Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001846.1 Hibiscus syriacus cultivar Beakdansim tig00003741_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: 130816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:558 original size:41 final size:41
Alignment explanation
Indices: 423--540 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 41
413 CATTGCGATT
* * *
423 TTATCGCGTTGTGATAGTCA-AATCGCGTTGTGATTTTGTA
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
* * *
463 TTATCGCGTTACGATAGTCAGAATCGCCTTACGATTTTGTA
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
* *
504 TTATCCCTTTGCGATAGTCAGAATCGCATTGCGATTT
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTT
541 ACATATTCGC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 18 0.27
41 49 0.73
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (41 bp):
TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
Found at i:628 original size:20 final size:19
Alignment explanation
Indices: 605--650 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
595 GGAAACTGAT
* *
605 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
625 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
644 TTGCGAT
1 TTGCGAT
651 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:640 original size:19 final size:19
Alignment explanation
Indices: 616--652 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
606 TGCGATACTG
*
616 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
635 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
653 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:5028 original size:29 final size:30
Alignment explanation
Indices: 4973--5033 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
4963 ATTTTGGGTC
*
4973 CTAAACTTTTCAAAGTTCATACTTTAGCCA
1 CTAAACTTTTCAAACTTCATACTTTAGCCA
* *
5003 CTAAAC-TTTCTAAACTT-ATATTTTAGTCA
1 CTAAACTTTTC-AAACTTCATACTTTAGCCA
5032 CT
1 CT
5034 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAACTTCATACTTTAGCCA
Found at i:8668 original size:21 final size:21
Alignment explanation
Indices: 8643--8695 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
8633 CACAACGGAA
8643 ACAAGCTCCAGTCTTCATTCT
1 ACAAGCTCCAGTCTTCATTCT
8664 ACAAGCTCCAGTCTTCATTCT
1 ACAAGCTCCAGTCTTCATTCT
*
8685 ACAAACTCCAG
1 ACAAGCTCCAG
8696 GGTGATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.28
Consensus pattern (21 bp):
ACAAGCTCCAGTCTTCATTCT
Found at i:9880 original size:18 final size:17
Alignment explanation
Indices: 9847--9882 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9837 GAACAATTAA
9847 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
9864 ATAAAATTATTAAAATAT
1 ATAAAA-TATCAAAATAT
9882 A
1 A
9883 ACAGACTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:12436 original size:29 final size:30
Alignment explanation
Indices: 12381--12441 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
12371 ATTTTGGGTC
*
12381 CTAAACTTTTCAAAGTTCATACTTTAGCCA
1 CTAAACTTTTCAAACTTCATACTTTAGCCA
* *
12411 CTAAAC-TTTCTAAACTT-ATATTTTAGTCA
1 CTAAACTTTTC-AAACTTCATACTTTAGCCA
12440 CT
1 CT
12442 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAACTTCATACTTTAGCCA
Found at i:28137 original size:32 final size:32
Alignment explanation
Indices: 28099--28161 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
28089 CTTGTTTAGT
*
28099 GGCGGTATG-GAGGTGCACCCCATTCTGGTGGC
1 GGCGGTA-GAGAGGTACACCCCATTCTGGTGGC
28131 GGCGGTAGAAGAGGTACACCCCATTCTGGTG
1 GGCGGTAG-AGAGGTACACCCCATTCTGGTG
28162 CCGCCGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.04
32 7 0.25
33 20 0.71
ACGTcount: A:0.17, C:0.24, G:0.38, T:0.21
Consensus pattern (32 bp):
GGCGGTAGAGAGGTACACCCCATTCTGGTGGC
Found at i:28871 original size:24 final size:21
Alignment explanation
Indices: 28820--28873 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
28810 AAAATTTTTA
*
28820 TTATTTTAAATATATAAAAAT
1 TTATTATAAATATATAAAAAT
* *
28841 ATGTTATAGAATATATAATAAGAT
1 TTATTATA-AATATATAA-AA-AT
28865 TTATTATAA
1 TTATTATAA
28874 GAAAGTGCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 3 0.12
24 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TTATTATAAATATATAAAAAT
Found at i:29111 original size:3 final size:3
Alignment explanation
Indices: 29103--29160 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
29093 AGTATCTAAT
*
29103 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29151 TTA TTA TTA T
1 TTA TTA TTA T
29161 CACATTTGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29888 original size:3 final size:3
Alignment explanation
Indices: 29880--29914 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29870 TCATAGTGTT
29880 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29915 TTCTTCTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38048 original size:2 final size:2
Alignment explanation
Indices: 38041--38081 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38031 AAATTTATCA
38041 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
38082 ATGTTAAGAT
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:53345 original size:15 final size:15
Alignment explanation
Indices: 53322--53353 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53312 CCCCCTTACT
*
53322 TTAATACTACTCCTC
1 TTAACACTACTCCTC
53337 TTAACACTACTCCTC
1 TTAACACTACTCCTC
53352 TT
1 TT
53354 TAAAACGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAACACTACTCCTC
Found at i:58729 original size:21 final size:20
Alignment explanation
Indices: 58692--58732 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
58682 CCAGAACCTC
*
58692 AGGGGGGTATCGATTCCCCT
1 AGGGGGGAATCGATTCCCCT
*
58712 AGGGGAGGAATCGGTTCCCCT
1 AGGGG-GGAATCGATTCCCCT
58733 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (20 bp):
AGGGGGGAATCGATTCCCCT
Found at i:72629 original size:14 final size:14
Alignment explanation
Indices: 72610--72648 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
72600 ATATTGACTC
72610 ATATTATGTTATGT
1 ATATTATGTTATGT
72624 ATATTATGTT-TGT
1 ATATTATGTTATGT
*
72637 AGAATTATGTTA
1 A-TATTATGTTA
72649 AAAATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (14 bp):
ATATTATGTTATGT
Found at i:78964 original size:2 final size:2
Alignment explanation
Indices: 78957--78987 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
78947 CAATTGTCAA
78957 AT AT AT AT AT AT AT -T 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
78988 TCATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:78977 original size:15 final size:15
Alignment explanation
Indices: 78957--78985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
78947 CAATTGTCAA
78957 ATATATATATATATT
1 ATATATATATATATT
78972 ATATATATATATAT
1 ATATATATATATAT
78986 ATTCATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:80852 original size:37 final size:37
Alignment explanation
Indices: 80795--80899 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
80785 CCTTTTCGTC
* *
80795 CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
80832 TTGCTATGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
80869 CTACTATAATTTAAACTCCTAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
80900 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:81439 original size:19 final size:19
Alignment explanation
Indices: 81417--81467 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
81407 TTTCATTTGG
*
81417 TTATTTTTTA-ATACTATAT
1 TTATTATTTATATA-TATAT
81436 TTATTATTTATATATATAT
1 TTATTATTTATATATATAT
* *
81455 ATA-TATATATATA
1 TTATTATTTATATA
81468 CTTTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.32
19 16 0.57
20 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTTATATATATAT
Found at i:81508 original size:2 final size:2
Alignment explanation
Indices: 81501--81526 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81491 AAGCGTATTA
81501 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
81527 TGTAATTATC
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:81648 original size:19 final size:19
Alignment explanation
Indices: 81621--81660 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
81611 TCATTATATG
81621 TATACTTTTATATTTGGTT
1 TATACTTTTATATTTGGTT
* * *
81640 TATATTTTTATTTTTGTTT
1 TATACTTTTATATTTGGTT
81659 TA
1 TA
81661 GGTTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (19 bp):
TATACTTTTATATTTGGTT
Found at i:81835 original size:16 final size:15
Alignment explanation
Indices: 81773--81841 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
81763 TCATTTATTT
*
81773 ATTTATTTATTTTTC
1 ATTTTTTTATTTTTC
*
81788 CTTTTATTT-TTTTT-
1 ATTTT-TTTATTTTTC
*
81802 ACTTATTTTTATTCTTC
1 A-TT-TTTTTATTTTTC
81819 ATTTTTTTATTTTTTC
1 ATTTTTTTA-TTTTTC
81835 ATTTTTT
1 ATTTTTT
81842 CCTCTAACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
15 19 0.44
16 23 0.53
17 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTTTATTTTTC
Found at i:86257 original size:17 final size:16
Alignment explanation
Indices: 86229--86310 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
86219 AGATCCAATC
*
86229 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAAAA
*
86244 AAGAAGCAAAAAAACA
1 AAGAAGCAAAAAAAAA
* * *
86260 AAGAAACAAAAGAAAC
1 AAGAAGCAAAAAAAAA
*
86276 AA-AAG-AAAAAAAGA
1 AAGAAGCAAAAAAAAA
*
86290 AAGAA-CAAAAATCAAA
1 AAGAAGCAAAAA-AAAA
86306 AAGAA
1 AAGAA
86311 AAAGGGACAA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
14 8 0.16
15 14 0.27
16 29 0.57
ACGTcount: A:0.78, C:0.09, G:0.12, T:0.01
Consensus pattern (16 bp):
AAGAAGCAAAAAAAAA
Found at i:86266 original size:8 final size:8
Alignment explanation
Indices: 86243--86291 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
86233 ACAAAAAAGA
*
86243 AAAGAAGC
1 AAAGAAAC
*
86251 AAAAAAAC
1 AAAGAAAC
86259 AAAGAAAC
1 AAAGAAAC
86267 AAAAGAAAC
1 -AAAGAAAC
*
86276 AAAAGAAAA
1 -AAAGAAAC
86285 AAAGAAA
1 AAAGAAA
86292 GAACAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
8 20 0.56
9 16 0.44
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAC
Found at i:86271 original size:9 final size:9
Alignment explanation
Indices: 86242--86291 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
86232 AACAAAAAAG
*
86242 AAAAGAAGC
1 AAAAGAAAC
86251 AAAA-AAAC
1 AAAAGAAAC
86259 -AAAGAAAC
1 AAAAGAAAC
86267 AAAAGAAAC
1 AAAAGAAAC
86276 AAAAGAAA-
1 AAAAGAAAC
86284 AAAAGAAA
1 AAAAGAAA
86292 GAACAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
7 3 0.08
8 15 0.39
9 20 0.53
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:86273 original size:30 final size:29
Alignment explanation
Indices: 86237--86299 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
86227 TCAAGAACAA
*
86237 AAAAGAAA-AGAAGCAAAAAAACAAAGAAAC
1 AAAAGAAACAAAAG-AAAAAAACAAAG-AAC
*
86267 AAAAGAAACAAAAGAAAAAAAGAAAGAAC
1 AAAAGAAACAAAAGAAAAAAACAAAGAAC
86296 AAAA
1 AAAA
86300 ATCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 19 0.63
31 4 0.13
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (29 bp):
AAAAGAAACAAAAGAAAAAAACAAAGAAC
Found at i:88053 original size:106 final size:106
Alignment explanation
Indices: 87925--88987 Score: 1761
Period size: 106 Copynumber: 10.0 Consensus size: 106
87915 ATATCGTGCC
* * * * *
87925 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
87990 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
88031 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
88096 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
88137 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
88202 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
88243 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
88308 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
88349 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
88414 AATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
88455 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
88520 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
88561 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
88626 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
88667 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAGTAAA-AATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
88731 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
88772 ACTCAAGACAACGAAAGTTCAACTTCATGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
88837 AATTTCAGAGTCAATTTCGACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
88878 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
88943 AATTCCAGAGCCAATTTCAACTTCA-TGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
88984 ACTC
1 ACTC
88988 GGAAAAATGC
Statistics
Matches: 894, Mismatches: 61, Indels: 4
0.93 0.06 0.00
Matches are distributed among these distances:
105 95 0.11
106 799 0.89
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:89771 original size:37 final size:37
Alignment explanation
Indices: 89720--89822 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
89710 TTTTCGTCCA
*
89720 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTCT
* * *
89757 GCTAGGATTCAAACTCCTAAAAATATGATAGAGTTCT
1 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTCT
* *
89794 ACTATGAATT-AAACTCCTAAAGATAGGAT
1 ACTA-GGATTCAAACTCCTAAAAATAGGAT
89823 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 53 0.93
38 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (37 bp):
ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTCT
Found at i:90320 original size:21 final size:23
Alignment explanation
Indices: 90285--90329 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
90275 TTGATTTTTT
90285 TACACTATATATTATTA-TTATA
1 TACACTATATATTATTATTTATA
*
90307 TACA-TATATTTTATTATTTATA
1 TACACTATATATTATTATTTATA
90329 T
1 T
90330 TCATTTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (23 bp):
TACACTATATATTATTATTTATA
Found at i:90687 original size:4 final size:4
Alignment explanation
Indices: 90651--90756 Score: 54
Period size: 4 Copynumber: 26.0 Consensus size: 4
90641 TATTTTACTC
* * * * *
90651 ATTT ATAT ATAT ATAT ATAT ATAT ATTT CATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT
* * * * * *
90700 -TTCCT -TTT ATTT TTTT ACTT ATTT TTATT CTTT ATTT TTTT ACTT ATTT
1 ATT--T ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
*
90749 TTTT ATTT
1 ATTT ATTT
90757 TTTCATTTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.04
4 69 0.84
5 10 0.12
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:90709 original size:24 final size:25
Alignment explanation
Indices: 90681--90750 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
90671 ATATATTTCA
* * *
90681 TTTATTTATTTATTTATTTTTCCT-
1 TTTATTTTTTTACTTATTTTTACTC
*
90705 TTTATTTTTTTACTTATTTTTATTC
1 TTTATTTTTTTACTTATTTTTACTC
90730 TTTATTTTTTTACTTATTTTT
1 TTTATTTTTTTACTTATTTTT
90751 TTATTTTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTATTTTTTTACTTATTTTTACTC
Found at i:90757 original size:8 final size:8
Alignment explanation
Indices: 90681--90767 Score: 61
Period size: 8 Copynumber: 10.2 Consensus size: 8
90671 ATATATTTCA
*
90681 TTTATTTA
1 TTTATTTT
90689 TTTATTTAT
1 TTTATTT-T
**
90698 TTT-TCCT
1 TTTATTTT
90705 TTTATTTT
1 TTTATTTT
90713 TTTACTTATT
1 TTTA-TT-TT
90723 TTTATTCTT
1 TTTATT-TT
90732 TATT-TTTT
1 T-TTATTTT
90740 TACTTATTTT
1 T--TTATTTT
90750 TTTATTTT
1 TTTATTTT
*
90758 TTCATTTT
1 TTTATTTT
90766 TT
1 TT
90768 CCTCTAACAC
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
7 4 0.06
8 33 0.52
9 14 0.22
10 13 0.20
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:90765 original size:25 final size:25
Alignment explanation
Indices: 90680--90756 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 25
90670 TATATATTTC
* * **
90680 ATTTATTTATTTATTTATTTTTCCT
1 ATTTATTTTTTTACTTATTTTTATT
90705 -TTTATTTTTTTACTTATTTTTATT
1 ATTTATTTTTTTACTTATTTTTATT
*
90729 CTTTATTTTTTTACTTATTTTT-TT
1 ATTTATTTTTTTACTTATTTTTATT
90753 ATTT
1 ATTT
90757 TTTCATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.54
25 21 0.46
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (25 bp):
ATTTATTTTTTTACTTATTTTTATT
Found at i:96361 original size:23 final size:23
Alignment explanation
Indices: 96309--96361 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
96299 AAATTTAATT
*
96309 AAAAA-TAAAAAACCAATAATAA
1 AAAAAGTAAAAAAACAATAATAA
*
96331 AAACAGTAAAAAAACAA-AATAA
1 AAAAAGTAAAAAAACAATAATAA
96353 AAATAAGTA
1 AAA-AAGTA
96362 CAAGGACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAGTAAAAAAACAATAATAA
Found at i:97450 original size:28 final size:28
Alignment explanation
Indices: 97418--97483 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
97408 AAACAGGGGG
*
97418 TTGTGGGCGTTGGTGTTGAAATATGGGA
1 TTGTGGGCGTTGGTGTTGAAATATGAGA
97446 TTGTGGGCGTTGGTGTTGAAATATGAGA
1 TTGTGGGCGTTGGTGTTGAAATATGAGA
*
97474 TGGT-GGCGTT
1 TTGTGGGCGTT
97484 TGAATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.17, C:0.05, G:0.42, T:0.36
Consensus pattern (28 bp):
TTGTGGGCGTTGGTGTTGAAATATGAGA
Found at i:98034 original size:39 final size:39
Alignment explanation
Indices: 97989--98387 Score: 611
Period size: 39 Copynumber: 10.3 Consensus size: 39
97979 AGTTTCTTAT
* * *
97989 AAAATCTTTTGTTTCGAGAGAAACCATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
98028 ACAATCTTCTGTTTCGAGGGAAACTATCTCAAGTGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
98067 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
98106 AAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAAAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * *
98145 AAAATCTTCTGTTTCAAGAGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
98184 AAAATCTTCTGTTTGGAGGGAAACTATCTCAAGCAAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
98223 AAAATCTTCAGTTTCGAGGGAAACTATCTCAAACGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
98262 AAAATCTTCAGTTTCGAGGGAAACTATCTCAAGCGATAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
98301 AAAATCTTCTGTTTCGAGAGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * *
98340 AAAATCTTTTGTTTCAAGGG-AACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
98378 AAAATCTTCT
1 AAAATCTTCT
98388 TTAAAACAAT
Statistics
Matches: 327, Mismatches: 33, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
38 26 0.08
39 301 0.92
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (39 bp):
AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
Found at i:98508 original size:76 final size:78
Alignment explanation
Indices: 98390--98534 Score: 190
Period size: 77 Copynumber: 1.9 Consensus size: 78
98380 AATCTTCTTT
* * *
98390 AAAACAATCTTGAGTGAAATGAAGTGTCTTCTTTTAAGT-AAAAATTGTCTCAAGCGAGACA-AA
1 AAAACAATCTTGAGTGAAATGAAATCTCTTCTTTTAAGTAAAAAACTGTCTCAAGCGAGACAGAA
98453 TCTTGTTTTAAGA
66 TCTTGTTTTAAGA
* * *
98466 AAAACAATCTTGAGTGAAAT-AAATCTTTTTTTTTCGAA-TAAAAAACTGTCTCAAGCGAGGCAG
1 AAAACAATCTTGAGTGAAATGAAATCTCTTCTTTT--AAGTAAAAAACTGTCTCAAGCGAGACAG
98529 AATCTT
64 AATCTT
98535 CTGTTTCAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
75 10 0.17
76 21 0.36
77 22 0.37
78 6 0.10
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (78 bp):
AAAACAATCTTGAGTGAAATGAAATCTCTTCTTTTAAGTAAAAAACTGTCTCAAGCGAGACAGAA
TCTTGTTTTAAGA
Found at i:98558 original size:39 final size:39
Alignment explanation
Indices: 98514--98588 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
98504 TAAAAAACTG
* * * *
98514 TCTCAAGCGAGGCAGAATCTTCTGTTTCAAGGGAAATTA
1 TCTCAAGCGAGACAAAATCTTATGTTTCAAGCGAAATTA
*
98553 TCTCAAGCGAGACAAAATCTTATGTTTTAAGCGAAA
1 TCTCAAGCGAGACAAAATCTTATGTTTCAAGCGAAA
98589 CAACTCTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTATGTTTCAAGCGAAATTA
Found at i:98618 original size:60 final size:60
Alignment explanation
Indices: 98536--98649 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
98526 CAGAATCTTC
* *
98536 TGTTTCAAGGGAAATTATCTCAAGCGAGACAAAATCTTATGTTTTAAGCGAAACAACTCT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTTAAGAGAAACAACTCT
* * * * * *
98596 TGTTTTAAGTGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTTGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTTAAGAGAAAC
98650 CATCTCAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTTAAGAGAAACAACTCT
Found at i:98655 original size:39 final size:39
Alignment explanation
Indices: 98596--98674 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
98586 AAACAACTCT
* * *
98596 TGTTTTAAGTGAAACTATCTCAAGTGAGATAAAATCTTC
1 TGTTTTAAGAGAAACCATCTCAAGTGAGATAAAATATTC
*
98635 TGTTTTGAGAGAAACCATCTCAAGTGAGATAAAATATTC
1 TGTTTTAAGAGAAACCATCTCAAGTGAGATAAAATATTC
98674 T
1 T
98675 TTAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (39 bp):
TGTTTTAAGAGAAACCATCTCAAGTGAGATAAAATATTC
Found at i:103925 original size:29 final size:30
Alignment explanation
Indices: 103855--103926 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
103845 TTACATTGAC
* *
103855 TAAAATGTAAGAAAATAAAAAGTTAGTAGT
1 TAAAATGAAATAAAATAAAAAGTTAGTAGT
* *
103885 TAATATGCAATAAAAT-AAAAGTTAGTAGT
1 TAAAATGAAATAAAATAAAAAGTTAGTAGT
103914 TAGAAAT-AAATAA
1 TA-AAATGAAATAA
103927 CATAGCAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.57, C:0.01, G:0.14, T:0.28
Consensus pattern (30 bp):
TAAAATGAAATAAAATAAAAAGTTAGTAGT
Found at i:110267 original size:31 final size:32
Alignment explanation
Indices: 110218--110299 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
110208 CTTTTTCATT
*
110218 TAAGTACTTAAAGTATTTTTTT-GG-TCAAAA
1 TAAGTACTAAAAGTATTTTTTTGGGATCAAAA
*
110248 TAAGTATCTAAAATTATTTTTTTGGGATCAAAA
1 TAAGTA-CTAAAAGTATTTTTTTGGGATCAAAA
110281 T-AGATAC-ATAAAGTATTTT
1 TAAG-TACTA-AAAGTATTTT
110300 ATGTCAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
30 6 0.14
31 15 0.34
32 14 0.32
33 9 0.20
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (32 bp):
TAAGTACTAAAAGTATTTTTTTGGGATCAAAA
Found at i:113178 original size:43 final size:43
Alignment explanation
Indices: 113122--113213 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 43
113112 TCTTATTACC
* * *
113122 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATTGATTATTTT
1 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
113165 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
1 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
113208 ATTAAA
1 ATTAAA
113214 TTAACTAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (43 bp):
ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
Found at i:119158 original size:602 final size:602
Alignment explanation
Indices: 118014--119820 Score: 3551
Period size: 602 Copynumber: 3.0 Consensus size: 602
118004 CCAAATGTGG
118014 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
1 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
*
118079 AGTTCTAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
66 AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
*
118144 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAATTTCAGCCACCATTTTCACCCGAATTATG
131 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
*
118209 TCTCTAAAGTCAACAAATGAGATATGAGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
196 TCTCTAAAGTCAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
118274 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
261 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
118339 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
326 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
118404 CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
391 CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
118469 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
456 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
118534 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
521 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
118599 CATCACAATAATGGCAA
586 CATCACAATAATGGCAA
118616 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
1 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
118681 AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
66 AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
118746 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
131 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
118811 TCTCTAAAGTCAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
196 TCTCTAAAGTCAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
118876 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
261 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
118941 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
326 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
119006 CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
391 CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
119071 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
456 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
119136 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
521 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
119201 CATCACAATAATGGCAA
586 CATCACAATAATGGCAA
119218 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
1 GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
119283 AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
66 AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
119348 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
131 AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
*
119413 TCTCTAAAGTTAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
196 TCTCTAAAGTCAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
119478 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
261 TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
119543 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
326 CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
* * *
119608 CTGGCAGACTCGAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAAATTTGATTCTACTGT
391 CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
119673 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
456 TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
119738 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
521 AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
119803 CATCACAATAATGGCAA
586 CATCACAATAATGGCAA
119820 G
1 G
119821 AATAGGAAGC
Statistics
Matches: 1198, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
602 1198 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (602 bp):
GCAGTTCGCAAGGAGACATATTTGGAGGCTTTGGATCTTTGGGAAGCAGTGGAAGAGGACTACAT
AGTTCCAGAAATTCCAGCCAATCCCACTTTGGCTCAGATCAAAGCACATAAGGAGAAGAAGATGA
AAAAAGCTAAGGCAAAATCCTGCTTGTTTGCTGCAGTTTCAGCCACCATTTTCACCCGAATTATG
TCTCTAAAGTCAACAAATGAGATATGGGATTATCTCAAGGCTGAGTACGAAGGGGATGAGAGAAT
TCGTGGGATGCAGGTGCTGAATTTAGTTCGTGATTTTGAGCTGTAAAAGATGAAGGAAACTGAGA
CAGTCAAGGAGTATGATGAAAGACTTCTTAGCATAGCAAACCGAGTCCGGTTGCTGGGATCATCT
CTGGCAGACTCAAGGATTGTGGAGAAAATCCTTGTAACATTGCCTGAAAATTTTGAGTCTACTGT
TACCACCTTGGATAATATCAAGGACTTGTCCAAGATTCCTCTGGCAGAACTCTTGAGTGCCTTGC
AAGCACAAGAGCAGAGGCATGCAATGAGACAAGAAGGAACTATTGAAGGAGCTCTAGCAGCTAAG
CATCACAATAATGGCAA
Found at i:124215 original size:11 final size:12
Alignment explanation
Indices: 124175--124218 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
124165 TATTTAAACG
*
124175 GGTATTGGGCCA
1 GGTATTGGGTCA
*
124187 GGTATTGGGTCG
1 GGTATTGGGTCA
124199 GGTATTGGGTC-
1 GGTATTGGGTCA
124210 GGTATTGGG
1 GGTATTGGG
124219 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:124217 original size:23 final size:24
Alignment explanation
Indices: 124173--124218 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
124163 ATTATTTAAA
124173 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
124197 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
124219 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:124300 original size:24 final size:25
Alignment explanation
Indices: 124236--124300 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
124226 TCGGGCCGGG
124236 TATATATATATATATATTTAAATTAAA
1 TATATAT-TATAT-TATTTAAATTAAA
*
124263 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
124287 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
124301 ATATATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.56
25 2 0.06
26 1 0.03
27 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:127037 original size:1 final size:1
Alignment explanation
Indices: 127031--127058 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
127021 TCTAAACCGC
127031 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
127059 CTAAACTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:130331 original size:25 final size:25
Alignment explanation
Indices: 130282--130341 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
130272 CTTAATCATC
130282 ATTTTAAAT-ATATTTAAAAATATT
1 ATTTTAAATAATATTTAAAAATATT
*
130306 ATTTTAAATAATTTTTAAATAA-ATT
1 ATTTTAAATAATATTTAAA-AATATT
130331 ATTTTAAATAA
1 ATTTTAAATAA
130342 GAAATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 9 0.27
25 22 0.67
26 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTAAATAATATTTAAAAATATT
Found at i:130339 original size:14 final size:14
Alignment explanation
Indices: 130294--130341 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
130284 TTTAAATATA
130294 TTTAAA-AATATTAT
1 TTTAAATAA-ATTAT
130308 TTTAAAT-AA-T-T
1 TTTAAATAAATTAT
130319 TTTAAATAAATTAT
1 TTTAAATAAATTAT
130333 TTTAAATAA
1 TTTAAATAA
130342 GAAATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.27
12 3 0.10
13 2 0.07
14 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATAAATTAT
Done.