGATTTTGGTT
1 TCGCGTTGCGA-TTTCATT
*
1698657 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATT-TCATT
1698676 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1698690 TAAGTTTCGT
Statistics
Matches: 110, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
14 17 0.15
16 10 0.09
17 5 0.05
18 40 0.36
19 38 0.35
ACGTcount: A:0.10, C:0.21, G:0.24, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:1698577 original size:14 final size:14
Alignment explanation
Indices: 1698558--1698613 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1698548 TTTCATTTCG
1698558 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1698572 CGTTGCGATTTTCATT
1 CGTTGCGATTCTC--T
*
1698588 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
1698604 CGTTGCGATT
1 CGTTGCGATT
1698614 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.57
16 6 0.17
18 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1698590 original size:32 final size:33
Alignment explanation
Indices: 1698542--1698632 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
1698532 CAAAATCGCA
1698542 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1698574 TTGCGATTTTCA-TTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1698606 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1698633 TTGGTTTGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 36 0.67
33 18 0.33
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1698628 original size:19 final size:19
Alignment explanation
Indices: 1698537--1698704 Score: 128
Period size: 19 Copynumber: 9.5 Consensus size: 19
1698527 GAAACCAAAA
*
1698537 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
1698555 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1698569 TCTCGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
* *
1698587 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1698603 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1698620 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1698639 T-GCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1698657 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1698676 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1698696 TCGTGTTGC
1 TCGCGTTGC
1698705 AAAAGTAAAC
Statistics
Matches: 121, Mismatches: 17, Indels: 22
0.76 0.11 0.14
Matches are distributed among these distances:
14 17 0.14
16 10 0.08
17 5 0.04
18 37 0.31
19 42 0.35
20 10 0.08
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1698664 original size:37 final size:38
Alignment explanation
Indices: 1698537--1698704 Score: 137
Period size: 32 Copynumber: 4.7 Consensus size: 38
1698527 GAAACCAAAA
*
1698537 TCGCATTGCGA-TTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1698571 T--CGTTGCGATTTTCA-TTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
1698603 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
1698639 T-GCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1698676 TCGCGTTGCGATTTTAAGTTTCGTGTTGC
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGC
1698705 AAAAGTAAAC
Statistics
Matches: 109, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.02
31 1 0.01
32 33 0.30
33 16 0.15
34 2 0.02
35 1 0.01
36 2 0.02
37 30 0.28
38 13 0.12
39 9 0.08
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:1700609 original size:14 final size:14
Alignment explanation
Indices: 1700590--1700625 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1700580 ATTGTTTAAT
1700590 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1700604 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1700618 TGATTTGT
1 TGATTTGT
1700626 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1700735 original size:19 final size:19
Alignment explanation
Indices: 1700711--1700796 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
1700701 TGCATATATT
1700711 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1700730 GAAATG--AATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1700745 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
1700761 GAAATGAAAATAGCAATGC
1 GAAATGAAAATCGCAATGC
1700780 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1700797 CGAGAGAATC
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 8 0.14
15 2 0.04
16 2 0.04
17 8 0.14
18 1 0.02
19 18 0.32
20 15 0.27
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1700807 original size:53 final size:50
Alignment explanation
Indices: 1700711--1700815 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 50
1700701 TGCATATATT
*
1700711 GAAATGAAAATCGCAATGCGAAATGAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATAGCAATGCGAAATGAATCGCAACGAGAGAATCGCAATGC
1700761 GAAATGAAAATAGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATAGCAATGC-GAAATG--AATCGCAACGAGAGAATCGCAATGC
1700814 GA
1 GA
1700816 TTTTCATTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
50 18 0.35
51 6 0.12
53 27 0.53
ACGTcount: A:0.46, C:0.16, G:0.25, T:0.13
Consensus pattern (50 bp):
GAAATGAAAATAGCAATGCGAAATGAATCGCAACGAGAGAATCGCAATGC
Found at i:1700833 original size:19 final size:19
Alignment explanation
Indices: 1700805--1701027 Score: 236
Period size: 19 Copynumber: 12.7 Consensus size: 19
1700795 AACGAGAGAA
*
1700805 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1700824 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1700843 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1700859 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1700875 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1700894 TCGCATTGCGA---TC-TC
1 TCGCATTGCGATTTTCATT
1700909 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1700926 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1700944 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1700961 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1700978 CTCG--TTGCGA-TTTCATT
1 -TCGCATTGCGATTTTCATT
1700995 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1701014 TCCGCATTGCGATT
1 T-CGCATTGCGATT
1701028 CTTGTTGGGA
Statistics
Matches: 177, Mismatches: 7, Indels: 39
0.79 0.03 0.17
Matches are distributed among these distances:
13 6 0.03
14 12 0.07
15 7 0.04
16 20 0.11
17 17 0.10
18 32 0.18
19 71 0.40
20 12 0.07
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1700876 original size:32 final size:33
Alignment explanation
Indices: 1700829--1701081 Score: 209
Period size: 32 Copynumber: 7.5 Consensus size: 33
1700819 TCATTTCGCA
1700829 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1700862 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * * *
1700897 CATTGCGATCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGAT-TTTCATTTCGCA-TTGCGATTCTCTCG
1700931 TTGCGA-TTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1700964 TTGCGATTTTCATTCTCG--TTGCGATTTCATTTCG
1 TTGCGATTTTCATT-TCGCATTGCGA-TTC-TCTCG
1700998 CATTGCGATTTTCATTTCCGCATTGCGATTCT-T-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
1701032 TTGGGATTTTCATTTCGCATTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
1701065 TTGCGATTGTAATTTCG
1 TTGCGATTTTCATTTCG
1701082 TGTGCGATAG
Statistics
Matches: 177, Mismatches: 20, Indels: 46
0.73 0.08 0.19
Matches are distributed among these distances:
30 5 0.03
31 18 0.10
32 49 0.28
33 33 0.19
34 19 0.11
35 7 0.04
36 19 0.11
37 9 0.05
38 8 0.05
39 10 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1700880 original size:51 final size:52
Alignment explanation
Indices: 1700811--1701081 Score: 339
Period size: 51 Copynumber: 5.3 Consensus size: 52
1700801 AGAATCGCAA
1700811 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1700863 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1700913 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1700965 TGCGATTTTCATTCTCG--TTGCGA-TTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGATTTTCATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * * * *
1701014 TCCGCA-TTGCGATTCTTG--TTGGGATTTTCATTTCGCATTGCAATTCTCTCGT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
1701066 TGCGATTGTAATTTCG
1 TGCGATTTTCATTTCG
1701082 TGTGCGATAG
Statistics
Matches: 196, Mismatches: 12, Indels: 24
0.84 0.05 0.10
Matches are distributed among these distances:
48 2 0.01
49 8 0.04
50 47 0.24
51 102 0.52
52 32 0.16
53 5 0.03
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1700889 original size:70 final size:64
Alignment explanation
Indices: 1700829--1701081 Score: 210
Period size: 70 Copynumber: 3.8 Consensus size: 64
1700819 TCATTTCGCA
1700829 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTCATT
1 TTGCGATTTTCATTTCG-ATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGA--TTC-TT
1700894 TCG
62 TCG
* * * * * *
1700897 CATTGCGATCTCTCGTTGCGATTTTC-ATT-TCGCATTGCGATTTCATTTCCGCATTGCGATTCT
1 --TTGCGAT-TTTCATTTCGA-TTGCGATTCTCTCGTTGCGATTTCATTT-CGCATTGCGATTCT
*
1700960 CTCG
61 TTCG
*
1700964 TTGCGATTTTCATTCTCG-TTGCGATTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATT-TCGATTGCGA-TTC-TCTCG--TTGCGA-TTTCATTT-CGCATTGCGATT
1701028 C-TT-G
59 CTTTCG
* * *
1701032 TTGGGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATTGTAATTTCG
1 TTGCGATTTTCATTTCG-ATTGCGATTCTCTCGTTGCGATT-TCATTTCG
1701082 TGTGCGATAG
Statistics
Matches: 150, Mismatches: 19, Indels: 34
0.74 0.09 0.17
Matches are distributed among these distances:
63 3 0.02
64 10 0.07
65 22 0.15
67 13 0.09
68 20 0.13
69 29 0.19
70 43 0.29
71 10 0.07
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (64 bp):
TTGCGATTTTCATTTCGATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTCTTTCG
Done.