Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 39
Found at i:5679678 original size:3 final size:3
Alignment explanation
Indices: 5679670--5679700 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5679660 TTTTGTCCGG
*
5679670 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5679701 CAGGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5681375 original size:2 final size:2
Alignment explanation
Indices: 5681368--5681428 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
5681358 TTTCATACTT
5681368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5681410 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5681429 CCTATACTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5682966 original size:28 final size:28
Alignment explanation
Indices: 5682933--5682987 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5682923 CCTCTGTTGC
5682933 TTTTAAGC-TCTGACTCGATGGCATAATA
1 TTTTAAGCAT-TGACTCGATGGCATAATA
* *
5682961 TTTTAAGCATTGGCTCGATGGTATAAT
1 TTTTAAGCATTGACTCGATGGCATAAT
5682988 GTAAACAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (28 bp):
TTTTAAGCATTGACTCGATGGCATAATA
Found at i:5685015 original size:2 final size:2
Alignment explanation
Indices: 5685008--5685034 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5684998 GAGTTAAAGT
5685008 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 T
5685035 GAGATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5685458 original size:2 final size:2
Alignment explanation
Indices: 5685453--5685478 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5685443 ACCACACACC
5685453 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5685479 GATAGATAGA
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):
TA
Found at i:5698309 original size:22 final size:22
Alignment explanation
Indices: 5698284--5698328 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5698274 AAAAATATTA
*
5698284 TGTACTTTAACTATGTATTTTT
1 TGTACTGTAACTATGTATTTTT
*
5698306 TGTACTGTAACTATGTCTTTTT
1 TGTACTGTAACTATGTATTTTT
5698328 T
1 T
5698329 AACTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (22 bp):
TGTACTGTAACTATGTATTTTT
Found at i:5698342 original size:14 final size:15
Alignment explanation
Indices: 5698313--5698346 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
5698303 TTTTGTACTG
5698313 TAACTATGTCTTTTT
1 TAACTATGTCTTTTT
5698328 TAACTATGT-TTTTT
1 TAACTATGTCTTTTT
5698342 TAACT
1 TAACT
5698347 TGTATTACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (15 bp):
TAACTATGTCTTTTT
Found at i:5704914 original size:21 final size:21
Alignment explanation
Indices: 5704884--5704931 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 21
5704874 TTTCTCGAGT
5704884 AATGAACATCCCTGTCATTGTG
1 AATG-ACATCCCTGTCATTGTG
5704906 AATGACATCCCTGTCATTGTG
1 AATGACATCCCTGTCATTGTG
5704927 AATGA
1 AATGA
5704932 TTTATTGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
AATGACATCCCTGTCATTGTG
Found at i:5711347 original size:60 final size:59
Alignment explanation
Indices: 5711270--5711437 Score: 166
Period size: 59 Copynumber: 2.8 Consensus size: 59
5711260 ACCCTCAACT
* *
5711270 TAAATT-GACCCCTAAACTTTTAA-ATGTTCTAATTTCATCCCTAAAGTATGACT-ATCATTC
1 TAAATTAG-CCCCTAAACTTTTAACAT-TT-TAATTTCATCCCCAAACTATG-CTGATCATTC
* * * *
5711330 TAAATTAG-TCCTCAAACTTTGAACATTTTAATTTCATCCCCAAACTATGGTGTTCATTC
1 TAAATTAGCCCCT-AAACTTTTAACATTTTAATTTCATCCCCAAACTATGCTGATCATTC
**
5711389 TAAATTAGCCCCTAAACTTTTTAGACATTCAAATTTCAT-CCCAAACTAT
1 TAAATTAGCCCCTAAAC-TTTTA-ACATTTTAATTTCATCCCCAAACTAT
5711438 ACTTATATAC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
58 1 0.01
59 40 0.44
60 34 0.37
61 16 0.18
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (59 bp):
TAAATTAGCCCCTAAACTTTTAACATTTTAATTTCATCCCCAAACTATGCTGATCATTC
Found at i:5717636 original size:30 final size:30
Alignment explanation
Indices: 5717602--5717672 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
5717592 ACAAGGATCA
*
5717602 CACCATCATCA-AAGGCTGCAACATCACAAG
1 CACCATCATCACAA-GCTACAACATCACAAG
*
5717632 CACCATCATCACAAGCTACAACATCATAAG
1 CACCATCATCACAAGCTACAACATCACAAG
5717662 CACCATCATCA
1 CACCATCATCA
5717673 TCACAAGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.08, T:0.15
Consensus pattern (30 bp):
CACCATCATCACAAGCTACAACATCACAAG
Found at i:5717673 original size:15 final size:15
Alignment explanation
Indices: 5717623--5717672 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
5717613 AAGGCTGCAA
5717623 CATCACAAGCACCAT
1 CATCACAAGCACCAT
*
5717638 CATCACAAGCTA-CAA
1 CATCACAAGC-ACCAT
*
5717653 CATCATAAGCACCAT
1 CATCACAAGCACCAT
5717668 CATCA
1 CATCA
5717673 TCACAAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.42, C:0.36, G:0.06, T:0.16
Consensus pattern (15 bp):
CATCACAAGCACCAT
Found at i:5724391 original size:2 final size:2
Alignment explanation
Indices: 5724334--5724374 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5724324 GATTTTTAAA
5724334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5724375 AATTAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5726679 original size:24 final size:24
Alignment explanation
Indices: 5726646--5726691 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5726636 ATTTTAATAG
*
5726646 AATTATAATTAA-AATATAATTTTT
1 AATTAAAATTAATAAT-TAATTTTT
5726670 AATTAAAATTAATAATTAATTT
1 AATTAAAATTAATAATTAATTT
5726692 AAGTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAAAATTAATAATTAATTTTT
Found at i:5726693 original size:18 final size:18
Alignment explanation
Indices: 5726651--5726690 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5726641 AATAGAATTA
**
5726651 TAATTAAAATATAATTTT
1 TAATTAAAATATAATAAT
5726669 TAATTAAAAT-TAATAAT
1 TAATTAAAATATAATAAT
5726686 TAATT
1 TAATT
5726691 TAAGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTAAAATATAATAAT
Found at i:5727141 original size:21 final size:20
Alignment explanation
Indices: 5727084--5727144 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
5727074 CTGGCATATC
*
5727084 AATTTACGGTGCTGACATAGT
1 AATTTACGGTG-TGACATGGT
* * *
5727105 GATTCACGATAGTGACATGGT
1 AATTTACGGT-GTGACATGGT
5727126 AATTTACGGTGTTGACATG
1 AATTTACGGTG-TGACATG
5727145 ACCGTTCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
AATTTACGGTGTGACATGGT
Found at i:5728416 original size:2 final size:2
Alignment explanation
Indices: 5728409--5728441 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5728399 AACTCGTGTT
5728409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5728442 TATTTGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5730062 original size:21 final size:22
Alignment explanation
Indices: 5730027--5730067 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5730017 TTGAGCGGTT
5730027 AATTTGATAAGATTA-AAAATA
1 AATTTGATAAGATTAGAAAATA
5730048 AATTTGATCAA-ATTAGAAAA
1 AATTTGAT-AAGATTAGAAAA
5730068 CAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (22 bp):
AATTTGATAAGATTAGAAAATA
Found at i:5731715 original size:21 final size:21
Alignment explanation
Indices: 5731673--5731726 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
5731663 ATAATTATTT
* *
5731673 AAAAAATTAAATAAAAGTATC
1 AAAAAATTTAATAAAAGAATC
5731694 AAAAACATTTAATAAAA-AATC
1 AAAAA-ATTTAATAAAAGAATC
5731715 AAAAAAATTTAA
1 -AAAAAATTTAA
5731727 GTTGAACCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAATTTAATAAAAGAATC
Found at i:5734285 original size:24 final size:22
Alignment explanation
Indices: 5734258--5734308 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
5734248 CACTAGGGGT
5734258 ACATATGATTTGTCCCGAAGGACC
1 ACATATGA--TGTCCCGAAGGACC
*
5734282 ACATA-GATGTCTCGAAGGACC
1 ACATATGATGTCCCGAAGGACC
5734303 ACATAT
1 ACATAT
5734309 AATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 18 0.72
23 2 0.08
24 5 0.20
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (22 bp):
ACATATGATGTCCCGAAGGACC
Found at i:5734297 original size:21 final size:21
Alignment explanation
Indices: 5734268--5734307 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5734258 ACATATGATT
5734268 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
5734289 TGTCTCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
5734308 TAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:5736687 original size:30 final size:30
Alignment explanation
Indices: 5736653--5736744 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
5736643 TTCATCATAT
5736653 ATAATTAAAACATAAACTTTACAAAATCAA
1 ATAATTAAAACATAAACTTTACAAAATCAA
** *
5736683 ATAATCT--TTC-T-TACTTTACAAAATCAA
1 ATAAT-TAAAACATAAACTTTACAAAATCAA
*
5736710 ATAATTAAAACATACACTTTACAAAATCAA
1 ATAATTAAAACATAAACTTTACAAAATCAA
5736740 ATAAT
1 ATAAT
5736745 CCTTCACATC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.02
27 20 0.39
28 2 0.04
29 2 0.04
30 25 0.49
31 1 0.02
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (30 bp):
ATAATTAAAACATAAACTTTACAAAATCAA
Found at i:5736758 original size:30 final size:28
Alignment explanation
Indices: 5736668--5736758 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 28
5736658 TAAAACATAA
* *
5736668 ACTTTACAAAATCAAATAATCTTTC-TT
1 ACTTTACAAAATCAAATAATCTTACATC
*
5736695 ACTTTACAAAATCAAATAAT-TAAAACATAC
1 ACTTTACAAAATCAAATAATCT--TACAT-C
5736725 ACTTTACAAAATCAAATAATCCTTCACATC
1 ACTTTACAAAATCAAATAAT-CTT-ACATC
5736755 ACTT
1 ACTT
5736759 GACATATCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
26 1 0.02
27 20 0.38
28 1 0.02
29 1 0.02
30 25 0.47
31 4 0.08
32 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (28 bp):
ACTTTACAAAATCAAATAATCTTACATC
Found at i:5747501 original size:24 final size:24
Alignment explanation
Indices: 5747474--5747523 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5747464 TGGTGGTTGA
*
5747474 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
5747498 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
5747522 TT
1 TT
5747524 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:5751877 original size:20 final size:20
Alignment explanation
Indices: 5751852--5751900 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5751842 TCAAAAATCG
* *
5751852 ACTAAGTAACCTAAACCTTC
1 ACTAAGCAACCCAAACCTTC
5751872 ACTAAGCAACCCAAACCTTC
1 ACTAAGCAACCCAAACCTTC
5751892 ACTAAGCAA
1 ACTAAGCAA
5751901 GAAAGCTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.33, G:0.06, T:0.18
Consensus pattern (20 bp):
ACTAAGCAACCCAAACCTTC
Found at i:5752195 original size:28 final size:28
Alignment explanation
Indices: 5752163--5752238 Score: 152
Period size: 28 Copynumber: 2.7 Consensus size: 28
5752153 AATTATCTCG
5752163 AAGATAATTTCAAATAATTAAATTCCCT
1 AAGATAATTTCAAATAATTAAATTCCCT
5752191 AAGATAATTTCAAATAATTAAATTCCCT
1 AAGATAATTTCAAATAATTAAATTCCCT
5752219 AAGATAATTTCAAATAATTA
1 AAGATAATTTCAAATAATTA
5752239 TTATGTCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (28 bp):
AAGATAATTTCAAATAATTAAATTCCCT
Found at i:5755273 original size:43 final size:43
Alignment explanation
Indices: 5755212--5755306 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
5755202 CCTCCAACCG
* *
5755212 AACACACCTTAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
5755255 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
5755298 AACACACCA
1 AACACACCA
5755307 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.36, C:0.37, G:0.11, T:0.17
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:5755453 original size:24 final size:24
Alignment explanation
Indices: 5755421--5755487 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
5755411 AAAACATAAT
5755421 TCAAGTATCAGATCAGAATCCATG
1 TCAAGTATCAGATCAGAATCCATG
*
5755445 TC-AGATATCATATCAGAATCCATG
1 TCAAG-TATCAGATCAGAATCCATG
5755469 TCAAGTATCAGATCAGAAT
1 TCAAGTATCAGATCAGAAT
5755488 TCAAATCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
TCAAGTATCAGATCAGAATCCATG
Found at i:5757545 original size:15 final size:15
Alignment explanation
Indices: 5757525--5757558 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5757515 GGTCAACATC
5757525 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
*
5757540 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
5757555 GGTC
1 GGTC
5757559 GAGTCGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:5770412 original size:42 final size:42
Alignment explanation
Indices: 5770365--5770449 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
5770355 AATTACTCCC
*
5770365 CCTTACTCTAACACTTCTCCCCTTTAAAACATTTTAACATTT
1 CCTTACTCTAACACTTCTCCCCTTTAAAACACTTTAACATTT
*
5770407 CCTTACTCTAACACTTCTCCCCTTTAAAACACTTTAATATTT
1 CCTTACTCTAACACTTCTCCCCTTTAAAACACTTTAACATTT
5770449 C
1 C
5770450 TCCCCCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (42 bp):
CCTTACTCTAACACTTCTCCCCTTTAAAACACTTTAACATTT
Found at i:5780080 original size:16 final size:16
Alignment explanation
Indices: 5780026--5780080 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
5780016 AATTATTCAA
*
5780026 ATATAGAATAATAAAT
1 ATATAAAATAATAAAT
* *
5780042 ATA-AAAATACTAAAA
1 ATATAAAATAATAAAT
* *
5780057 ATAAAAAATAATACAT
1 ATATAAAATAATAAAT
5780073 ATATAAAA
1 ATATAAAA
5780081 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (16 bp):
ATATAAAATAATAAAT
Found at i:5784195 original size:21 final size:21
Alignment explanation
Indices: 5784169--5784239 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
5784159 AATTACACCC
* *
5784169 TAAACCTTAAATCCTAAATTA
1 TAAACCCTAAACCCTAAATTA
5784190 TAAACCCTAAACCCTAAA-TA
1 TAAACCCTAAACCCTAAATTA
** * *
5784210 CTAAATACTAAACCCTAAACTC
1 -TAAACCCTAAACCCTAAATTA
5784232 TAAACCCT
1 TAAACCCT
5784240 TAATCTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATTA
Found at i:5784199 original size:28 final size:28
Alignment explanation
Indices: 5784165--5784235 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
5784155 GTTAAATTAC
* *
5784165 ACCCTAAACCTTAAATCCTAAATTA-TAA
1 ACCCTAAACCCTAAATACTAAA-TACTAA
5784193 ACCCTAAACCCTAAATACTAAATACTAA
1 ACCCTAAACCCTAAATACTAAATACTAA
*
5784221 ACCCTAAACTCTAAA
1 ACCCTAAACCCTAAA
5784236 CCCTTAATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 2 0.05
28 37 0.95
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (28 bp):
ACCCTAAACCCTAAATACTAAATACTAA
Found at i:5784229 original size:7 final size:7
Alignment explanation
Indices: 5784165--5784239 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
5784155 GTTAAATTAC
5784165 ACCCTAA
1 ACCCTAA
*
5784172 ACCTTAA
1 ACCCTAA
*
5784179 ATCCTAA
1 ACCCTAA
***
5784186 ATTATAA
1 ACCCTAA
5784193 ACCCTAA
1 ACCCTAA
5784200 ACCCTAA
1 ACCCTAA
**
5784207 ATACTAA
1 ACCCTAA
**
5784214 ATACTAA
1 ACCCTAA
5784221 ACCCTAA
1 ACCCTAA
*
5784228 ACTCTAA
1 ACCCTAA
5784235 ACCCT
1 ACCCT
5784240 TAATCTAATT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (7 bp):
ACCCTAA
Found at i:5786540 original size:30 final size:30
Alignment explanation
Indices: 5786504--5786575 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
5786494 GGAACTTAAT
5786504 TTGACATGTTGCAATATTTTGTAAGCAAAC
1 TTGACATGTTGCAATATTTTGTAAGCAAAC
* * *
5786534 TTGACATGTTACAATATTTTGTAAGTAAAT
1 TTGACATGTTGCAATATTTTGTAAGCAAAC
5786564 TTGACATGTTGC
1 TTGACATGTTGC
5786576 TGCCATCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (30 bp):
TTGACATGTTGCAATATTTTGTAAGCAAAC
Found at i:5786733 original size:37 final size:36
Alignment explanation
Indices: 5786682--5786754 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
5786672 GAAAATAGTG
* *
5786682 TCATCTTGTATAAATTTGGATATGTTGTCATTTTTT
1 TCATCTTGTATAAATTTAGATATGTTGTCATATTTT
* *
5786718 TCATCTTTTTATAAATTTAGATGTGTTGTCATATTTT
1 TCATC-TTGTATAAATTTAGATATGTTGTCATATTTT
5786755 GTAAACTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 5 0.16
37 27 0.84
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.56
Consensus pattern (36 bp):
TCATCTTGTATAAATTTAGATATGTTGTCATATTTT
Found at i:5787455 original size:15 final size:15
Alignment explanation
Indices: 5787435--5787464 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5787425 CCGAGATATC
*
5787435 ACTTTGACTTTTAAA
1 ACTTTGACTCTTAAA
5787450 ACTTTGACTCTTAAA
1 ACTTTGACTCTTAAA
5787465 GAAAAACCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
ACTTTGACTCTTAAA
Found at i:5787834 original size:20 final size:20
Alignment explanation
Indices: 5787794--5787834 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5787784 TTTGATCATG
*
5787794 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
5787814 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
5787834 A
1 A
5787835 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:5794296 original size:15 final size:15
Alignment explanation
Indices: 5794276--5794305 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5794266 CCGAGGTGTC
*
5794276 ACTTTGACTTTTAAA
1 ACTTTGACTCTTAAA
5794291 ACTTTGACTCTTAAA
1 ACTTTGACTCTTAAA
5794306 GAAAAACCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
ACTTTGACTCTTAAA
Found at i:5794675 original size:20 final size:20
Alignment explanation
Indices: 5794635--5794675 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5794625 TTTGATCATG
*
5794635 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
5794655 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
5794675 A
1 A
5794676 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:5794914 original size:15 final size:15
Alignment explanation
Indices: 5794894--5794928 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5794884 CCGTAGGACC
*
5794894 ACTACGTCTCGAAGG
1 ACTACGTCCCGAAGG
5794909 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
5794924 ACTAC
1 ACTAC
5794929 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:5811343 original size:2 final size:2
Alignment explanation
Indices: 5811336--5811369 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5811326 CTTCTTCAAG
5811336 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5811370 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5811374 original size:2 final size:2
Alignment explanation
Indices: 5811369--5811403 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5811359 TCTCTCTCTC
5811369 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
5811404 TTGTATCATC
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:5817448 original size:37 final size:36
Alignment explanation
Indices: 5817407--5817476 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
5817397 TAGATCCTAA
*
5817407 AACCCAAAACCTTAAAACTCTAAAATAATAAACCATG
1 AACCCAAAACCTTAAAAC-CCAAAATAATAAACCATG
* *
5817444 AACCCAAAATCTTAAAACCCAAAATCATAAACC
1 AACCCAAAACCTTAAAACCCAAAATAATAAACC
5817477 CAAAATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.17
Consensus pattern (36 bp):
AACCCAAAACCTTAAAACCCAAAATAATAAACCATG
Found at i:5817459 original size:29 final size:29
Alignment explanation
Indices: 5817436--5817511 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
5817426 CTAAAATAAT
* *
5817436 AAACCATGAACCCAAAATCTTAAAACCCA
1 AAACCATAAACCCAAAATCTTAAAACCAA
* * *
5817465 AAATCATAAACCCAAAATCTTAAATCCTA
1 AAACCATAAACCCAAAATCTTAAAACCAA
*
5817494 AAACCATAAGCCCTAAAA
1 AAACCATAAACCC-AAAA
5817512 CACTAAACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (29 bp):
AAACCATAAACCCAAAATCTTAAAACCAA
Found at i:5817464 original size:15 final size:15
Alignment explanation
Indices: 5817444--5817488 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
5817434 ATAAACCATG
5817444 AACCCAAAATCTTAA
1 AACCCAAAATCTTAA
*
5817459 AACCCAAAATCAT-A
1 AACCCAAAATCTTAA
5817473 AACCCAAAATCTTAA
1 AACCCAAAATCTTAA
5817488 A
1 A
5817489 TCCTAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCCAAAATCTTAA
Found at i:5817477 original size:14 final size:14
Alignment explanation
Indices: 5817444--5817521 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 14
5817434 ATAAACCATG
*
5817444 AACCCAAAATCTTAA
1 AACCCAAAATCAT-A
5817459 AACCCAAAATCATA
1 AACCCAAAATCATA
*
5817473 AACCCAAAATCTTA
1 AACCCAAAATCATA
* *
5817487 AATCCTAAAACCATA
1 AA-CCCAAAATCATA
*
5817502 AGCCCTAAAA-CACTA
1 AACCC-AAAATCA-TA
5817517 AACCC
1 AACCC
5817522 TAAGCTATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 20 0.38
15 32 0.62
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (14 bp):
AACCCAAAATCATA
Found at i:5817522 original size:15 final size:15
Alignment explanation
Indices: 5817436--5817524 Score: 60
Period size: 15 Copynumber: 6.1 Consensus size: 15
5817426 CTAAAATAAT
*
5817436 AAACCATGAACCC-A
1 AAACCATAAACCCTA
* *
5817450 AAATCTTAAAACCC-A
1 AAACCAT-AAACCCTA
*
5817465 AAATCATAAACCC-A
1 AAACCATAAACCCTA
* * *
5817479 AAATCTTAAATCCTA
1 AAACCATAAACCCTA
*
5817494 AAACCATAAGCCCTA
1 AAACCATAAACCCTA
5817509 AAA-CACTAAACCCTA
1 AAACCA-TAAACCCTA
5817524 A
1 A
5817525 GCTATAAACC
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
14 25 0.41
15 36 0.59
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (15 bp):
AAACCATAAACCCTA
Found at i:5817588 original size:15 final size:15
Alignment explanation
Indices: 5817570--5817629 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
5817560 CTTGAACCAA
5817570 TAAACTCATAAATCC
1 TAAACTCATAAATCC
*
5817585 TAAAATCATAAATCC
1 TAAACTCATAAATCC
*
5817600 TAAACT-ATAAACTCA
1 TAAACTCATAAA-TCC
*
5817615 TAAAC-CCTAAATCC
1 TAAACTCATAAATCC
5817629 T
1 T
5817630 TAAATCCCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.21
15 30 0.79
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAACTCATAAATCC
Found at i:5817619 original size:8 final size:8
Alignment explanation
Indices: 5817569--5817619 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 8
5817559 CCTTGAACCA
5817569 ATAAACTC
1 ATAAACTC
5817577 ATAAA-TC
1 ATAAACTC
* *
5817584 CTAAAATC
1 ATAAACTC
5817592 ATAAA-TC
1 ATAAACTC
*
5817599 CTAAACT-
1 ATAAACTC
5817606 ATAAACTC
1 ATAAACTC
5817614 ATAAAC
1 ATAAAC
5817620 CCTAAATCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 18 0.50
8 18 0.50
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAACTC
Found at i:5817634 original size:37 final size:37
Alignment explanation
Indices: 5817569--5817641 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
5817559 CCTTGAACCA
* *
5817569 ATAAACTCATAAATCCTAAAATCATAAATCCTAAACT
1 ATAAACTCATAAACCCTAAAATCATAAATCCCAAACT
*
5817606 ATAAACTCATAAACCCT-AAATCCTTAAATCCCAAAC
1 ATAAACTCATAAACCCTAAAAT-CATAAATCCCAAAC
5817642 ACAAATATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (37 bp):
ATAAACTCATAAACCCTAAAATCATAAATCCCAAACT
Found at i:5817772 original size:29 final size:29
Alignment explanation
Indices: 5817739--5817794 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5817729 TTTAATATCT
*
5817739 AAACCTTAAACTCATTA-ATACTAAATCCC
1 AAACCCTAAAC-CATTAGATACTAAATCCC
*
5817768 AAACCCTAAACCCTTAGATACTAAATC
1 AAACCCTAAACCATTAGATACTAAATC
5817795 ATAAACTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.25
Consensus pattern (29 bp):
AAACCCTAAACCATTAGATACTAAATCCC
Found at i:5817800 original size:29 final size:29
Alignment explanation
Indices: 5817738--5817800 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
5817728 ATTTAATATC
* *
5817738 TAAACCTTAAACTCATTAATACTAAATCC
1 TAAACCCTAAACTCATTAATACTAAATCA
* *
5817767 CAAACCCTAAAC-CCTTAGATACTAAATCA
1 TAAACCCTAAACTCATTA-ATACTAAATCA
5817796 TAAAC
1 TAAAC
5817801 TCTATCATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (29 bp):
TAAACCCTAAACTCATTAATACTAAATCA
Found at i:5817873 original size:7 final size:7
Alignment explanation
Indices: 5817863--5817902 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5817853 ATCATAAGTT
5817863 CTAAACC
1 CTAAACC
*
5817870 CTAAACT
1 CTAAACC
*
5817877 ATAAACC
1 CTAAACC
*
5817884 CTAAACT
1 CTAAACC
5817891 CTAAACC
1 CTAAACC
5817898 CTAAA
1 CTAAA
5817903 TCAATGACCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:5817881 original size:14 final size:14
Alignment explanation
Indices: 5817864--5817902 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
5817854 TCATAAGTTC
5817864 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
5817878 TAAACCCTAAACTC
1 TAAACCCTAAACTA
5817892 TAAACCCTAAA
1 TAAACCCTAAA
5817903 TCAATGACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:5817912 original size:28 final size:28
Alignment explanation
Indices: 5817862--5817915 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5817852 AATCATAAGT
*
5817862 TCTAAACCCTAAACTATAAACCCTAAAC
1 TCTAAACCCTAAACAATAAACCCTAAAC
*
5817890 TCTAAACCCTAAATCAAT-GACCCTAA
1 TCTAAACCCTAAA-CAATAAACCCTAA
5817916 CCACTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.22
Consensus pattern (28 bp):
TCTAAACCCTAAACAATAAACCCTAAAC
Found at i:5817964 original size:14 final size:14
Alignment explanation
Indices: 5817937--5818001 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
5817927 AAAATCTTAA
*
5817937 AAATC-TAAACCTT
1 AAATCATAAACCCT
* *
5817950 AAATCATAAATCTT
1 AAATCATAAACCCT
*
5817964 AAATCTTAAACCCT
1 AAATCATAAACCCT
* *
5817978 AAACCATAAAACCT
1 AAATCATAAACCCT
*
5817992 AAACCATAAA
1 AAATCATAAA
5818002 ATCATAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
13 5 0.11
14 39 0.89
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATCATAAACCCT
Found at i:5817980 original size:21 final size:20
Alignment explanation
Indices: 5817937--5818001 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
5817927 AAAATCTTAA
*
5817937 AAATCTAAACCTTAAATCAT
1 AAATCTAAACCTTAAACCAT
* *
5817957 AAATCTTAAATCTTAAACCCT
1 AAATC-TAAACCTTAAACCAT
*
5817978 AAACCATAAAACC-TAAACCAT
1 AAATC-T-AAACCTTAAACCAT
5817999 AAA
1 AAA
5818002 ATCATAAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.14
21 27 0.75
22 4 0.11
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATCTAAACCTTAAACCAT
Found at i:5818038 original size:37 final size:36
Alignment explanation
Indices: 5817964--5818073 Score: 93
Period size: 36 Copynumber: 3.1 Consensus size: 36
5817954 CATAAATCTT
*
5817964 AAATCTTAAACCCTAAACCATAAAACCTAAACCATA
1 AAATCATAAACCCTAAACCATAAAACCTAAACCATA
* *
5818000 AAATCATAAATCCCTAAA-CACT-AAACACTAAGCTAT-
1 AAATCATAAA-CCCTAAACCA-TAAAAC-CTAAACCATA
* * * *
5818036 AAACCTTAAACACTAAATCATAAAA-CTATAACCATA
1 AAATCATAAACCCTAAACCATAAAACCTA-AACCATA
5818072 AA
1 AA
5818074 CCCTAAAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
34 3 0.05
35 11 0.19
36 30 0.51
37 15 0.25
ACGTcount: A:0.54, C:0.25, G:0.01, T:0.21
Consensus pattern (36 bp):
AAATCATAAACCCTAAACCATAAAACCTAAACCATA
Found at i:5818052 original size:14 final size:14
Alignment explanation
Indices: 5817970--5818080 Score: 70
Period size: 14 Copynumber: 7.8 Consensus size: 14
5817960 TCTTAAATCT
*
5817970 TAAACCCTAAACCA
1 TAAACACTAAACCA
5817984 TAAA-ACCTAAACCA
1 TAAACA-CTAAACCA
*
5817998 TAAA-ATCATAAATCCC
1 TAAACA-C-TAAA-CCA
5818014 TAAACACTAAA-CA
1 TAAACACTAAACCA
* *
5818027 CTAAGCTA-TAAACCT
1 -TAAAC-ACTAAACCA
*
5818042 TAAACACTAAATCA
1 TAAACACTAAACCA
5818056 TAAA-ACTATAACCA
1 TAAACACTA-AACCA
*
5818070 TAAACCCTAAA
1 TAAACACTAAA
5818081 ATTCTAAACC
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
13 6 0.08
14 49 0.64
15 13 0.17
16 7 0.09
17 1 0.01
ACGTcount: A:0.53, C:0.26, G:0.01, T:0.20
Consensus pattern (14 bp):
TAAACACTAAACCA
Found at i:5818068 original size:28 final size:28
Alignment explanation
Indices: 5817977--5818080 Score: 81
Period size: 28 Copynumber: 3.6 Consensus size: 28
5817967 TCTTAAACCC
*
5817977 TAAACCATAAA-ACCTAAAC-CATAAAATCA
1 TAAACCATAAACA-CTAAACAC-TAAACT-A
* *
5818006 TAAATCCCTAAACACTAAACACTAAGCTA
1 TAAA-CCATAAACACTAAACACTAAACTA
*
5818035 TAAACCTTAAACACTAAATCA-TAAAACTA
1 TAAACCATAAACACTAAA-CACT-AAACTA
*
5818064 T-AACCATAAACCCTAAA
1 TAAACCATAAACACTAAA
5818081 ATTCTAAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
28 28 0.44
29 17 0.27
30 16 0.25
31 2 0.03
ACGTcount: A:0.54, C:0.25, G:0.01, T:0.20
Consensus pattern (28 bp):
TAAACCATAAACACTAAACACTAAACTA
Found at i:5818179 original size:22 final size:22
Alignment explanation
Indices: 5818162--5818208 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5818152 CCTAAAGCTC
5818162 AAAACCATATACCTTAAACCAT
1 AAAACCATATACCTTAAACCAT
* *
5818184 AAAACCATATACTTTAAATCAT
1 AAAACCATATACCTTAAACCAT
5818206 AAA
1 AAA
5818209 CACTAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAACCATATACCTTAAACCAT
Found at i:5818239 original size:22 final size:21
Alignment explanation
Indices: 5818205--5818253 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
5818195 CTTTAAATCA
*
5818205 TAAACACTAAAACCTTGAACCC
1 TAAA-ACTAAAACCATGAACCC
*
5818227 TAAAACTATAAACCATGCACCC
1 TAAAACTA-AAACCATGAACCC
5818249 TAAAA
1 TAAAA
5818254 ATTGAGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.49, C:0.29, G:0.04, T:0.18
Consensus pattern (21 bp):
TAAAACTAAAACCATGAACCC
Found at i:5818512 original size:15 final size:15
Alignment explanation
Indices: 5818496--5818564 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
5818486 TCTAAACCTA
* *
5818496 AAATCATAAATCC-T
1 AAATCCTAAAACCAT
*
5818510 AAACCCTAAAACCAT
1 AAATCCTAAAACCAT
* *
5818525 AAATCCCAAAATCAT
1 AAATCCTAAAACCAT
5818540 AAA-CCATAAAACCAT
1 AAATCC-TAAAACCAT
*
5818555 AAATCTTAAA
1 AAATCCTAAA
5818565 GTATGAACAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
14 12 0.28
15 30 0.70
16 1 0.02
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCTAAAACCAT
Found at i:5818520 original size:22 final size:22
Alignment explanation
Indices: 5818467--5818530 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 22
5818457 TCCTAAGCCA
5818467 TAAACCCT-AAATCATGAAAT-C
1 TAAACCCTAAAATCAT-AAATCC
5818488 TAAA-CCTAAAATCATAAATCC
1 TAAACCCTAAAATCATAAATCC
*
5818509 TAAACCCTAAAACCATAAATCC
1 TAAACCCTAAAATCATAAATCC
5818531 CAAAATCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 7 0.18
21 16 0.41
22 16 0.41
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAACCCTAAAATCATAAATCC
Found at i:5818543 original size:30 final size:30
Alignment explanation
Indices: 5818503--5818559 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
5818493 CTAAAATCAT
* *
5818503 AAATCCTAAACCCTAAAACCATAAATCCCA
1 AAATCATAAACCATAAAACCATAAATCCCA
5818533 AAATCATAAACCATAAAACCATAAATC
1 AAATCATAAACCATAAAACCATAAATC
5818560 TTAAAGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (30 bp):
AAATCATAAACCATAAAACCATAAATCCCA
Found at i:5818602 original size:22 final size:22
Alignment explanation
Indices: 5818489--5818628 Score: 79
Period size: 22 Copynumber: 6.4 Consensus size: 22
5818479 CATGAAATCT
* * *
5818489 AAACCTAAAATCATAAATCCTA
1 AAACCTTAAACCATAAACCCTA
* *
5818511 AACCCTAAAACCATAAATCCC-A
1 AAACCTTAAACCATAAA-CCCTA
* * *
5818533 AAATCATAAACCATAAAACC-A
1 AAACCTTAAACCATAAACCCTA
* ** * **
5818554 TAAATCTTAAAGTATGAACATTA
1 -AAACCTTAAACCATAAACCCTA
*
5818577 AAACCTTAAACCTATAACCCCT-
1 AAACCTTAAACC-ATAAACCCTA
* *
5818599 AAACCCTAAAGCATAAACCCTA
1 AAACCTTAAACCATAAACCCTA
5818621 AAACCTTA
1 AAACCTTA
5818629 GAATATTGAT
Statistics
Matches: 87, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
21 11 0.13
22 68 0.78
23 8 0.09
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (22 bp):
AAACCTTAAACCATAAACCCTA
Found at i:5818662 original size:15 final size:14
Alignment explanation
Indices: 5818642--5818698 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
5818632 TATTGATTCA
5818642 TAAACCTTAAAAATC
1 TAAACCTTAAAAA-C
5818657 TAAACCTTAAACAA-
1 TAAACCTTAAA-AAC
**
5818671 TAGAACCTTGAAACCC
1 TA-AACCTT-AAAAAC
5818687 TAAACCTTAAAA
1 TAAACCTTAAAA
5818699 TCTTAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 5 0.14
15 23 0.66
16 7 0.20
ACGTcount: A:0.51, C:0.23, G:0.04, T:0.23
Consensus pattern (14 bp):
TAAACCTTAAAAAC
Found at i:5818920 original size:7 final size:7
Alignment explanation
Indices: 5818879--5818957 Score: 68
Period size: 7 Copynumber: 11.1 Consensus size: 7
5818869 GCCTAAGTTA
5818879 TAAATCT
1 TAAATCT
* *
5818886 TAAACCC
1 TAAATCT
* *
5818893 TAAAACC
1 TAAATCT
5818900 TAAATCT
1 TAAATCT
5818907 TACAATCT
1 TA-AATCT
5818915 TAAATCT
1 TAAATCT
*
5818922 TAAATCA
1 TAAATCT
* *
5818929 TAAACCA
1 TAAATCT
*
5818936 TAAACCT
1 TAAATCT
*
5818943 TAAATTT
1 TAAATCT
5818950 TAAATCT
1 TAAATCT
5818957 T
1 T
5818958 GAAACCAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
7 53 0.88
8 7 0.12
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (7 bp):
TAAATCT
Found at i:5818952 original size:28 final size:28
Alignment explanation
Indices: 5818913--5818974 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5818903 ATCTTACAAT
5818913 CTTAAATCTTAAATCAT-AAACCATAAAC
1 CTTAAATCTTAAATCATGAAACCA-AAAC
* *
5818941 CTTAAATTTTAAATCTTGAAACCAAAAC
1 CTTAAATCTTAAATCATGAAACCAAAAC
*
5818969 CCTAAA
1 CTTAAA
5818975 CACTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (28 bp):
CTTAAATCTTAAATCATGAAACCAAAAC
Found at i:5818954 original size:71 final size:70
Alignment explanation
Indices: 5818849--5819013 Score: 169
Period size: 71 Copynumber: 2.3 Consensus size: 70
5818839 ACCCTAAACC
* * *
5818849 CTTAAA-CATTAAACCATAAAGCCTAAGTTATAAATCTT-AAACCCTAAAA-CCTAAATC-TTAC
1 CTTAAATCA-TAAACCATAAA-CCTAAATTATAAATCTTGAAA-CC-AAAACCCTAAA-CACTAA
*
5818910 AATCTTAAAT
61 AATCATAAAT
*
5818920 CTTAAATCATAAACCATAAACCTTAAATTTTAAATCTTGAAACCAAAACCCTAAACACTAAAATC
1 CTTAAATCATAAACCATAAACC-TAAATTATAAATCTTGAAACCAAAACCCTAAACACTAAAATC
*
5818985 ATACAT
65 ATAAAT
5818991 CTTAAATCATGAAACTC-TAAACC
1 CTTAAATCAT-AAAC-CATAAACC
5819014 CCATATCCTA
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
70 7 0.09
71 58 0.72
72 15 0.19
73 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.28
Consensus pattern (70 bp):
CTTAAATCATAAACCATAAACCTAAATTATAAATCTTGAAACCAAAACCCTAAACACTAAAATCA
TAAAT
Found at i:5828591 original size:13 final size:13
Alignment explanation
Indices: 5828573--5828597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5828563 GTGGCACCCG
5828573 ACATTCAAGCTGC
1 ACATTCAAGCTGC
5828586 ACATTCAAGCTG
1 ACATTCAAGCTG
5828598 AAATCAGTCA
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:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
ACATTCAAGCTGC
Found at i:5842826 original size:8 final size:8
Alignment explanation
Indices: 5842813--5842838 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5842803 AAAAATAATG
5842813 TTATTTCT
1 TTATTTCT
5842821 TTATTTCT
1 TTATTTCT
5842829 TTATTTCT
1 TTATTTCT
5842837 TT
1 TT
5842839 TCCTTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTCT
Found at i:5857471 original size:40 final size:42
Alignment explanation
Indices: 5857341--5857481 Score: 196
Period size: 42 Copynumber: 3.4 Consensus size: 42
5857331 ATCCTATGAA
* *
5857341 GGCGTTTGTAAGAAAAATGTCACTAATGTACTAGCCTATTGC
1 GGCGTTTGTAAGAAAAATGCCACTAATGTACTAGTCTATTGC
* * *
5857383 GGCGTTTGTGAGAAAAACGCCACTAATATACTAGTCTATTGC
1 GGCGTTTGTAAGAAAAATGCCACTAATGTACTAGTCTATTGC
* * *
5857425 GACGTTTGCAAGAAAAATGCCA-TAATGTACT-GTCTATTGT
1 GGCGTTTGTAAGAAAAATGCCACTAATGTACTAGTCTATTGC
5857465 GGCGTTTGTAAGAAAAA
1 GGCGTTTGTAAGAAAAA
5857482 CACCAATAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 23 0.27
41 8 0.09
42 55 0.64
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
GGCGTTTGTAAGAAAAATGCCACTAATGTACTAGTCTATTGC
Found at i:5857563 original size:82 final size:81
Alignment explanation
Indices: 5857477--5857658 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 81
5857467 CGTTTGTAAG
* ** * *
5857477 AAAAACACCAATAAAAAGTACTAGGTTTTAGTGGTGTTTGTCTAAAAACACCATGATATTTGTAC
1 AAAAACACCAAT--AAAGTACTAGGTTTTAGCGGCATTTGTCTAAAAACACCACGATATATGTAC
* *
5857542 CCTGTTGCGGCGTTTATAA
64 CCTATTACGGCGTTTAT-A
* * **
5857561 AAAAACGCCACTAAAGTACTAGGTTTTAGCGGCATTTGTCTAAAAATGCCACGATATATGTACCC
1 AAAAACACCAATAAAGTACTAGGTTTTAGCGGCATTTGTCTAAAAACACCACGATATATGTACCC
*
5857626 TATTACGGCGTTTGTTA
66 TATTACGGCGTTT-ATA
* *
5857643 AAAAACGCCACTAAAG
1 AAAAACACCAATAAAG
5857659 AGCGAATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
82 74 0.87
83 1 0.01
84 10 0.12
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (81 bp):
AAAAACACCAATAAAGTACTAGGTTTTAGCGGCATTTGTCTAAAAACACCACGATATATGTACCC
TATTACGGCGTTTATA
Found at i:5860851 original size:32 final size:31
Alignment explanation
Indices: 5860788--5860851 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
5860778 GGTCGGGTTT
* * * *
5860788 CGACCAACCCGAAAATTGTACATCCTTTACC
1 CGACCAACCCGAAAAATATACACCCTCTACC
*
5860819 CGACTCAACCCGAAAAATATATACCCTCTACC
1 CGAC-CAACCCGAAAAATATACACCCTCTACC
5860851 C
1 C
5860852 AAACCCGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.34, C:0.38, G:0.08, T:0.20
Consensus pattern (31 bp):
CGACCAACCCGAAAAATATACACCCTCTACC
Found at i:5862118 original size:25 final size:25
Alignment explanation
Indices: 5862087--5862151 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
5862077 ATAAATACAT
5862087 AATATAATAGACAAAGTAATTGATA
1 AATATAATAGACAAAGTAATTGATA
5862112 AATATAATAGACAAAGTAATTGATA
1 AATATAATAGACAAAGTAATTGATA
* *
5862137 AATAAAATAAACAAA
1 AATATAATAGACAAA
5862152 TAACTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.25
Consensus pattern (25 bp):
AATATAATAGACAAAGTAATTGATA
Found at i:5862647 original size:122 final size:123
Alignment explanation
Indices: 5862430--5862676 Score: 399
Period size: 122 Copynumber: 2.0 Consensus size: 123
5862420 AAACAAAATT
* *
5862430 ATAACCTCAATTTTGGGTATGACAACTCTCCCCTCCTTAATGAAATTTCATCTTCAATTTTTTTT
1 ATAACCTCAATTTTGGGTATGACAACTCTCCCCACCTTAATGAAATTTCATCTTCAAATTTTTTT
* *
5862495 TCGACTTGATGGTATATTGATATCATAGATTTAAC-AAAAAATATTACTCAAACACAG
66 TCGACTTGATGGTAGATTGATATCATAGATTTAACAAAAAAAAATTACTCAAACACAG
* *
5862552 ATAACCTCGATTTTGGGTATGACAACTCTCCCCACCTTAATGAAATTTCGTCCTT-AAATTTTTT
1 ATAACCTCAATTTTGGGTATGACAACTCTCCCCACCTTAATGAAATTTCAT-CTTCAAATTTTTT
*
5862616 TTCTACTTGATGGTAGATTGATATCATAGATTTAACAAAAAAAAAATTACTCAAACACAG
65 TTCGACTTGATGGTAGATTGATATCATAGATTTAAC-AAAAAAAAATTACTCAAACACAG
5862676 A
1 A
5862677 GAAAAACAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
122 90 0.78
123 3 0.03
124 22 0.19
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (123 bp):
ATAACCTCAATTTTGGGTATGACAACTCTCCCCACCTTAATGAAATTTCATCTTCAAATTTTTTT
TCGACTTGATGGTAGATTGATATCATAGATTTAACAAAAAAAAATTACTCAAACACAG
Found at i:5863061 original size:15 final size:15
Alignment explanation
Indices: 5863028--5863061 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5863018 TTATTATCAC
*
5863028 TTTATCAAAAAATAT
1 TTTATCAAAAAATAA
*
5863043 TTTATCAAAATATAA
1 TTTATCAAAAAATAA
5863058 TTTA
1 TTTA
5863062 AATCCGAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTATCAAAAAATAA
Found at i:5873474 original size:156 final size:155
Alignment explanation
Indices: 5873166--5873482 Score: 417
Period size: 156 Copynumber: 2.0 Consensus size: 155
5873156 AGAATGTCAT
* ** * *
5873166 AATCCTATGCTCGAATTTTCTAAAGTTTTCGTCTATGTTTTCCGGGAGTCCAGTGAGTGTCAAAT
1 AATCCTATGCTCAAATTTTCTAAACATTTCGTCTATGTTTTCCGAGAGTCCAGTGAGTGCCAAAT
* * * *
5873231 ACAAGAGTATGTCGCAATACCATGCTCGAATTTTCTAAGTTTTCGTCTATGTTTTCCAGGAGTCC
66 ACAAGAATATGTCGCAATACCATGATCGAATTTTCTAACTTTTAGTC-ATGTTTTCCAGGAGTCC
* *
5873296 AGTGGTGTCGAATATGAGTATGTCGC
130 AGTGGTGTCGAATATGACTATGTCGA
* *
5873322 AATCCTATTCTCAAATTTTCTAAACATTTCGTCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAAT
1 AATCCTATGCTCAAATTTTCTAAACATTTCGTCTATGTTTTCCGAGAGTCCAGTGAGTGCCAAAT
**
5873387 ACAAGAATATGTCGCAAT-CCTATGATCGAATTTTCTAACTTTTAGTC-TGTTTT-TGGGAGTCC
66 ACAAGAATATGTCGCAATACC-ATGATCGAATTTTCTAACTTTTAGTCATGTTTTCCAGGAGTCC
5873449 AGTGAGTG-CTGAATATGGGACTATGTCGA
130 AGTG-GTGTC-GAATAT--GACTATGTCGA
5873478 AATCC
1 AATCC
5873483 ATTATCCAAT
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
153 12 0.09
154 15 0.11
155 2 0.01
156 112 0.79
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (155 bp):
AATCCTATGCTCAAATTTTCTAAACATTTCGTCTATGTTTTCCGAGAGTCCAGTGAGTGCCAAAT
ACAAGAATATGTCGCAATACCATGATCGAATTTTCTAACTTTTAGTCATGTTTTCCAGGAGTCCA
GTGGTGTCGAATATGACTATGTCGA
Found at i:5873482 original size:76 final size:79
Alignment explanation
Indices: 5873122--5873456 Score: 386
Period size: 80 Copynumber: 4.3 Consensus size: 79
5873112 TTGTTTGTCG
* * **
5873122 ATGTTTAT-CGGGAGTCCAGTTAGTGTCAAATACAAGA--ATGTCATAATCCTATGCTCGAATTT
1 ATGTTT-TCCGGGAGTCCAGTGAGTGTCGAATACAAGAGTATGTCGCAATCCTATGCTCGAATTT
*
5873184 TCTAAAGTTTTCGTC
65 TCTAAACTTTTCGTC
*
5873199 TATGTTTTCCGGGAGTCCAGTGAGTGTCAAATACAAGAGTATGTCGCAATACC-ATGCTCGAATT
1 -ATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGAGTATGTCGCAAT-CCTATGCTCGAATT
*
5873263 TTCT-AAGTTTTCGTC
64 TTCTAAACTTTTCGTC
* * * *
5873278 TATGTTTTCCAGGAGTCCAGTG-GTGTCGAAT--ATGAGTATGTCGCAATCCTATTCTCAAATTT
1 -ATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGAGTATGTCGCAATCCTATGCTCGAATTT
*
5873340 TCTAAACATTTCGTC
65 TCTAAACTTTTCGTC
* * * *
5873355 TATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGCAATCCTATGATCGAATTT
1 -ATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGAGTATGTCGCAATCCTATGCTCGAATTT
*
5873420 TCT-AACTTTTAGTC
65 TCTAAACTTTTCGTC
*
5873434 -TGTTTT-TGGGAGTCCAGTGAGTG
1 ATGTTTTCCGGGAGTCCAGTGAGTG
5873457 CTGAATATGG
Statistics
Matches: 226, Mismatches: 22, Indels: 20
0.84 0.08 0.07
Matches are distributed among these distances:
75 2 0.01
76 43 0.19
77 36 0.16
78 50 0.22
79 41 0.18
80 52 0.23
81 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (79 bp):
ATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGAGTATGTCGCAATCCTATGCTCGAATTTT
CTAAACTTTTCGTC
Found at i:5876583 original size:18 final size:18
Alignment explanation
Indices: 5876560--5876613 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
5876550 GAGGGATTAT
5876560 TAGTGGTCTTTCGGGACA
1 TAGTGGTCTTTCGGGACA
*
5876578 TAGTGGTCCTTCGGGACA
1 TAGTGGTCTTTCGGGACA
5876596 TAGTGGTCTTTCGGGACA
1 TAGTGGTCTTTCGGGACA
5876614 AATATTCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
TAGTGGTCTTTCGGGACA
Found at i:5879373 original size:36 final size:36
Alignment explanation
Indices: 5879331--5879433 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
5879321 AGTTGAGTAG
5879331 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
5879367 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
5879403 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
5879434 CCAGCATCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:5888960 original size:17 final size:17
Alignment explanation
Indices: 5888938--5888996 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 17
5888928 CTAATATAAA
5888938 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
*
5888955 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--ATTTTT
5888975 TTAAACAAAATA-TTTT
1 TTAAACAAAATATTTTT
5888991 TTAAAC
1 TTAAAC
5888997 GTAAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 9 0.24
17 9 0.24
18 3 0.08
19 3 0.08
20 13 0.35
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:5889585 original size:4 final size:4
Alignment explanation
Indices: 5889576--5889660 Score: 86
Period size: 4 Copynumber: 21.8 Consensus size: 4
5889566 GTTTGGAACT
* **
5889576 TTTC TTTC TTTC TTTC -TTC -TTC TTTC TTTCC TTTC TCTC -TTC TCCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC
* * *
5889622 TTTC TTTA TTTA TTTC TGTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5889661 TTTGTGCTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
3 8 0.12
4 56 0.82
5 4 0.06
ACGTcount: A:0.02, C:0.27, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:5892949 original size:76 final size:76
Alignment explanation
Indices: 5892823--5892979 Score: 287
Period size: 76 Copynumber: 2.1 Consensus size: 76
5892813 CTTTAATAAA
*
5892823 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAGAAAAATGGAGACAATGGTCA
1 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
5892888 CACAAAATTTC
66 CACAAAATTTC
*
5892899 AACAATAGAACGAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
1 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
5892964 CACAAAATTTC
66 CACAAAATTTC
*
5892975 TACAA
1 AACAA
5892980 AAATAAAAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (76 bp):
AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
CACAAAATTTC
Found at i:5893013 original size:67 final size:74
Alignment explanation
Indices: 5892823--5893013 Score: 180
Period size: 76 Copynumber: 2.6 Consensus size: 74
5892813 CTTTAATAAA
* ** * * *
5892823 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAGAAAAATGGAGACAATGGTCA
1 AACAATAGAACGAAAAATAATTACAACACA-T-AAGCATACAAAAAAAAATGGAGACAATGGTCA
5892888 CACAAAATTTC
64 CACAAAATTTC
** * *
5892899 AACAATAGAACGAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
1 AACAATAGAACGAAAAATAATTACAACACA-T-AAGCATACAAAAAAAAATGGAGACAATGGTCA
5892964 CACAAAATTTC
64 CACAAAATTTC
* * *
5892975 TACAA-A-AA-TAAAAAT-ATTA-AACCCA-AAG-ATACAAAAAAA
1 AACAATAGAACGAAAAATAATTACAACACATAAGCATACAAAAAAA
5893014 TAAAACATTC
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
67 9 0.08
68 3 0.03
71 5 0.05
72 4 0.04
73 4 0.04
74 2 0.02
75 1 0.01
76 78 0.74
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.18
Consensus pattern (74 bp):
AACAATAGAACGAAAAATAATTACAACACATAAGCATACAAAAAAAAATGGAGACAATGGTCACA
CAAAATTTC
Found at i:5893993 original size:28 final size:29
Alignment explanation
Indices: 5893947--5894035 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
5893937 GGAATCAAAG
* *
5893947 AAAATTATAGGCTCC-AATT-TAAACATAA
1 AAAATTAAAGG-TCCTAATTATAAATATAA
*
5893975 AAAATTAAAGGTCCTAATTATAAATATTA
1 AAAATTAAAGGTCCTAATTATAAATATAA
** *
5894004 AAAATTGGAGGCCCTAATTATAAATATAA
1 AAAATTAAAGGTCCTAATTATAAATATAA
5894033 AAA
1 AAA
5894036 TTGAGAGCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.06
28 14 0.27
29 35 0.67
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (29 bp):
AAAATTAAAGGTCCTAATTATAAATATAA
Found at i:5895044 original size:2 final size:2
Alignment explanation
Indices: 5895037--5895086 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5895027 TCAATTACAA
5895037 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
5895079 AT AT AT AT
1 AT AT AT AT
5895087 TATTCAATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5895716 original size:15 final size:16
Alignment explanation
Indices: 5895687--5895717 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5895677 AACCCCATTT
5895687 AAATAAAATAATAAAA
1 AAATAAAATAATAAAA
5895703 AAATAAAA-AATAAAA
1 AAATAAAATAATAAAA
5895718 CCAGTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAATAATAAAA
Found at i:5904061 original size:14 final size:14
Alignment explanation
Indices: 5904026--5904067 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5904016 ACTATATGAA
5904026 TGAAAATTTTAGAAAC
1 TGAAAA-TTTA-AAAC
*
5904042 TG-AAATTTAAAAT
1 TGAAAATTTAAAAC
5904055 TGAAAATTTAAAA
1 TGAAAATTTAAAA
5904068 AGATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 3 0.12
16 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (14 bp):
TGAAAATTTAAAAC
Found at i:5905916 original size:25 final size:26
Alignment explanation
Indices: 5905870--5905921 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
5905860 TAATAAAAAA
5905870 ATATATCTAATGACAAATA-TTTAAT
1 ATATATCTAATGACAAATATTTTAAT
* *
5905895 ATATTTCTAATGA-TAATAATTTTAAT
1 ATATATCTAATGACAAAT-ATTTTAAT
5905921 A
1 A
5905922 ACTGATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 13 0.57
26 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATATCTAATGACAAATATTTTAAT
Found at i:5919068 original size:29 final size:29
Alignment explanation
Indices: 5918982--5919069 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 29
5918972 TAAAATATAT
* * *
5918982 AACTTTTAAAAATTACAATTTAGTCTCTA
1 AACTTTCAAAAATTATAATTTAGTCACTA
* ** * **
5919011 AATTTTTCAAAGTTTATACTTTAACCACTA
1 AA-CTTTCAAAAATTATAATTTAGTCACTA
* *
5919041 AACTTTCAAAACTTATATTTTAGTCACTA
1 AACTTTCAAAAATTATAATTTAGTCACTA
5919070 TACAAAATTT
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (29 bp):
AACTTTCAAAAATTATAATTTAGTCACTA
Found at i:5927211 original size:2 final size:2
Alignment explanation
Indices: 5927194--5927276 Score: 102
Period size: 2 Copynumber: 43.5 Consensus size: 2
5927184 AAGATACAAC
*
5927194 AT AT AA AT AT AT -T AT AT AT AT AT AT A- 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
* * *
5927234 AT -T AT GT AT AT AT AT AT AT AT AT AT GT AT A- AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5927274 AT A
1 AT A
5927277 CCTTTTTTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
1 4 0.06
2 65 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5927218 original size:15 final size:15
Alignment explanation
Indices: 5927194--5927276 Score: 105
Period size: 15 Copynumber: 5.6 Consensus size: 15
5927184 AAGATACAAC
* *
5927194 ATATAAATATATTAT
1 ATATATATATAATAT
5927209 ATATATATATAATAT
1 ATATATATATAATAT
*
5927224 ATATATATATATTAT
1 ATATATATATAATAT
*
5927239 GTATATATAT-ATAT
1 ATATATATATAATAT
*
5927253 ATATATGTATAATAT
1 ATATATATATAATAT
*
5927268 ATATTTATA
1 ATATATATA
5927277 CCTTTTTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATATATATAATAT
Found at i:5927939 original size:84 final size:83
Alignment explanation
Indices: 5927840--5929303 Score: 1217
Period size: 84 Copynumber: 17.7 Consensus size: 83
5927830 CGGAGTGTAA
* * * * * *
5927840 TCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAAAGGTGT
1 TCGAACTCGAAGGTCTT-GGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *
5927905 ACCTTGGAGTTGAGCGTAT
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
5927924 TCGAACTTGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * ** *
5927988 TGCCCTCGAAGCTGGGTATAA
64 TG-CCTTGGAGCTGAGCGTAG
* * * * * *
5928009 TCGAACTCGAAGGTC-T--TTGGTAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTA
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
5928071 CCTTAGAGCAGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * * *
5928089 TCAAACTTGAAGGTCTT--TTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TCGAACTCGAAGGTCTTGGTTGG-C--AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * * *
5928152 GTGCCCTCGAAGCTGAGTGTAA
63 GTG-CCTTGGAGCTGAGCGTAG
* * * * * *
5928174 TCGAACTCGAGGGTC-T--TTGGTAGATAGCCCTTCTCGACTTAAGTTGTGCTACAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
5928236 CTTTGGAGCTGAGCGTAA
66 CCTTGGAGCTGAGCGTAG
* * * *
5928254 TCGAACTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
5928319 ACCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * ** * * * *
5928338 TCGAACTCGAAGGCCTT--TTGGTCACAGATAACCCTTCTAGCCTTGGGTTATGTTGTAAATAAC
1 TCGAACTCGAAGGTCTTGGTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * * *
5928401 GTGCCCTCGAAGCTGAGTGTAA
63 GTG-CCTTGGAGCTGAGCGTAG
* * *
5928423 TCGAACTCGAGGGTC-T--TTGGCAGATAACCTTTCT-GACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
5928484 CCTTGGAGATGAGCATAG
66 CCTTGGAGCTGAGCGTAG
* * ** * *
5928502 TCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGCTAT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
5928567 GCCTTAGAGTTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * *
5928586 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * *
5928650 TGTCCTCGAAGCTGAGTGTAA
64 TG-CCTTGGAGCTGAGCGTAG
* * * * *
5928671 TCAAACTCGAGGGTC-T--TTGGCAGATAA-CCTTCTCGACTTAAGCTATG-TCGCAAATGATAT
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCT-GCAAATGATGT
* * *
5928731 GTCTTGGGGCTAAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * * **
5928750 TCGAACTCGAAGGTCTTTG-TGGTAGATAGCCCTTCTAGCCTTGAGATATGCTACAAAAAATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
5928814 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* ** * * * * *
5928832 TCGAACTCGAAGGTCTTGGATGTTAGACAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
*
5928897 CCTTGGAGCTGAGTGTAG
66 CCTTGGAGCTGAGCGTAG
** * * * *
5928915 TCGAACTCGAAGGTC-T--TTAACAGATAGCCCTTCTAGACTTAAG-CATTGCTGTAAATGGTGT
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTA-TGCTGCAAATGATGT
5928976 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * *
5928995 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
5929059 TGCCTTGGAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * *
5929079 TCGAACTCGAAGGTC-T--TTAGCATATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
5929141 CCCTGGAGCTGAGCATAG
66 CCTTGGAGCTGAGCGTAG
** * * * * **
5929159 TCGAACTCGAAGGTCTTTTGG-TGATAGATAACCCTTATAGCCTTGAGTTATGTTTTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
*
5929223 TGCCTTGGAGCTGAACGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * * *
5929243 TCAAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATG
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
5929304 TTTCTTTACA
Statistics
Matches: 1092, Mismatches: 242, Indels: 92
0.77 0.17 0.06
Matches are distributed among these distances:
79 52 0.05
80 229 0.21
81 108 0.10
82 61 0.06
83 94 0.09
84 438 0.40
85 108 0.10
86 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:5928063 original size:165 final size:163
Alignment explanation
Indices: 5927840--5929303 Score: 1329
Period size: 164 Copynumber: 8.9 Consensus size: 163
5927830 CGGAGTGTAA
* * * * * * *
5927840 TCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAAAGGTGT
1 TCGAACTCGAAGGTCTT---TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * * *
5927905 ACCTTGGAGTTGAGCGTATTCGAACTTGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
63 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTG-CAGATAACCCTTCTAGACTTAA
* * * * * ** *
5927970 GTTATGTTGTAAATGATGTGCCCTCGAAGCTGGGTATAA
126 GTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * *
5928009 TCGAACTCGAAGGTC-TTTGGTAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTACC
1 TCGAACTCGAAGGTCTTTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
* * * * * *
5928073 TTAGAGCAGAGCGTAGTCAAACTTGAAGGTCTTTTGGT-CATAGATAACCCTTCTAGCCTTGAGT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGC--AGATAACCCTTCTAGACTTAAGT
* * * * *
5928137 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
128 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * *
5928174 TCGAACTCGAGGGTC-TTTGGTAGATAGCCCTTCTCGACTTAAGTTGTGCTACAAATGATGTGCT
1 TCGAACTCGAAGGTCTTTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
* * *
5928238 TTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GCAGATAACCCTTCTAGACTTAAGTT
* *
5928303 ATGCTGCAAATGATATACCTTGGAGCTGAGCGTAG
129 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * ** * * * *
5928338 TCGAACTCGAAGGCCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTATGTTGTAAATAACGT
1 TCGAACTCGAAGGTCTTTTGGT---AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * * *
5928403 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-GCAGATAACCTTTCT-GACTTAAG
63 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAG
* * *
5928465 CTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAG
127 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
5928502 TCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGCTAT
1 TCGAACTCGAAGGTC-TT--TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
5928567 GCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
63 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTG-CAGATAACCCTTCTAGACTTAA
* * * * *
5928632 GTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAA
126 GTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * *
5928671 TCAAACTCGAGGGTC-TTTGGCAGATAA-CCTTCTCGACTTAAGCTATG-TCGCAAATGATATGT
1 TCGAACTCGAAGGTCTTTTGGTAGATAACCCTTCTCGACTTAAGTTATGCT-GCAAATGATGTGC
* * * * * * *
5928733 CTTGGGGCTAAGCGTAGTCGAACTCGAAGGTCTTT-GTGGTAGATAGCCCTTCTAGCCTTGAGAT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GCAGATAACCCTTCTAGACTTAAGTT
* **
5928797 ATGCTACAAAAAATGTGCCTTGGAGCTGAGCGTAG
129 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * * * * *
5928832 TCGAACTCGAAGGTCTTGGATGTTAGACAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTT--TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* ** * *
5928897 CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTT--AACAGATAGCCCTTCTAGACTTAAG-C
64 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGTT
* *
5928959 ATTGCTGTAAATGGTGTGCCTTGGAGCTGAGCGTAG
129 A-TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * *
5928995 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGT---AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
5929060 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT--AGCATATAACCCTTCTCGACTTAAGC
63 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGT
* * *
5929123 TATGATGCAAATGATGTGCCCTGGAGCTGAGCATAG
128 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * * **
5929159 TCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTATAGCCTTGAGTTATGTTTTAAATGATGT
1 TCGAACTCGAAGGTCTTTT-G-G-TAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * *
5929224 GCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAA
63 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GCAGATAACCCTTCTAGACTTAA
*
5929289 GCTATGCTGCAAATG
126 GTTATGCTGCAAATG
5929304 TTTCTTTACA
Statistics
Matches: 1090, Mismatches: 167, Indels: 77
0.82 0.13 0.06
Matches are distributed among these distances:
161 30 0.03
162 39 0.04
163 98 0.09
164 398 0.37
165 341 0.31
166 3 0.00
167 21 0.02
168 89 0.08
169 71 0.07
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (163 bp):
TCGAACTCGAAGGTCTTTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGTTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:5928588 original size:248 final size:248
Alignment explanation
Indices: 5927948--5929303 Score: 1493
Period size: 248 Copynumber: 5.5 Consensus size: 248
5927938 CTTTTGGTGA
* * * * * * * * ** *
5927948 CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGGGTATAATCGA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* * * * *
5928013 ACTCGAAGGTC--T-TTGGTAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTACCTT
65 ACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * * * *
5928075 AGAGCAGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
5928140 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
195 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * * * * *
5928194 TAGATAGCCCTTCTCGACTTAAGTTGTGCTACAAATGATGTGCTTTGGAGCTGAGCGTAATCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
5928259 CTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATACCTT
66 CTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* *
5928324 GGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
5928389 GTTGTAAATAACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
195 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
5928443 CAGATAACCTTTCT-GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
5928507 CTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGCTATGCCTT
66 CTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
5928572 AGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
* *
5928637 GCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGG
195 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * *
5928691 CAGATAA-CCTTCTCGACTTAAGCTATG-TCGCAAATGATATGTCTTGGGGCTAAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGCTATGCT-GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * * * * * **
5928754 ACTCGAAGGTCTTTG-TGGTAGATAGCCCTTCTAGCCTTGAGATATGCTACAAAAAATGTGCCTT
65 ACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
*** *
5928818 GGAGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGATGTTAGACAACCCTTCTAGCCTTGAGTTA
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTA
* * * * * **
5928881 TACTGTAAATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTAA
194 TGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
5928935 CAGATAGCCCTTCTAGACTTAAGC-ATTGCTGTAAATGGTGTGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGCTA-TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * * * *
5928999 ACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCT
65 ACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* * * * * *
5929064 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTAG---CATATAACCCTTCTCGACTTAAGCTA
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTA
* * * ** * *
5929125 TGATGCAAATGATGTGCCCT-GGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGGTG
194 TGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTT-G-G
* * * * * * ** * *
5929182 ATAGATAACCCTTATAGCCTTGAGTTATGTTTTAAATGATGTGCCTTGGAGCTGAACGTAGTCAA
1 -CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * *
5929247 ACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATG
65 ACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
5929304 TTTCTTTACA
Statistics
Matches: 949, Mismatches: 141, Indels: 38
0.84 0.12 0.03
Matches are distributed among these distances:
244 101 0.11
245 130 0.14
246 103 0.11
247 81 0.09
248 370 0.39
249 164 0.17
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (248 bp):
CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:5930086 original size:26 final size:26
Alignment explanation
Indices: 5930031--5930088 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5930021 GAATCAAGAG
* *
5930031 CTCTTTTAATGCTTTAAGAGTCATAG
1 CTCTTTTAATGCTTTAAGAGTCACAA
* *
5930057 CTCTTTTAATGCTTTCAGAGTTACAA
1 CTCTTTTAATGCTTTAAGAGTCACAA
5930083 CTCTTT
1 CTCTTT
5930089 GAAAAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (26 bp):
CTCTTTTAATGCTTTAAGAGTCACAA
Found at i:5942043 original size:31 final size:31
Alignment explanation
Indices: 5942007--5942066 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
5941997 AACTTAAAAG
* *
5942007 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
5942038 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
5942067 CATACAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:5942579 original size:20 final size:19
Alignment explanation
Indices: 5942531--5942579 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
5942521 AACTTAAATC
*
5942531 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
5942551 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
5942569 AAAATAATTTA
1 AAAATAATTTA
5942580 TATGATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:5942657 original size:12 final size:12
Alignment explanation
Indices: 5942640--5942720 Score: 67
Period size: 12 Copynumber: 6.4 Consensus size: 12
5942630 ATTTATTTAA
5942640 AAAATTAATATT
1 AAAATTAATATT
5942652 AAAATTAATATCT
1 AAAATTAATAT-T
*
5942665 ATAATATAATATT
1 AAAAT-TAATATT
5942678 AAAAAAATTAATATT
1 ---AAAATTAATATT
* *
5942693 -TAATTTAT-TT
1 AAAATTAATATT
5942703 AAAAATTAATATT
1 -AAAATTAATATT
5942716 AAAAT
1 AAAAT
5942721 CAAATATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 22 0.40
13 8 0.15
14 6 0.11
15 7 0.13
16 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:5942691 original size:15 final size:14
Alignment explanation
Indices: 5942607--5942719 Score: 70
Period size: 14 Copynumber: 8.8 Consensus size: 14
5942597 ATCTATAATA
5942607 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
5942621 TAATATT---TAAT
1 TAATATTAAAAAAT
*
5942632 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
5942645 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
5942657 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
5942671 TAATATTAAAAAAAT
1 TAATATT-AAAAAAT
*
5942686 TAATATT---TAAT
1 TAATATTAAAAAAT
*
5942697 T--TATTTAAAAAT
1 TAATATTAAAAAAT
5942709 TAATATTAAAA
1 TAATATTAAAA
5942720 TCAAATATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
9 4 0.05
10 2 0.03
11 10 0.13
12 15 0.20
13 8 0.11
14 26 0.35
15 10 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:5942693 original size:65 final size:64
Alignment explanation
Indices: 5942588--5942741 Score: 244
Period size: 64 Copynumber: 2.4 Consensus size: 64
5942578 TATATGATAT
5942588 AAATTAAATATCTATAATATAATATT-AAAAAATTAATATTTAATTTATTTAAAAAATTAATATT
1 AAATT-AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTT-AAAAATTAATATT
5942652 A
64 A
5942653 AAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
1 AAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
* *
5942717 AAATCAA-A--TATAATATAAAATTAAA
1 AAATTAATATCTATAATATAATATTAAA
5942742 TATAAAACCT
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
61 16 0.19
63 1 0.01
64 40 0.47
65 29 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (64 bp):
AAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
Found at i:5942735 original size:17 final size:18
Alignment explanation
Indices: 5942705--5942746 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
5942695 ATTTATTTAA
5942705 AAAT-TAATATTAAAATC
1 AAATATAATATTAAAATC
*
5942722 AAATATAATA-TAAAATT
1 AAATATAATATTAAAATC
5942739 AAATATAA
1 AAATATAA
5942747 AACCTCTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATATTAAAATC
Found at i:5943798 original size:29 final size:27
Alignment explanation
Indices: 5943735--5943799 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
5943725 ATAAAACAAT
*
5943735 ATAATAATATTTTTTGTAATATTAATTA
1 ATAAT-ATATTTTTTGTAAAATTAATTA
* *
5943763 A-AGTATATTATTTTGATAAAATTTATTA
1 ATAATATATT-TTTTG-TAAAATTAATTA
5943791 ATAATATAT
1 ATAATATAT
5943800 GTATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.17
27 7 0.23
28 12 0.40
29 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
ATAATATATTTTTTGTAAAATTAATTA
Found at i:5945827 original size:15 final size:15
Alignment explanation
Indices: 5945807--5945837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5945797 TTAAAACTAA
5945807 AATAAAATACGATTT
1 AATAAAATACGATTT
*
5945822 AATAAAATACTATTT
1 AATAAAATACGATTT
5945837 A
1 A
5945838 TATCTAATAA
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:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (15 bp):
AATAAAATACGATTT
Found at i:5952154 original size:23 final size:21
Alignment explanation
Indices: 5952102--5952163 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
5952092 TTTTGGTGCA
*
5952102 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
5952122 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
5952143 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
5952164 ACATCGATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:5955945 original size:22 final size:22
Alignment explanation
Indices: 5955918--5955961 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5955908 AATAATCACG
*
5955918 CGCTAAATTTTTTACTTAGTGA
1 CGCTAAATTTTTTAATTAGTGA
5955940 CGCTAAATTTTTTAATTAGTGA
1 CGCTAAATTTTTTAATTAGTGA
5955962 GGTAACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (22 bp):
CGCTAAATTTTTTAATTAGTGA
Found at i:5956465 original size:12 final size:12
Alignment explanation
Indices: 5956448--5956491 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
5956438 ATTCGTACCC
5956448 AAAATCATATAA
1 AAAATCATATAA
*
5956460 AAAATCATTTAA
1 AAAATCATATAA
* *
5956472 AAACTCA-GTAA
1 AAAATCATATAA
5956483 AAAATCATA
1 AAAATCATA
5956492 ACATAATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.25
Consensus pattern (12 bp):
AAAATCATATAA
Found at i:5956857 original size:160 final size:162
Alignment explanation
Indices: 5956652--5956977 Score: 620
Period size: 160 Copynumber: 2.0 Consensus size: 162
5956642 TTGGTTTGAT
5956652 TTGTTTTTGTTTTCGATCACGATCTTCATATCATCAATTTCCTAACATAAACAATTTCGAATACG
1 TTGTTTTTGTTTTCGATCACGATCTTCATATCATCAATTTCCTAACATAAACAATTTCGAATACG
* *
5956717 AATTAGTACTTTAACTAATAATATAATATTCGTTTATAATCAAACAACTTT-A-AAAAAATCGAC
66 AATCAGTACTTTAACTAATAATATAATATTCATTTATAATCAAACAACTTTAATAAAAAATCGAC
5956780 ACATATTCGAAACTAATTTCTCTCCCTTAATC
131 ACATATTCGAAACTAATTTCTCTCCCTTAATC
5956812 TTGTTTTTGTTTTCGATCACGATCTTCATATCATCAATTTCCTAACATAAACAATTTCGAATACG
1 TTGTTTTTGTTTTCGATCACGATCTTCATATCATCAATTTCCTAACATAAACAATTTCGAATACG
5956877 AATCAGTACTTTAACTAATAATATAATATTCATTTATAATCAAACAACTTTAATAAAAAATCGAC
66 AATCAGTACTTTAACTAATAATATAATATTCATTTATAATCAAACAACTTTAATAAAAAATCGAC
5956942 ACATATTCGAAACTAATTTCTCTCCCTTAATC
131 ACATATTCGAAACTAATTTCTCTCCCTTAATC
5956974 TTGT
1 TTGT
5956978 GAAACTTTCC
Statistics
Matches: 162, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
160 114 0.70
161 1 0.01
162 47 0.29
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (162 bp):
TTGTTTTTGTTTTCGATCACGATCTTCATATCATCAATTTCCTAACATAAACAATTTCGAATACG
AATCAGTACTTTAACTAATAATATAATATTCATTTATAATCAAACAACTTTAATAAAAAATCGAC
ACATATTCGAAACTAATTTCTCTCCCTTAATC
Found at i:5961416 original size:21 final size:20
Alignment explanation
Indices: 5961330--5961484 Score: 80
Period size: 21 Copynumber: 7.7 Consensus size: 20
5961320 AAATGACCAA
**
5961330 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5961349 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5961369 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5961389 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5961410 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5961431 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5961451 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5961472 GAAAATCGCAACG
1 CAAAATCGCAACG
5961485 TGAACACATA
Statistics
Matches: 101, Mismatches: 29, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 38 0.38
21 47 0.47
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5961478 original size:20 final size:20
Alignment explanation
Indices: 5961454--5961763 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
5961444 CGATTTTCCA
* ** *
5961454 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
5961474 AAATCGCAACGTGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
5961494 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
5961514 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
5961534 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
5961554 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
5961574 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
5961594 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5961614 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5961634 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5961654 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5961674 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5961694 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5961714 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5961734 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5961754 AAATCACAAC
1 AAATCGCAAC
5961764 ACTGAAATTT
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
20 253 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:5962482 original size:24 final size:24
Alignment explanation
Indices: 5962443--5962489 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5962433 GAATTTGGTC
5962443 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5962467 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5962490 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5964978 original size:19 final size:19
Alignment explanation
Indices: 5964909--5965025 Score: 103
Period size: 19 Copynumber: 6.7 Consensus size: 19
5964899 GCAACGAGAG
5964909 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5964928 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5964942 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5964962 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
5964980 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
5964994 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
* *
5965013 AACCGCATTGCGA
1 AATCGCAATGCGA
5965026 TTCTCCCGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
13 1 0.01
14 21 0.27
16 5 0.06
17 1 0.01
18 10 0.13
19 25 0.32
20 16 0.20
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5965058 original size:19 final size:19
Alignment explanation
Indices: 5965034--5965130 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 19
5965024 GATTCTCCCG
*
5965034 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
5965053 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5965072 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
5965086 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5965105 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5965124 TTGCGAT
1 TTGCGAT
5965131 AGTCAATTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 49 0.72
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5965073 original size:52 final size:52
Alignment explanation
Indices: 5965016--5965130 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 52
5965006 AAATTAAAAC
5965016 CGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTT
* * *
5965068 CGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTT
5965120 CGCATTGCGAT
1 CGCATTGCGAT
5965131 AGTCAATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (52 bp):
CGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTT
Found at i:5965256 original size:14 final size:14
Alignment explanation
Indices: 5965237--5965273 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5965227 CATCAATTAC
5965237 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5965251 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5965265 ACAAATCAA
1 ACAAATCAA
5965274 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5967266 original size:14 final size:14
Alignment explanation
Indices: 5967247--5967303 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5967237 GCGAAATGAA
*
5967247 AATCGCAACGACAG
1 AATCGCAACGAAAG
5967261 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5967278 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5967294 AATCGCAACG
1 AATCGCAACG
5967304 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5967274 original size:33 final size:33
Alignment explanation
Indices: 5967228--5967320 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5967218 GCGAAACCAA
*
5967228 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5967261 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5967294 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5967321 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5967285 original size:19 final size:19
Alignment explanation
Indices: 5967191--5967325 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5967181 TAGTTTACTT
* *
5967191 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5967211 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5967230 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5967249 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5967263 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5967282 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5967296 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5967315 TCGCAATGCGA
1 TCGCAACGCGA
5967326 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Done.