Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 23
Found at i:3607013 original size:19 final size:18
Alignment explanation
Indices: 3606991--3607037 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3606981 AGTGAATAAT
3606991 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
3607010 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
3607029 AATA-AAGAA
1 AATATAAGAA
3607038 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:3608385 original size:30 final size:31
Alignment explanation
Indices: 3608345--3608404 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3608335 ACATGCTGCC
**
3608345 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
3608376 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
3608405 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:3611639 original size:238 final size:238
Alignment explanation
Indices: 3611221--3611655 Score: 746
Period size: 238 Copynumber: 1.8 Consensus size: 238
3611211 CTGGAAAAGA
* *
3611221 AGTCGAAGTGTTGGAATTGTCCATCAAGCCAGGAAATAGAAGACTGATGTTTCCTTGTACATTCG
1 AGTCGAAGTGTTGGAATTGTCCACCAAGCCAGGAAATAGAAGAATGATGTTTCCTTGTACATTCG
* *
3611286 ATGAAGATATATGAAATCACGCAATCTAACGTGATTTGTAGTTTCCATCTGCCTCAGTGTATTGA
66 ATGAAGATATATGAAATCACGCAATATAACGTGAGTTGTAGTTTCCATCTGCCTCAGTGTATTGA
* *
3611351 TACATTGTGTATTATATGGAAGTTTTTTTATGACAATTAATTTGGGATCAATTCTTTCTTTGCAT
131 GACATTGTGTATTATATGGAAGTTGTTTTATGACAATTAATTTGGGATCAATTCTTTCTTTGCAT
3611416 TTACATTTTGCATTCCCATCTTTGCATCTTTGCATTTGCATGT
196 TTACATTTTGCATTCCCATCTTTGCATCTTTGCATTTGCATGT
*
3611459 AGTCGAAGTGTTGGAATTGTCCACCAAGCCAGTAAATAGAAGAATGATGTTTCCTTGTACATTCG
1 AGTCGAAGTGTTGGAATTGTCCACCAAGCCAGGAAATAGAAGAATGATGTTTCCTTGTACATTCG
*
3611524 ATGAAGATATATGAAATCGA-GCAATATGACGTGAGTTGTAGTTTCCATCTGCCTCAGTGTATTG
66 ATGAAGATATATGAAATC-ACGCAATATAACGTGAGTTGTAGTTTCCATCTGCCTCAGTGTATTG
* * * *
3611588 AGACATTGTGTGTTCTTTGGAAGTTGTTTTATGACAATTAATTTGGGATCAATTCTTTTTTTGCA
130 AGACATTGTGTATTATATGGAAGTTGTTTTATGACAATTAATTTGGGATCAATTCTTTCTTTGCA
3611653 TTT
195 TTT
3611656 TGCATTCTCA
Statistics
Matches: 184, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
238 183 0.99
239 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (238 bp):
AGTCGAAGTGTTGGAATTGTCCACCAAGCCAGGAAATAGAAGAATGATGTTTCCTTGTACATTCG
ATGAAGATATATGAAATCACGCAATATAACGTGAGTTGTAGTTTCCATCTGCCTCAGTGTATTGA
GACATTGTGTATTATATGGAAGTTGTTTTATGACAATTAATTTGGGATCAATTCTTTCTTTGCAT
TTACATTTTGCATTCCCATCTTTGCATCTTTGCATTTGCATGT
Found at i:3611682 original size:22 final size:21
Alignment explanation
Indices: 3611647--3611690 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
3611637 CAATTCTTTT
*
3611647 TTTGCATTTTGCATTCTCATC
1 TTTGCATTTTGCATTATCATC
3611668 TTTGCATATTTGCATTATCATC
1 TTTGCAT-TTTGCATTATCATC
3611690 T
1 T
3611691 ATACATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTGCATTTTGCATTATCATC
Found at i:3612613 original size:18 final size:18
Alignment explanation
Indices: 3612587--3612740 Score: 155
Period size: 18 Copynumber: 8.6 Consensus size: 18
3612577 CCAGAATATG
* * *
3612587 TATGTGTATGTGTATGCG
1 TATGCGTATGCGTATGCA
*
3612605 TATGCGTATTCGTATGCA
1 TATGCGTATGCGTATGCA
* *
3612623 TATACGTATGCATATGCA
1 TATGCGTATGCGTATGCA
* * **
3612641 TATGTGTATGCATATATA
1 TATGCGTATGCGTATGCA
*
3612659 TATACGTATGCGTATGCA
1 TATGCGTATGCGTATGCA
* *
3612677 TATGCGTATGCGTATACG
1 TATGCGTATGCGTATGCA
* * *
3612695 TATGCATATGCATATGCG
1 TATGCGTATGCGTATGCA
3612713 TATGCGTATGCGTATGCA
1 TATGCGTATGCGTATGCA
*
3612731 TATGTGTATG
1 TATGCGTATG
3612741 TATACAATAA
Statistics
Matches: 110, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 110 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (18 bp):
TATGCGTATGCGTATGCA
Found at i:3612741 original size:6 final size:6
Alignment explanation
Indices: 3612586--3612740 Score: 139
Period size: 6 Copynumber: 25.8 Consensus size: 6
3612576 CCCAGAATAT
* * * * *
3612586 GTATGT GTATGT GTATGC GTATGC GTATTC GTATGC ATATAC GTATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
* * * * ** * * *
3612634 ATATGC ATATGT GTATGC ATATAT ATATAC GTATGC GTATGC ATATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
* * *
3612682 GTATGC GTATAC GTATGC ATATGC ATATGC GTATGC GTATGC GTATGC
1 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC
* *
3612730 ATATGT GTATG
1 GTATGC GTATG
3612741 TATACAATAA
Statistics
Matches: 123, Mismatches: 26, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (6 bp):
GTATGC
Found at i:3614203 original size:37 final size:37
Alignment explanation
Indices: 3614100--3614420 Score: 209
Period size: 37 Copynumber: 9.1 Consensus size: 37
3614090 TTGGGTGTTG
** * * *
3614100 TTTCTCTCGAAACAAAATATCGTCTCGCTAGAGACATT
1 TTTCTCTTAAAAC-AAATTTCGTCTCACTTGAGACATT
* *
3614138 GTTT-TCTTAAAAAATAATTTTGTCTCACTTGAGACATT
1 -TTTCTCTTAAAACA-AATTTCGTCTCACTTGAGACATT
3614176 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACA-T
1 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
** * ** *
3614212 TTTCATTCGGAACACAAA-TT--TCAAAGTT--G---TT
1 TTTC--TCTTAAAACAAATTTCGTCTCACTTGAGACATT
* *
3614243 TTTCT-TAAAAACAAATTTTGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
3614279 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACA-T
1 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
** *
3614315 TTTC-CTTCGAAACACAAA-TT--TCAAAGTT--G---TT
1 TTTCTCTT--AAA-ACAAATTTCGTCTCACTTGAGACATT
* *
3614346 TTTCT-TAAAAACAAATTTTGTCTCACTTGAGACATT
1 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
* * *
3614382 TTTCTCTTAAAACGAATTTCGTTTCACTTGAGATATT
1 TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
3614419 TT
1 TT
3614421 CCTTCGGAGC
Statistics
Matches: 219, Mismatches: 35, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
28 12 0.05
29 8 0.04
31 21 0.10
33 4 0.02
35 13 0.06
36 24 0.11
37 86 0.39
38 48 0.22
39 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (37 bp):
TTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATT
Found at i:3614318 original size:103 final size:103
Alignment explanation
Indices: 3614139--3614519 Score: 570
Period size: 103 Copynumber: 3.7 Consensus size: 103
3614129 AGAGACATTG
3614139 TTTTCTTAAAAA-ATAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCAC
1 TTTTCTTAAAAACA-AATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCAC
*
3614203 TTGAGACATTTTCATTCGGAACACAAATTTCAAAGTTGT
65 TTGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTGT
3614242 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
*
3614307 TGAGACATTTTCCTTCGAAACACAAATTTCAAAGTTGT
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTGT
* *
3614345 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACGAATTTCGTTTCACT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
* * * *
3614410 TGAGATATTTTCCTTCGGAGCGCAAATTTCAAAGTTAT
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTGT
* * * * * * ** * *
3614448 TTTACTT-GAACCAAATTTTGTCTCGCTTGAGACA-ATTTCTCTCAAAACAAACATAGTCTCGCT
1 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
3614511 TGAGACATT
66 TGAGACATT
3614520 CCCCTAAAAT
Statistics
Matches: 255, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
101 29 0.11
102 24 0.09
103 201 0.79
104 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (103 bp):
TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTGT
Found at i:3614653 original size:66 final size:65
Alignment explanation
Indices: 3614583--3614712 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 65
3614573 TCCAAAGAAC
* * * *
3614583 AAATTTTGTCTCCCTTGAAACAATTTCTTTTAAAACAAAATCTTTGATTAT-GTTTCCCTTTAAA
1 AAATTTTATCTCCCTTGAAACAATTTCTCTTAAAAC-AAATCTTTGA-CATCATTTCCCTTTAAA
3614647 CA
64 CA
* * * * *
3614649 AAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTTGACATCATTTCCCTTTAAAC
1 AAATTTTATCTCCCTTGAAACAATTTCTCTTAAAACAAATCTTTGACATCATTTCCCTTTAAAC
3614713 GGATTTTGTC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
64 2 0.04
65 22 0.41
66 30 0.56
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (65 bp):
AAATTTTATCTCCCTTGAAACAATTTCTCTTAAAACAAATCTTTGACATCATTTCCCTTTAAACA
Found at i:3614685 original size:37 final size:37
Alignment explanation
Indices: 3614634--3614943 Score: 101
Period size: 36 Copynumber: 8.5 Consensus size: 37
3614624 CTTTGATTAT
*
3614634 GTTTCCCTTTAAACAAAATTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACA
* *
3614671 GTTTCTCTTGAAAC--AA----AT-T-T-TTGACATCA
1 GTTTCCCTTGAAACAAAATTTTATCTCTCTTGAGA-CA
* ** * *
3614700 -TTTCCCTTTAAAC-GGATTTTGTCTCTCTGGAGACA
1 GTTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACA
* * * **
3614735 GTGTCCCTTGAAAAACAAAA-TGTATCTCACTTGAGATG
1 GTTTCCCTTG--AAACAAAATTTTATCTCTCTTGAGACA
** * * * *
3614773 GTTTTTCTTAAAAC-CAACTTTGTCTCGT-TTGAGACA
1 GTTTCCCTTGAAACAAAATTTTATCTC-TCTTGAGACA
* * * **
3614809 GTTTTCCCTTGAAATAAAA-TTTATCTCACTCGAGATT
1 G-TTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACA
** * * * **
3614846 GTTTTTCTTAAAACCGGAAGATTTTATCTCGCTTGAGATT
1 GTTTCCCTTGAAA-C--AAAATTTTATCTCTCTTGAGACA
* * * *
3614886 GTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATA
1 GTTTCCCTTGAAACA-AA-ATTTTATCTCTCTTGAGACA
*
3614925 GTTTCGCTTGAAACAAAAT
1 GTTTCCCTTGAAACAAAAT
3614944 ATTTTTAGAA
Statistics
Matches: 195, Mismatches: 54, Indels: 48
0.66 0.18 0.16
Matches are distributed among these distances:
28 16 0.08
29 4 0.02
30 1 0.01
31 2 0.01
33 1 0.01
34 1 0.01
35 7 0.04
36 37 0.19
37 37 0.19
38 27 0.14
39 37 0.19
40 25 0.13
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAATTTTATCTCTCTTGAGACA
Found at i:3614915 original size:39 final size:39
Alignment explanation
Indices: 3614862--3614948 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
3614852 CTTAAAACCG
*
3614862 GAAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACA
1 GAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
* *
3614901 GAAGATTTTATCTCGCTTGAGATAGTTTCGCTTGAAACA
1 GAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
* *
3614940 AAATATTTT
1 GAAGATTTT
3614949 TAGAAACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (39 bp):
GAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
Found at i:3615021 original size:53 final size:52
Alignment explanation
Indices: 3614950--3615100 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 52
3614940 AAATATTTTT
* * *
3614950 AGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAA
1 AGAAATTAAGCCTAATTTT-AGGGGTTTCTCGATGTTTTCAAATGAATTTCAA
* * *
3615003 AGAATTTAAGCCTAATTTTAGGGGTTTTTCAATGTTTTCAAATGAATTTCAA
1 AGAAATTAAGCCTAATTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTCAA
* * *
3615055 AGAAATTAAGCCTAATTTTTAGGGTTTTCTTGATATTTTCAAATGA
1 AGAAATTAAGCCTAA-TTTTAGGGGTTTCTCGATGTTTTCAAATGA
3615101 GTTTTTAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 44 0.52
53 41 0.48
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (52 bp):
AGAAATTAAGCCTAATTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTCAA
Found at i:3615137 original size:52 final size:52
Alignment explanation
Indices: 3614945--3615189 Score: 183
Period size: 52 Copynumber: 4.6 Consensus size: 52
3614935 AAACAAAATA
* * * *
3614945 TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGA-
1 TTTTTAAAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAG
* * * * * *
3614996 ATTTGAAAGAATTTAAGCCTAATTTT-AGGGGTTT-TTCAATGTTTTCAAATGAA
1 TTTTTAAA-AA-CTAAGCCTAATTTTCAGGGGTTTCTT-GATATTTTCAAATGAG
** * * *
3615049 TTTCAAAGAAATTAAGCCTAATTTTTAGGGTTTTCTTGATATTTTCAAATGAG
1 TTTTTAA-AAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAG
* * *
3615102 TTTTTAAAAACTAAACCTGATTTTCAGGGATTTCTTGATGATGATTTTC-AATGAG
1 TTTTTAAAAACTAAGCCTAATTTTCAGGGGTTTC-T--TGAT-ATTTTCAAATGAG
*
3615157 TTTTTAAAAGGAAACTAAGCCTAATTTTTAGGG
1 TTTTT--AA--AAACTAAGCCTAATTTTCAGGG
3615190 TGTTGAACTA
Statistics
Matches: 155, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
51 6 0.04
52 60 0.39
53 44 0.28
54 3 0.02
55 15 0.10
56 6 0.04
57 2 0.01
59 19 0.12
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (52 bp):
TTTTTAAAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAG
Found at i:3615252 original size:34 final size:30
Alignment explanation
Indices: 3615214--3615282 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
3615204 TCGATATAAA
*
3615214 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
3615248 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
3615277 AATTTA
1 AATTTA
3615283 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:3615290 original size:31 final size:31
Alignment explanation
Indices: 3615223--3615282 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3615213 AAATTTAAGG
*
3615223 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3615254 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3615283 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3615375 original size:19 final size:19
Alignment explanation
Indices: 3615347--3615412 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
3615337 AATGTTTTTA
* *
3615347 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
3615366 TGAACGGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* * *
3615385 TGAACAGTAAATCATTGTT
1 TGAACAGTAAATTACTATT
3615404 TGAACAGTA
1 TGAACAGTA
3615413 CCCCGAGGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:3615545 original size:21 final size:21
Alignment explanation
Indices: 3615519--3615560 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3615509 ATTTGAATAT
*
3615519 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3615540 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3615561 CCCATTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3615626 original size:21 final size:23
Alignment explanation
Indices: 3615588--3615629 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3615578 ATTTTTGTAG
3615588 AAAAATCATTCCCAAACGGCTCC
1 AAAAATCATTCCCAAACGGCTCC
*
3615611 AAAAA-CA-TCCCTAACGGCT
1 AAAAATCATTCCCAAACGGCT
3615630 AGATATGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.40, C:0.33, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAAATCATTCCCAAACGGCTCC
Found at i:3616798 original size:19 final size:20
Alignment explanation
Indices: 3616774--3616821 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3616764 AACGATTTTC
*
3616774 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3616793 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3616813 TTTTGAAAA
1 TTTTGAAAA
3616822 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3618129 original size:29 final size:32
Alignment explanation
Indices: 3618073--3618138 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 32
3618063 ATTTAAGGAA
*
3618073 AAAATGGTTTTTGGACTTGAATTGAATT-TAC
1 AAAATGGTATTTGGACTTGAATTGAATTATAC
*
3618104 AAAAT-GTATTTGGACTT-AATTGAATTATTC
1 AAAATGGTATTTGGACTTGAATTGAATTATAC
3618134 AAAAT
1 AAAAT
3618139 TTACAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 9 0.28
30 18 0.56
31 5 0.16
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (32 bp):
AAAATGGTATTTGGACTTGAATTGAATTATAC
Found at i:3618253 original size:19 final size:19
Alignment explanation
Indices: 3618208--3618260 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
3618198 ATAGTAATTT
* *
3618208 ACTATTTGAACAATAAATT
1 ACTATTTGAACAGTAAATC
3618227 ACTATTTGAACAGTAAATC
1 ACTATTTGAACAGTAAATC
* *
3618246 ATTGTTTGAACAGTA
1 ACTATTTGAACAGTA
3618261 CCCCGAGGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (19 bp):
ACTATTTGAACAGTAAATC
Found at i:3618372 original size:21 final size:21
Alignment explanation
Indices: 3618346--3618387 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3618336 ATTTGAATAT
*
3618346 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3618367 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3618388 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3618450 original size:21 final size:21
Alignment explanation
Indices: 3618417--3618456 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3618407 TTTTACAGAA
*
3618417 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3618439 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3618457 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3619490 original size:144 final size:145
Alignment explanation
Indices: 3619117--3619568 Score: 622
Period size: 145 Copynumber: 3.1 Consensus size: 145
3619107 AGCAAGATGA
** *
3619117 TAAGTCCTTCTGGCCATCCATAAGACCTTCGGGAAGGATGTTTTCAACATTTCCTTTGCTTGATT
1 TAAGTCCTTCTGGCCATCCATAAGACCTTCGGGCGGGATGTTTTCAACATTTCCTTTGCTCGATT
* * * * * *
3619182 CACAACACTTCGAATCAGAAACGTCCTACTAGAGGGGTTAACATTTCTTATTGCTTGATTCACAA
66 CAAAACACTTCGAATCAGTAACGCCCCACTAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
*
3619247 CACTTCGAATCAGCT
131 CACTTCGAATCAGTT
* * * *
3619262 TAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAGGG-TGTTTTCAACATTTACTTTGCTCGAA
1 TAAGTCCTTCTGGCCATCCATAAGACCTTCGGGC-GGGATGTTTTCAACATTTCCTTTGCTCGAT
* * * *
3619326 TCAAAACACTTCGGAA-CAGTAACACCCCACCAGAGGGTTTAACATTTCCTATTGCTCGATTCAC
65 TCAAAACACTTC-GAATCAGTAACGCCCCACTAGAGGGGTTAACATTTCATATTGCTCGATTCAC
*
3619390 AACACTTTGAATCAGTT
129 AACACTTCGAATCAGTT
* * * *
3619407 TAAGTTCTTCAGGCCAT-CATAAGACCTTCAGGCGGGATGTTTTCAACATTTCCTTTACTCGATT
1 TAAGTCCTTCTGGCCATCCATAAGACCTTCGGGCGGGATGTTTTCAACATTTCCTTTGCTCGATT
* * *
3619471 CAAAACACTTCCAATCAGTAATGCCCCACTAGAGGGGTTAACATTTCATATTGCTCGATTCATAA
66 CAAAACACTTCGAATCAGTAACGCCCCACTAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
3619536 CACTTCGAATCAGTT
131 CACTTCGAATCAGTT
*
3619551 GAAGTCCTTCTGGCCATC
1 TAAGTCCTTCTGGCCATC
3619569 AGTAAGTCTT
Statistics
Matches: 266, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
143 5 0.02
144 122 0.46
145 134 0.50
146 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (145 bp):
TAAGTCCTTCTGGCCATCCATAAGACCTTCGGGCGGGATGTTTTCAACATTTCCTTTGCTCGATT
CAAAACACTTCGAATCAGTAACGCCCCACTAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
CACTTCGAATCAGTT
Found at i:3629552 original size:25 final size:25
Alignment explanation
Indices: 3629523--3629570 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3629513 TATTTTATAT
*
3629523 AAATTATT-TAATTTCATATCCCTTG
1 AAATT-TTATAATCTCATATCCCTTG
*
3629548 AAATTTTATAATCTCGTATCCCT
1 AAATTTTATAATCTCATATCCCT
3629571 AAGATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (25 bp):
AAATTTTATAATCTCATATCCCTTG
Found at i:3632411 original size:16 final size:16
Alignment explanation
Indices: 3632390--3632421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3632380 TGTTGCTCGA
*
3632390 CTCGTTGTTCGTTAAG
1 CTCGTTGCTCGTTAAG
3632406 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCGTTAAG
3632422 TTTAGTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (16 bp):
CTCGTTGCTCGTTAAG
Found at i:3633005 original size:49 final size:49
Alignment explanation
Indices: 3632933--3633028 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
3632923 CTAATTGCAA
3632933 TTCTTCCATTTAACCAAAGGGAGCCAAGCGTCTTGCCAAACTATGGCGC
1 TTCTTCCATTTAACCAAAGGGAGCCAAGCGTCTTGCCAAACTATGGCGC
3632982 TTCTTCCATTTAACCAAAGGGAGCCAAGCGTCTTGCCAAACTATGGC
1 TTCTTCCATTTAACCAAAGGGAGCCAAGCGTCTTGCCAAACTATGGC
3633029 TCATGCGCGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (49 bp):
TTCTTCCATTTAACCAAAGGGAGCCAAGCGTCTTGCCAAACTATGGCGC
Found at i:3634493 original size:27 final size:29
Alignment explanation
Indices: 3634459--3634513 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3634449 AGAGTACTTT
3634459 TAAAATTTC-AG-GAC-AAACTTAAATTTA
1 TAAAATTTCAAGAGACGAAA-TTAAATTTA
3634486 TAAAATTTCAAGAGACGAAATTAAATTT
1 TAAAATTTCAAGAGACGAAATTAAATTT
3634514 TTTTATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 2 0.08
29 11 0.44
30 3 0.12
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (29 bp):
TAAAATTTCAAGAGACGAAATTAAATTTA
Found at i:3635349 original size:3 final size:3
Alignment explanation
Indices: 3635341--3635416 Score: 143
Period size: 3 Copynumber: 25.0 Consensus size: 3
3635331 TGCTATTGAT
3635341 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3635389 ATA ATA ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA
3635417 GTTAATTGCT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3638122 original size:8 final size:8
Alignment explanation
Indices: 3638105--3638137 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
3638095 CAACTGAGGT
*
3638105 TGAACTAG
1 TGAACCAG
3638113 TGAACCAG
1 TGAACCAG
3638121 TGAACCAG
1 TGAACCAG
3638129 TGAACCAG
1 TGAACCAG
3638137 T
1 T
3638138 ATCTTCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (8 bp):
TGAACCAG
Found at i:3641641 original size:25 final size:24
Alignment explanation
Indices: 3641620--3641692 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
3641610 AATATAACAC
3641620 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGATAAA-A
* * * *
3641645 TAACTACTAAG-TAGTTTAGTTTAAAT
1 TAACT-CTTAGAAAG-TTAG-ATAAAA
3641671 TAACTCTTAGAAAGTTAGATAA
1 TAACTCTTAGAAAGTTAGATAA
3641693 GGATATCTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
24 3 0.08
25 15 0.41
26 15 0.41
27 4 0.11
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (24 bp):
TAACTCTTAGAAAGTTAGATAAAA
Found at i:3641678 original size:51 final size:51
Alignment explanation
Indices: 3641620--3641724 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
3641610 AATATAACAC
*
3641620 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACCAAGTAGTTTAGTTTAAAT
* *
3641671 TAACTCTTAGAAAGTTAGATAAGGATATCTACCAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACCAAGTAGTTTAGTTTAAAT
3641722 TAA
1 TAA
3641725 ATATTTGTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (51 bp):
TAACTCTTAGAAAGTTAGATAAAGATAACTACCAAGTAGTTTAGTTTAAAT
Found at i:3643442 original size:21 final size:21
Alignment explanation
Indices: 3643404--3643443 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3643394 GAAAAAATTA
*
3643404 GATATCCGAAATTTTGGATCG
1 GATATCCGAAATTCTGGATCG
3643425 GATATCCG-AATATCTGGAT
1 GATATCCGAAAT-TCTGGAT
3643444 ACAAATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
GATATCCGAAATTCTGGATCG
Found at i:3644391 original size:50 final size:51
Alignment explanation
Indices: 3644316--3644450 Score: 173
Period size: 59 Copynumber: 2.5 Consensus size: 51
3644306 TCAAGCCATG
* *
3644316 TAAAATACAAGCTAGAATCCAGAAAT-GAGAAATCTATACGTGCTGTATAT
1 TAAAATACAAGCTAGAATCCAGAAATACAAAAATCTATACGTGCTGTATAT
3644366 TAAAATACAAGCTAGAATCCAGAAATCTATACATACAAAAATCTATACGTGCTGTATAT
1 TAAAATACAAGCTAGAATCCAG------A-A-ATACAAAAATCTATACGTGCTGTATAT
3644425 TAAAATACAAGCTAGAATCCAGAAAT
1 TAAAATACAAGCTAGAATCCAGAAAT
3644451 CTATACATAC
Statistics
Matches: 74, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
50 22 0.30
51 2 0.03
52 1 0.01
53 1 0.01
56 1 0.01
57 1 0.01
58 2 0.03
59 44 0.59
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.25
Consensus pattern (51 bp):
TAAAATACAAGCTAGAATCCAGAAATACAAAAATCTATACGTGCTGTATAT
Found at i:3644437 original size:59 final size:59
Alignment explanation
Indices: 3644345--3644469 Score: 241
Period size: 59 Copynumber: 2.1 Consensus size: 59
3644335 CAGAAATGAG
3644345 AAATCTATACGTGCTGTATATTAAAATACAAGCTAGAATCCAGAAATCTATACATACAA
1 AAATCTATACGTGCTGTATATTAAAATACAAGCTAGAATCCAGAAATCTATACATACAA
*
3644404 AAATCTATACGTGCTGTATATTAAAATACAAGCTAGAATCCAGAAATCTATACATACAG
1 AAATCTATACGTGCTGTATATTAAAATACAAGCTAGAATCCAGAAATCTATACATACAA
3644463 AAATCTA
1 AAATCTA
3644470 ATACAGCCCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (59 bp):
AAATCTATACGTGCTGTATATTAAAATACAAGCTAGAATCCAGAAATCTATACATACAA
Found at i:3647127 original size:22 final size:22
Alignment explanation
Indices: 3647099--3647146 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3647089 CTACGACGAC
*
3647099 ATCCATCCCTATCTCCGGCAAA
1 ATCCATCCCCATCTCCGGCAAA
*
3647121 ATCCATCCCCATCTCCGGCGAA
1 ATCCATCCCCATCTCCGGCAAA
3647143 ATCC
1 ATCC
3647147 GTCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGGCAAA
Found at i:3649164 original size:21 final size:21
Alignment explanation
Indices: 3649118--3649167 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3649108 GTTAGGGGAA
* *
3649118 TTACATGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
*
3649139 TTACGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACT
3649160 TTACGTGA
1 TTACGTGA
3649168 AGACAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:3649622 original size:21 final size:20
Alignment explanation
Indices: 3649575--3649680 Score: 104
Period size: 21 Copynumber: 5.1 Consensus size: 20
3649565 GGTTCACATG
* *
3649575 TCATCATTCAAGAGGTCTCT
1 TCATCATTCAAGAGGCCCCT
*
3649595 CCTATCATTCAAGAGGCCCCT
1 TC-ATCATTCAAGAGGCCCCT
3649616 ATCATCATTCAAGAGGCCCCT
1 -TCATCATTCAAGAGGCCCCT
* * *
3649637 CTCACCGTTCAAGAGGCCCGT
1 -TCATCATTCAAGAGGCCCCT
* *
3649658 GTCATCGTTCAAGAGGTCCCT
1 -TCATCATTCAAGAGGCCCCT
3649679 TC
1 TC
3649681 CACCGGTTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
20 3 0.04
21 68 0.94
22 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (20 bp):
TCATCATTCAAGAGGCCCCT
Found at i:3649685 original size:42 final size:41
Alignment explanation
Indices: 3649573--3649698 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 41
3649563 CCGGTTCACA
* * * *
3649573 TGTCATCATTCAAGAGGTCTCTCCTATCATTCAAGAGGCCCC
1 TGTCATCATTCAAGAGGTCCCTCC-ACCGTTCAAGAGGCCCG
* *
3649615 TATCATCATTCAAGAGGCCCCTCTCACCGTTCAAGAGGCCCG
1 TGTCATCATTCAAGAGGTCCCTC-CACCGTTCAAGAGGCCCG
* *
3649657 TGTCATCGTTCAAGAGGTCCCTTCCACCGGTTCGAGA-GCCCG
1 TGTCATCATTCAAGAGGTCCC-TCCACC-GTTCAAGAGGCCCG
3649699 ATTCACATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 61 0.86
43 10 0.14
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (41 bp):
TGTCATCATTCAAGAGGTCCCTCCACCGTTCAAGAGGCCCG
Found at i:3651060 original size:13 final size:14
Alignment explanation
Indices: 3651035--3651081 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
3651025 AAATTGATGT
3651035 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
3651049 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
3651062 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
3651076 ATTTGT
1 ATTTGT
3651082 TTAATTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.41
14 19 0.59
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:3651095 original size:27 final size:27
Alignment explanation
Indices: 3651038--3651097 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
3651028 TTGATGTATT
*
3651038 TGTAAAAGTTGATTTGTAAAGTTGATT
1 TGTAAAAGTTGATTTGTAAAGTTGATG
*
3651065 TGTAAAAGTTGATTTGTTTAA-TTGATG
1 TGTAAAAGTTGATTTG-TAAAGTTGATG
3651092 TGTAAA
1 TGTAAA
3651098 TAATTCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (27 bp):
TGTAAAAGTTGATTTGTAAAGTTGATG
Found at i:3651230 original size:20 final size:20
Alignment explanation
Indices: 3651205--3651266 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
3651195 AAGGTACACT
* *
3651205 TTCGCAGCGCGAAAGTTAAA
1 TTCGCAACGCGAAAGTCAAA
*
3651225 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
3651245 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
3651265 TT
1 TT
3651267 TGCGTTGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:3654643 original size:16 final size:15
Alignment explanation
Indices: 3654621--3654659 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3654611 GAAATCATTG
3654621 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
3654637 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
3654652 AAAAATTA
1 AAAAATTA
3654660 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:3654843 original size:20 final size:20
Alignment explanation
Indices: 3654818--3654918 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
3654808 ACTAAAACCT
3654818 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
** *
3654838 GTTGCGAAAAC-AAAATTCGC
1 GTTGCGAATTCGAAAA-TCGA
*
3654858 GTTGCAAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* * *
3654878 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTCGAAAATC-GA
*
3654899 GTTGCGAATTTGGAAAATCG
1 GTTGCGAA-TTCGAAAATCG
3654919 CAATGCAGAT
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 4 0.06
20 37 0.59
21 14 0.22
22 8 0.13
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:3654930 original size:21 final size:20
Alignment explanation
Indices: 3654901--3654950 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
3654891 AATTCAGTGT
3654901 TGCGAATTTGGAAAATCGCAA
1 TGCG-ATTTGGAAAATCGCAA
* *
3654922 TGCAGATTTGGAAAATTGTAA
1 TGC-GATTTGGAAAATCGCAA
3654943 TGCGATTT
1 TGCGATTT
3654951 ATATATTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (20 bp):
TGCGATTTGGAAAATCGCAA
Found at i:3655396 original size:3 final size:3
Alignment explanation
Indices: 3655388--3655477 Score: 90
Period size: 3 Copynumber: 28.3 Consensus size: 3
3655378 ATCGAGTTTT
3655388 GAA GAA GAA GAA GAAA GAA GAA GAA GAAA GAA GAAA GAA GAAA GAA GAAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA G-AA GAA G-AA GAA G-AA GAA G-AA
* * * * *
3655438 GAA GAA GAA GAA AAA GAA AAA GAG GAT GAG GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3655478 CTGCCATGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
3 59 0.80
4 15 0.20
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:3655407 original size:7 final size:7
Alignment explanation
Indices: 3655389--3655460 Score: 109
Period size: 7 Copynumber: 11.0 Consensus size: 7
3655379 TCGAGTTTTG
3655389 AAGAAG-
1 AAGAAGA
3655395 AAGAAGA
1 AAGAAGA
3655402 AAGAAG-
1 AAGAAGA
3655408 AAGAAGA
1 AAGAAGA
3655415 AAGAAGA
1 AAGAAGA
3655422 AAGAAGA
1 AAGAAGA
3655429 AAGAAGA
1 AAGAAGA
3655436 AAGAAG-
1 AAGAAGA
3655442 AAGAAGA
1 AAGAAGA
3655449 AA-AAGA
1 AAGAAGA
3655455 AA-AAGA
1 AAGAAGA
3655461 GGATGAGGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
6 28 0.44
7 35 0.56
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:3655407 original size:10 final size:10
Alignment explanation
Indices: 3655388--3655460 Score: 75
Period size: 10 Copynumber: 7.5 Consensus size: 10
3655378 ATCGAGTTTT
3655388 GAAGAAG-AA
1 GAAGAAGAAA
3655397 GAAGAA-AGAA
1 GAAGAAGA-AA
3655407 GAAGAAGAAA
1 GAAGAAGAAA
3655417 GAAGAA-AGAA
1 GAAGAAGA-AA
3655427 GAAAGAAGAAA
1 G-AAGAAGAAA
3655438 GAAGAAG-AA
1 GAAGAAGAAA
*
3655447 GAAAAAGAAA
1 GAAGAAGAAA
3655457 -AAGA
1 GAAGA
3655461 GGATGAGGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
9 18 0.33
10 27 0.49
11 9 0.16
12 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:3660737 original size:2 final size:2
Alignment explanation
Indices: 3660730--3660760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3660720 AAATTAATCC
3660730 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 T
3660761 TTGATTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3661479 original size:60 final size:60
Alignment explanation
Indices: 3661366--3661488 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 60
3661356 ATTCTATAAC
* * *
3661366 TTTTAATAGTTGAGAGACTCAACAAAGCAACATCCTATAATTGAGGAACCATTT-TGTAAT
1 TTTTAATAGTTGAGAAAATCAACAAAGCAACAACCTATAATTGAGGAACCATTTGTGT-AT
* * * * *
3661426 TTTTAATAGTTGGGAAAATCAAGAAAGCAACAACCTATAGTT-AGGGGATCATTTGTGTAT
1 TTTTAATAGTTGAGAAAATCAACAAAGCAACAACCTATAATTGA-GGAACCATTTGTGTAT
3661486 TTT
1 TTT
3661489 ACCCAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.02
60 49 0.92
61 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (60 bp):
TTTTAATAGTTGAGAAAATCAACAAAGCAACAACCTATAATTGAGGAACCATTTGTGTAT
Found at i:3667938 original size:90 final size:90
Alignment explanation
Indices: 3667821--3667998 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
3667811 TAATCCCGAA
* * * ** * *
3667821 TATTTAATTTCAATTAATTAAATATAGATATATTTAATTTGAAATAATAAAATTCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATATAATTAATTTGAAATAATAAAAACCCTAATATGAC
3667886 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
3667911 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATATAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
3667976 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
3667999 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATATAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:3669614 original size:44 final size:45
Alignment explanation
Indices: 3669461--3669675 Score: 260
Period size: 45 Copynumber: 4.9 Consensus size: 45
3669451 ATTATAACAT
*
3669461 CTTTT-TGTTGATAATGCACCC-TATGCATTTCAACTATA-TATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * *
3669503 CTTTTATGTTGATAGTGTACCCATATACATTACAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* * * * *
3669548 CTTTTCTATTGATAATGTACCCATATACATATAAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* *
3669593 C-TTTCTGTTGATAATGCACCCATTTGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
3669637 CTTTTCTGTTAATAATGCACCCATATGCATTTCAACTCT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
3669676 GGCATCCTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.03
43 14 0.10
44 50 0.34
45 77 0.52
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:3669614 original size:89 final size:89
Alignment explanation
Indices: 3669468--3669713 Score: 255
Period size: 89 Copynumber: 2.8 Consensus size: 89
3669458 CATCTTTTTG
* * * *
3669468 TTGATAATGCACCC-TATGCATTTCAACTATA-TATACTTTTATGTTGATAGTGTACCCATATAC
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATAC-TTTCTGTTGATAATGCACCCATATAC
*
3669531 ATTACAAC-CATAGTATACTTTTCTA
65 ATTACAACTC-TAGCATACTTTTCTA
* * * * * *
3669556 TTGATAATGTACCCATATACATATAAACTCTAGTATACTTTCTGTTGATAATGCACCCATTTGCA
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTCTGTTGATAATGCACCCATATACA
* *
3669621 TTTCAACTCTAGCATACTTTTCTG
66 TTACAACTCTAGCATACTTTTCTA
* * * * *** *
3669645 TTAATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATTC
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTC-TGTTGATAATGCACCCATATAC
3669710 ATTA
65 ATTA
3669714 TTCTTTTATG
Statistics
Matches: 127, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
88 13 0.10
89 88 0.69
90 26 0.20
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (89 bp):
TTGATAATGCACCCATATGCATTTCAACTCTAGTATACTTTCTGTTGATAATGCACCCATATACA
TTACAACTCTAGCATACTTTTCTA
Found at i:3669696 original size:45 final size:43
Alignment explanation
Indices: 3669603--3669791 Score: 146
Period size: 45 Copynumber: 4.5 Consensus size: 43
3669593 CTTTCTGTTG
* * **
3669603 ATAATGCACCCATTTGCATTTCAACTCTAGCATACTTTTC-TGTTA
1 ATAATGCACCCATATGCATTTCAA-TCTGGCAT-C-TTTCATGCCA
3669648 ATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAA-TCTGGCAT-CTTTCATGCCA
* **
3669693 ATAATGCACCCATATTCA-TT--AT-T--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTCAATCTGGCATCTTTCATGCCA
* * * *
3669727 ACAATGTACCCATATACATTTCAGATATGGCATCATTTCATGCCA
1 ATAATGCACCCATATGCATTTCA-ATCTGGCATC-TTTCATGCCA
3669772 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
3669792 ATTCTTTTAC
Statistics
Matches: 116, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
34 19 0.16
35 5 0.04
37 1 0.01
38 3 0.03
39 1 0.01
40 1 0.01
41 2 0.02
42 2 0.02
44 9 0.08
45 73 0.63
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (43 bp):
ATAATGCACCCATATGCATTTCAATCTGGCATCTTTCATGCCA
Found at i:3669768 original size:79 final size:79
Alignment explanation
Indices: 3669650--3669800 Score: 241
Period size: 79 Copynumber: 1.9 Consensus size: 79
3669640 TTCTGTTAAT
* * * *
3669650 AATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATTCATTAT
1 AATGCACCCATATACATTTCAACTATGGCATCATTTCATGCCAATAATGCACCCATATGCATTAT
3669715 TCTTTTATGCTGAC
66 TCTTTTATGCTGAC
*
3669729 AATGTACCCATATACATTTCAGA-TATGGCATCATTTCATGCCAATAATGCACCCATATGCATTA
1 AATGCACCCATATACATTTCA-ACTATGGCATCATTTCATGCCAATAATGCACCCATATGCATTA
3669793 TTCTTTTA
65 TTCTTTTA
3669801 CATTCGTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 65 0.98
80 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATGGCATCATTTCATGCCAATAATGCACCCATATGCATTAT
TCTTTTATGCTGAC
Found at i:3670219 original size:22 final size:20
Alignment explanation
Indices: 3670181--3670233 Score: 88
Period size: 22 Copynumber: 2.5 Consensus size: 20
3670171 TGGCCCTTCA
3670181 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
3670201 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
3670223 GTATCGATACC
1 GTATCGATACC
3670234 AAAGTTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.35
22 20 0.65
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:3670307 original size:22 final size:20
Alignment explanation
Indices: 3670258--3670329 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
3670248 TGTGGTCCAA
*
3670258 TATCGATACCCTTACCATAGG
1 TATCGATACCCTTACTAT-GG
3670279 TATCGATACCACTATACTATGG
1 TATCGATACC-CT-TACTATGG
* *
3670301 TACCGATACCTTTA-TATGG
1 TATCGATACCCTTACTATGG
3670320 TATCGATACC
1 TATCGATACC
3670330 AAAATTAGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 14 0.31
20 2 0.04
21 11 0.24
22 13 0.29
23 5 0.11
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (20 bp):
TATCGATACCCTTACTATGG
Found at i:3672028 original size:20 final size:20
Alignment explanation
Indices: 3671988--3672026 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3671978 ATTTGCAAGA
3671988 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
3672008 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
3672027 GACATTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:3685270 original size:21 final size:21
Alignment explanation
Indices: 3685244--3685287 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3685234 CTCCTTGGCA
*
3685244 AAAACTAGCAATGTCATTGCG
1 AAAACTACCAATGTCATTGCG
3685265 AAAACTACCAATGTCATTGCG
1 AAAACTACCAATGTCATTGCG
3685286 AA
1 AA
3685288 GCTGAGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (21 bp):
AAAACTACCAATGTCATTGCG
Found at i:3698993 original size:94 final size:95
Alignment explanation
Indices: 3698888--3699066 Score: 238
Period size: 94 Copynumber: 1.9 Consensus size: 95
3698878 CAAAAGTAAA
* * * *
3698888 GTATCGATACCAT-AGATTCCAGAATGCCA-AAATGGTATCGATACTGAAAGGGAGTATC-GTAC
1 GTATCAATACCATGA-ATTACAGAATG-CATAAATAGTATCAATACTGAAAGGGAGTATCAGTAC
*
3698950 CATAGTATAGTAGTATCAATACTGAGAGAAAG
64 CATAGTATAGAAGTATCAATACTGAGAGAAAG
* *
3698982 GTATCAATACCATGAATTACAGAATGTATAAATAGTATCAATACTGAAAGGGGGTATCAGTACCA
1 GTATCAATACCATGAATTACAGAATGCATAAATAGTATCAATACTGAAAGGGAGTATCAGTACCA
* *
3699047 TATTATAGAAGTATCGATAC
66 TAGTATAGAAGTATCAATAC
3699067 CATGGTAGGG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 1 0.01
94 48 0.66
95 24 0.33
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (95 bp):
GTATCAATACCATGAATTACAGAATGCATAAATAGTATCAATACTGAAAGGGAGTATCAGTACCA
TAGTATAGAAGTATCAATACTGAGAGAAAG
Found at i:3699431 original size:45 final size:45
Alignment explanation
Indices: 3699362--3699599 Score: 343
Period size: 45 Copynumber: 5.3 Consensus size: 45
3699352 GTTTCCATTA
3699362 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
3699407 CATAAATAAAATGCATAACAGTGCATTAAAGGCATGAAAGAATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
3699452 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAAGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * * *
3699497 TATAAATGAAATGCATAACAGTGCATTAATGGCATGAAAGAATGA
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
3699542 CATAAATAAAATGCATAACGGCT-CATTAAAGGCGTGAAAGGATGC
1 CATAAATGAAATGCATAACGG-TGCATTAAAGGCATGAAAGGATGC
3699587 CATAAATGGAAAT
1 CATAAAT-GAAAT
3699600 AATGAATAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
45 163 0.97
46 5 0.03
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:3699515 original size:90 final size:90
Alignment explanation
Indices: 3699361--3699599 Score: 390
Period size: 90 Copynumber: 2.6 Consensus size: 90
3699351 TGTTTCCATT
*
3699361 ACATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAAC
1 ACATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
3699426 AGTGCATTAAAGGCATGAAAGAATG
66 AGTGCATTAAAGGCATGAAAGAATG
* * *
3699451 TCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAAGATGCTATAAATGAAATGCATAAC
1 ACATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
*
3699516 AGTGCATTAATGGCATGAAAGAATG
66 AGTGCATTAAAGGCATGAAAGAATG
* *
3699541 ACATAAATAAAATGCATAACGGCT-CATTAAAGGCGTGAAAGGATGCCATAAATGGAAAT
1 ACATAAATGAAATGCATAACGG-TGCATTAAAGGCATGAAAGGATGCCATAAAT-GAAAT
3699600 AATGAATAAT
Statistics
Matches: 137, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
90 131 0.96
91 6 0.04
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (90 bp):
ACATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
AGTGCATTAAAGGCATGAAAGAATG
Found at i:3701575 original size:55 final size:55
Alignment explanation
Indices: 3701491--3701860 Score: 546
Period size: 55 Copynumber: 6.7 Consensus size: 55
3701481 AAGTGTGCAA
*
3701491 AAACTTAATAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
*
3701546 AAACTTAAGAAATTCATTCTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * *
3701601 AAACTTAAGAAATTCATACTAAGTGAATGAATTTTCGTATGGGCAATTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* *
3701656 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTAT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * * *
3701711 AAACTTAAGAAATTCATATTAAGTGGATGAATTTCCATATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * *
3701766 AAACTGAAGAAATTCATAGTAAGTGGATGAA-TTTCTGTATGGGCACTATATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTC-GTATGGGCACTATATGTG-T
* * * *
3701822 AAAC-TAGGAAATTCATACTAAGTGTATAAATTTCCGTAT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTAT
3701861 TGGTACTGGG
Statistics
Matches: 287, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
54 3 0.01
55 277 0.97
56 7 0.02
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
Found at i:3702260 original size:22 final size:24
Alignment explanation
Indices: 3702235--3702278 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3702225 TATGTAATTA
3702235 AGTTTAA-TAC-ATGTTTTATATT
1 AGTTTAATTACAATGTTTTATATT
3702257 AGTTTAATTACAATGTTTTATA
1 AGTTTAATTACAATGTTTTATA
3702279 AAAAGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (24 bp):
AGTTTAATTACAATGTTTTATATT
Found at i:3707435 original size:22 final size:21
Alignment explanation
Indices: 3707381--3707438 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
3707371 TGCAAAAATG
*
3707381 GTATTGATACCATAG--TAGA
1 GTATCGATACCATAGTATAGA
*
3707400 GTATCAGTTA-CATAGTATAGTA
1 GTATC-GATACCATAGTATAG-A
3707422 GTATCGATACCATAGTA
1 GTATCGATACCATAGTA
3707439 GGGGTATCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 9 0.29
20 3 0.10
21 6 0.19
22 13 0.42
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:3707855 original size:46 final size:46
Alignment explanation
Indices: 3707787--3707874 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
3707777 TACCAAATGA
3707787 CACTAAGTGTGCAAAAACTTAATAAATTCATACTAAGTGGATAAAT
1 CACTAAGTGTGCAAAAACTTAATAAATTCATACTAAGTGGATAAAT
*
3707833 CACTAAGTGTGCAAAAATTTAATAAATTCATACTAAGTGGAT
1 CACTAAGTGTGCAAAAACTTAATAAATTCATACTAAGTGGAT
3707875 GAATTTCCGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (46 bp):
CACTAAGTGTGCAAAAACTTAATAAATTCATACTAAGTGGATAAAT
Found at i:3707935 original size:55 final size:55
Alignment explanation
Indices: 3707851--3708271 Score: 610
Period size: 55 Copynumber: 7.7 Consensus size: 55
3707841 GTGCAAAAAT
* *
3707851 TTAATAAATTCATACTAAGTGGATGAATTTCCGTATGGGTACTATATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* ** *
3707906 TTAATAAATTCATACTAAGTGGATGAATTTTTGTATGGACACTATATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* *
3707961 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGCCACTATATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
*
3708016 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * *
3708071 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTATAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * * *
3708126 TTAAGAAGTTCATACTAAATGGATGAATTTCCGTATGGGCATTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * * *
3708181 TGAAGAAATTCATATTAAGTGGATGAATTTCTGTATGGGCACTATATGTGCAAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTG-TAAAC
* * * *
3708237 -TAGGAAATTCATACTAAATGTATAAATTTCCGTAT
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
3708272 TGGTATTGGG
Statistics
Matches: 333, Mismatches: 32, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
55 329 0.99
56 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
Found at i:3708671 original size:22 final size:24
Alignment explanation
Indices: 3708646--3708689 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3708636 TATGTAATTA
3708646 AGTTTAA-TAC-ATGTTTTATATT
1 AGTTTAATTACAATGTTTTATATT
3708668 AGTTTAATTACAATGTTTTATA
1 AGTTTAATTACAATGTTTTATA
3708690 AAAAGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (24 bp):
AGTTTAATTACAATGTTTTATATT
Found at i:3709924 original size:17 final size:17
Alignment explanation
Indices: 3709899--3709938 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3709889 AGTATTTGTT
*
3709899 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
3709916 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
3709933 CATTTA
1 CATTTA
3709939 GGGAAGTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:3711037 original size:139 final size:135
Alignment explanation
Indices: 3710863--3711141 Score: 409
Period size: 139 Copynumber: 2.0 Consensus size: 135
3710853 CTTTCATATA
* *
3710863 CATATTTATATATACATGTTTCTCTTCTTGTAACGTTGTTTGTGCATTTTCAGCCTTCAATCAAA
1 CATATTTATATATACATATTTCTCTTCTTGTAACGTTGTTTGTGCATTTTCAACCTTCAATCAAA
*
3710928 GCAATACGAAGTTCTTACTAGAATCACGATCGAACACACTCACTCATATATGACTC-GAAACACA
66 GCAATACGAAGTTCTTACTAGAATCACGA-C---CACACACACTCATATATGACTCAG-AACACA
3710992 TAATCAAGAT
126 TAATCAAGAT
*
3711002 CATATTTATATATACATATTTC-CATTCTTGTAACGTTGTTTGTGCATTTTCAATCTTCAATCAA
1 CATATTTATATATACATATTTCTC-TTCTTGTAACGTTGTTTGTGCATTTTCAACCTTCAATCAA
* * ** *
3711066 AGCACTGCGAAGTTCTTACTAGAATCACGACCAGGCACACTCATATATGACTCAGAACACATGAT
65 AGCAATACGAAGTTCTTACTAGAATCACGACCACACACACTCATATATGACTCAGAACACATAAT
3711131 CAAGAT
130 CAAGAT
3711137 CATAT
1 CATAT
3711142 CAGGTGGGAG
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
135 39 0.30
136 1 0.01
138 2 0.02
139 87 0.67
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (135 bp):
CATATTTATATATACATATTTCTCTTCTTGTAACGTTGTTTGTGCATTTTCAACCTTCAATCAAA
GCAATACGAAGTTCTTACTAGAATCACGACCACACACACTCATATATGACTCAGAACACATAATC
AAGAT
Found at i:3711350 original size:38 final size:42
Alignment explanation
Indices: 3711308--3711385 Score: 119
Period size: 38 Copynumber: 2.0 Consensus size: 42
3711298 GTTATGATAA
*
3711308 TATAATATATGTATAT-ATAT-TATAAG-GTATAT-TATACT
1 TATAATATATGTACATAATATATATAAGTGTATATATATACT
3711346 TATAATATATGTACATAATATATATAAGTGTATATATATA
1 TATAATATATGTACATAATATATATAAGTGTATATATATA
3711386 TATTAATTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 15 0.43
39 4 0.11
40 6 0.17
41 6 0.17
42 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (42 bp):
TATAATATATGTACATAATATATATAAGTGTATATATATACT
Found at i:3711384 original size:18 final size:18
Alignment explanation
Indices: 3711317--3711388 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 18
3711307 ATATAATATA
3711317 TGTATATATAT-TATAAG
1 TGTATATATATATATAAG
3711334 -GTATATTATACTTATAATATA-
1 TGTATA-TATA--TAT-ATA-AG
*
3711355 TGTACATAATATATATAAG
1 TGTATAT-ATATATATAAG
3711374 TGTATATATATATAT
1 TGTATATATATATAT
3711389 TAATTGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 9 0.20
19 10 0.23
20 4 0.09
21 4 0.09
22 8 0.18
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (18 bp):
TGTATATATATATATAAG
Found at i:3724772 original size:21 final size:20
Alignment explanation
Indices: 3724737--3724795 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
3724727 CTGTTGAGAG
3724737 TGGTATCGATACCTTAAGGGA
1 TGGTATCGATACCTTAA-GGA
3724758 TGGGTATCG-TACCTTAAGGA
1 T-GGTATCGATACCTTAAGGA
*
3724778 TGGTATCTATACCCTTAA
1 TGGTATCGATA-CCTTAA
3724796 ACATCGAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 15 0.44
22 7 0.21
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCTTAAGGA
Found at i:3724912 original size:22 final size:21
Alignment explanation
Indices: 3724885--3724938 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3724875 TACATGCAGA
3724885 GGTATCGATACCCCGTAAAGGT
1 GGTATCGATACCCC-TAAAGGT
* * *
3724907 GGTATCGGTA-CCCTTAGGGT
1 GGTATCGATACCCCTAAAGGT
3724927 GGTATCGATACC
1 GGTATCGATACC
3724939 TCCAAGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 14 0.52
21 4 0.15
22 9 0.33
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (21 bp):
GGTATCGATACCCCTAAAGGT
Found at i:3725307 original size:21 final size:22
Alignment explanation
Indices: 3725281--3725331 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3725271 ATGTTATGGA
* *
3725281 AATGTGAACC-TTGAATAAGTT
1 AATGTGAACCTTTGAACAAGTG
*
3725302 AATGTG-ACCTTTGAACCAGTG
1 AATGTGAACCTTTGAACAAGTG
3725323 AATGTGAAC
1 AATGTGAAC
3725332 AAACTCTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (22 bp):
AATGTGAACCTTTGAACAAGTG
Found at i:3732090 original size:21 final size:21
Alignment explanation
Indices: 3732064--3732113 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3732054 TTGTTATGGA
*
3732064 AATGTGAACCTTGAATAAGTG
1 AATGTGAACCTTGAACAAGTG
* *
3732085 AATGTGAACTTTGAACCAGTG
1 AATGTGAACCTTGAACAAGTG
3732106 AATGTGAA
1 AATGTGAA
3732114 TAAACTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (21 bp):
AATGTGAACCTTGAACAAGTG
Found at i:3732304 original size:21 final size:21
Alignment explanation
Indices: 3732280--3732376 Score: 74
Period size: 21 Copynumber: 4.5 Consensus size: 21
3732270 TGTGGTCCTC
*
3732280 CGGTACAAATATGTGGCACTT
1 CGGTGCAAATATGTGGCACTT
*
3732301 CGGTGCAACCCTATGTGGCACTT
1 CGGTGCAA--ATATGTGGCACTT
** *
3732324 CAATGCAAACTATATGGTC-CTT
1 CGGTGCAAA-TATGTGG-CACTT
3732346 CGG-G-ATAATTATGTGGCACTT
1 CGGTGCA-AA-TATGTGGCACTT
3732367 CGGTGCAAAT
1 CGGTGCAAAT
3732377 TACGAGCTGT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
20 2 0.03
21 23 0.40
22 13 0.22
23 20 0.34
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
CGGTGCAAATATGTGGCACTT
Found at i:3733229 original size:20 final size:20
Alignment explanation
Indices: 3733206--3733258 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
3733196 ACTGTAAAGG
*
3733206 TGGTATTGATACCTGATGGA
1 TGGTATCGATACCTGATGGA
3733226 TGGTATCGATACCTGATGGA
1 TGGTATCGATACCTGATGGA
3733246 TGGTATCGATACC
1 TGGTATCGATACC
3733259 CTTAAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCTGATGGA
Found at i:3733330 original size:22 final size:20
Alignment explanation
Indices: 3733281--3733354 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
3733271 AATGCCAAAT
*
3733281 TAGTATCGGTACC-TT-GAG
1 TAGTATCGATACCATTAGAG
* * *
3733299 GAGGTATCGATACCCTTGAAGGG
1 TA-GTATCGATACCATT--AGAG
3733322 TAGTATCGATACCATTAGAG
1 TAGTATCGATACCATTAGAG
3733342 TAGTATCGATACC
1 TAGTATCGATACC
3733355 TCCAAGCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 10 0.22
20 18 0.40
22 13 0.29
23 3 0.07
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (20 bp):
TAGTATCGATACCATTAGAG
Found at i:3733969 original size:23 final size:23
Alignment explanation
Indices: 3733907--3733956 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3733897 GGACAATTAC
* *
3733907 GTGGCACTTCGGTGCAAACCTAT
1 GTGGCACTTCGGTACAAAACTAT
3733930 GTGGCACTTCGGTACAAAACTAT
1 GTGGCACTTCGGTACAAAACTAT
3733953 GTGG
1 GTGG
3733957 TCCTTCAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (23 bp):
GTGGCACTTCGGTACAAAACTAT
Found at i:3736584 original size:19 final size:21
Alignment explanation
Indices: 3736552--3736590 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3736542 AAACATTAAA
3736552 TTCAAACTAATC-AAACCAAG
1 TTCAAACTAATCAAAACCAAG
3736572 TTCAAAC-AATCAAAACCAA
1 TTCAAACTAATCAAAACCAA
3736591 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.18
Consensus pattern (21 bp):
TTCAAACTAATCAAAACCAAG
Found at i:3748655 original size:20 final size:20
Alignment explanation
Indices: 3748611--3748682 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
3748601 TGCAAGGTTT
* *
3748611 GTATCGATACCTGTTGATAGTG
1 GTATCGATA-CTG-TAATGGTG
3748633 GTATCGATACTGTAATGGTG
1 GTATCGATACTGTAATGGTG
*
3748653 GTATCGATAC-CTAATGGATG
1 GTATCGATACTGTAATGG-TG
3748673 GTATCGATAC
1 GTATCGATAC
3748683 CCTTAAAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 6 0.13
20 28 0.61
21 3 0.07
22 9 0.20
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (20 bp):
GTATCGATACTGTAATGGTG
Found at i:3748795 original size:54 final size:54
Alignment explanation
Indices: 3748672--3748797 Score: 164
Period size: 54 Copynumber: 2.3 Consensus size: 54
3748662 CCTAATGGAT
* *
3748672 GGTATCGATACCCTTAAAACATCGAATGCGAAATTGGTAACGGTACCTTGAGAA
1 GGTATCGATACCCTTGAAACATCGAATGCGAAATTGGTAACGGTACCATGAGAA
** * ** *
3748726 GGTATCGATACCCTTGAAACATCGAATG-TTATTTCGGTATTGGTACCATGATAA
1 GGTATCGATACCCTTGAAACATCGAATGCGAAATT-GGTAACGGTACCATGAGAA
3748780 GGTATCGATACCCTTGAA
1 GGTATCGATACCCTTGAA
3748798 GAATAGTATC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 3 0.05
54 60 0.95
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATGCGAAATTGGTAACGGTACCATGAGAA
Found at i:3751127 original size:13 final size:13
Alignment explanation
Indices: 3751109--3751142 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3751099 AGCATTGTGA
3751109 AAAGAAAAT-AAT
1 AAAGAAAATAAAT
3751121 GAAAGAAAATAAAT
1 -AAAGAAAATAAAT
3751135 AAAGAAAA
1 AAAGAAAA
3751143 GTGGAGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAGAAAATAAAT
Found at i:3754203 original size:18 final size:19
Alignment explanation
Indices: 3754168--3754206 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3754158 TTATTGAAGG
3754168 AGTATCGATACCTAAAGGGT
1 AGTATCGATACC-AAAGGGT
*
3754188 AGTATGGATACC-AAGGGT
1 AGTATCGATACCAAAGGGT
3754206 A
1 A
3754207 CCGATACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGT
Found at i:3754712 original size:7 final size:7
Alignment explanation
Indices: 3754700--3754725 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3754690 TTATATGTTT
3754700 TGATATA
1 TGATATA
3754707 TGATATA
1 TGATATA
3754714 TGATATA
1 TGATATA
3754721 TGATA
1 TGATA
3754726 CATAGGAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (7 bp):
TGATATA
Found at i:3756831 original size:17 final size:17
Alignment explanation
Indices: 3756786--3756832 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3756776 TAGGTCCTTG
3756786 TACT-TATTTTATTTTT
1 TACTATATTTTATTTTT
* * *
3756802 TATTCTATGTTATTTTT
1 TACTATATTTTATTTTT
*
3756819 TACTATTTTTTATT
1 TACTATATTTTATT
3756833 ATTATTTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (17 bp):
TACTATATTTTATTTTT
Found at i:3756875 original size:22 final size:21
Alignment explanation
Indices: 3756826--3756882 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
3756816 TTTTACTATT
3756826 TTTTATT-ATTA-TTTATTTA
1 TTTTATTAATTATTTTATTTA
*
3756845 TTGGT-TTAATTATTTTATTTTA
1 TT-TTATTAATTATTTTA-TTTA
*
3756867 TTTTATTAATTGTTTT
1 TTTTATTAATTATTTT
3756883 GATATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 5 0.17
22 16 0.53
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTATTAATTATTTTATTTA
Found at i:3763617 original size:21 final size:22
Alignment explanation
Indices: 3763571--3763623 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3763561 ACACCTAACA
* * *
3763571 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACATCCATGAAG
3763593 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCATGAAG
*
3763614 GTGCACCGAT
1 GTGCATCGAT
3763624 GCACGCCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATACATCCATGAAG
Found at i:3763646 original size:23 final size:23
Alignment explanation
Indices: 3763571--3763647 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
3763561 ACACCTAACA
*
3763571 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
3763593 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
3763614 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
3763637 GTACATCGATG
1 GTGCATCGATG
3763648 TACAAGGCCA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.35
22 10 0.23
23 17 0.40
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:3765237 original size:21 final size:21
Alignment explanation
Indices: 3765195--3765238 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3765185 ACTCCGGGAG
*
3765195 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3765216 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3765237 CT
1 CT
3765239 CCCCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3765829 original size:2 final size:2
Alignment explanation
Indices: 3765822--3765854 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3765812 CAGCTTAAGC
3765822 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
3765855 TTAATCAATT
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:3766439 original size:65 final size:65
Alignment explanation
Indices: 3766319--3766525 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 65
3766309 TTTATCAAAG
* * * **
3766319 TGATGCACCGATG-CACCAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGACACCAA-CCATGCATCGATGCACTATGGA-TATTTTGAAACATCGAATGCA
3766382 TT
64 TT
*
3766384 TCATGCATCGATGA-A-CATACCATGCATCGATGCACTGAT-GAT-TTTATGAAAACATCGAATG
1 TGATGCATCGATGACACCA-ACCATGCATCGATGCACT-ATGGATATTT-TG-AAACATCGAATG
3766445 CATT
62 CATT
* * * *
3766449 TGATGCATCGAT-ACACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGACACCAACCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCATT
3766513 TGATGCATCGATG
1 TGATGCATCGATG
3766526 CACTCTTAGT
Statistics
Matches: 120, Mismatches: 11, Indels: 22
0.78 0.07 0.14
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 48 0.40
65 63 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGACACCAACCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCATT
Found at i:3769673 original size:114 final size:114
Alignment explanation
Indices: 3769473--3769687 Score: 349
Period size: 114 Copynumber: 1.9 Consensus size: 114
3769463 CATGTTCTTG
* * * *
3769473 TAGTAGAAATAAAGAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTT
1 TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* **
3769538 GATAGGAACCCTTAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GATAAGAACCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
*
3769587 TAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
*
3769652 GGTAAGAACCCAAAAACCAATCATTGGATTTGAAAG
66 GATAAGAACCCAAAAACCAATCATTGGATTTGAAAG
3769688 CCATTTGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 92 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GATAAGAACCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:3771899 original size:22 final size:22
Alignment explanation
Indices: 3771873--3771942 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
3771863 CTCTTAAAAT
3771873 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
* *
3771895 ATGATAGGTTCTCTTTTTAAAG
1 ATGATAGATTCTCTTTTCAAAG
3771917 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
3771939 ATGA
1 ATGA
3771943 AAGCTTTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTCAAAG
Found at i:3772894 original size:76 final size:76
Alignment explanation
Indices: 3772795--3773753 Score: 1659
Period size: 76 Copynumber: 12.6 Consensus size: 76
3772785 CTATTTCCTA
* *
3772795 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTATCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3772860 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3772871 CACCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3772936 AACCTTAGGGT
66 AGCCTTAGGGT
* *
3772947 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773012 AGCCTTAGGGT
66 AGCCTTAGGGT
3773023 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773088 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3773099 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773164 AGCCTTAGGGT
66 AGCCTTAGGGT
3773175 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773240 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3773251 CATCTGTAAGTCCTACGGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773316 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
3773327 CATCTGTAAGTCCTTCAGTGCATAATGTTTCCAAAAAACCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
3773392 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
3773404 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3773469 AACCTTAGGGT
66 AGCCTTAGGGT
* * *
3773480 CATCTGTAAGTCCTTCAATGGATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773545 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3773556 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGCGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3773621 AACCTTAGGGT
66 AGCCTTAGGGT
*
3773632 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3773697 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * * *
3773708 CATCTGTTA-TCCCTTCAGTGCTTGATGTTTTCAAAAAACCTTCGGG
1 CATCTGTAAGT-CCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
3773754 TCATCTCTAA
Statistics
Matches: 837, Mismatches: 44, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
75 1 0.00
76 763 0.91
77 73 0.09
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3773769 original size:47 final size:47
Alignment explanation
Indices: 3773684--3773788 Score: 142
Period size: 47 Copynumber: 2.3 Consensus size: 47
3773674 CGGGAGCTTT
* * * *
3773684 TTGATGTTTTC--AAAGCCTTAGGGTCATCTGTTATCCCTTCAGTGC
1 TTGATGTTTTCAAAAAACCTTAGGGTCATCTCTAAGCCCTTCAGTGC
*
3773729 TTGATGTTTTCAAAAAACCTTCGGGTCATCTCTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAAAACCTTAGGGTCATCTCTAAGCCCTTCAGTGC
*
3773776 TTGATGATTTCAA
1 TTGATGTTTTCAA
3773789 CATTTCAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 11 0.21
47 41 0.79
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (47 bp):
TTGATGTTTTCAAAAAACCTTAGGGTCATCTCTAAGCCCTTCAGTGC
Found at i:3773909 original size:3 final size:3
Alignment explanation
Indices: 3773895--3773968 Score: 85
Period size: 3 Copynumber: 23.7 Consensus size: 3
3773885 TAATTTTTTC
* * * *
3773895 TAT TAT TTT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT
3773942 TAT TAT TAT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TA
3773969 AATAAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 55 0.89
4 7 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3776045 original size:27 final size:25
Alignment explanation
Indices: 3776002--3776063 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 25
3775992 AAATTGAACG
*
3776002 ACCGG-TTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTTACCGGATAAAAA
*
3776026 ACCGTTTTTTTTTAAACCGGATAAAAA
1 ACCGGTTTTTTTT--ACCGGATAAAAA
3776053 ACCGGTTTTTT
1 ACCGGTTTTTT
3776064 ATCTGAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.12
25 7 0.22
27 21 0.66
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (25 bp):
ACCGGTTTTTTTTACCGGATAAAAA
Found at i:3776090 original size:39 final size:37
Alignment explanation
Indices: 3776047--3776129 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 37
3776037 TTAAACCGGA
* *
3776047 TAAAAAACCGGTTTTTTATCTGAAAACAATCCAGTTTTT
1 TAAAAAACCGGATTTTTATCTGAAAA-AAT-CAGGTTTT
**
3776086 TAAAAAATTGGATTTTTATCTGAAAAAATCAGGTTTT
1 TAAAAAACCGGATTTTTATCTGAAAAAATCAGGTTTT
3776123 TAAAAAA
1 TAAAAAA
3776130 AATGATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 14 0.35
38 3 0.08
39 23 0.57
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (37 bp):
TAAAAAACCGGATTTTTATCTGAAAAAATCAGGTTTT
Found at i:3776122 original size:21 final size:21
Alignment explanation
Indices: 3776059--3776124 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
3776049 AAAAACCGGT
3776059 TTTTTATCTGAAAACAATCCA-G
1 TTTTTATCTGAAAA-AAT-CAGG
*
3776081 -TTTT-T-T-AAAAAAT-TGG
1 TTTTTATCTGAAAAAATCAGG
3776097 ATTTTTATCTGAAAAAATCAGG
1 -TTTTTATCTGAAAAAATCAGG
3776119 TTTTTA
1 TTTTTA
3776125 AAAAAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 8 0.23
19 2 0.06
20 2 0.06
21 17 0.49
22 2 0.06
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (21 bp):
TTTTTATCTGAAAAAATCAGG
Found at i:3776122 original size:38 final size:38
Alignment explanation
Indices: 3776059--3776139 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 38
3776049 AAAAACCGGT
* *
3776059 TTTTTATCTGAAAACAATCCAGTTTTTTAAAAAATTGGA
1 TTTTTATCTGAAAACAATCCAGTTTTTAAAAAAAAT-GA
3776098 TTTTTATCTGAAAA-AAT-CAGGTTTTTAAAAAAAATGA
1 TTTTTATCTGAAAACAATCCA-GTTTTTAAAAAAAATGA
3776135 TTTTT
1 TTTTT
3776140 TTGCAAAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 9 0.23
38 16 0.41
39 14 0.36
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (38 bp):
TTTTTATCTGAAAACAATCCAGTTTTTAAAAAAAATGA
Found at i:3776130 original size:39 final size:37
Alignment explanation
Indices: 3776059--3776139 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 37
3776049 AAAAACCGGT
*
3776059 TTTTTATCTGAAAACAATCCAGTTTTTTAAAAAATTGGA
1 TTTTTATCTGAAAACAATCCAG-TTTTTAAAAAAAT-GA
3776098 TTTTTATCTGAAAA-AAT-CAGGTTTTTAAAAAAAATGA
1 TTTTTATCTGAAAACAATCCA-GTTTTT-AAAAAAATGA
3776135 TTTTT
1 TTTTT
3776140 TTGCAAAACG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
37 14 0.36
38 11 0.28
39 14 0.36
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (37 bp):
TTTTTATCTGAAAACAATCCAGTTTTTAAAAAAATGA
Found at i:3786425 original size:14 final size:13
Alignment explanation
Indices: 3786406--3786446 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3786396 TTTAGATTTT
3786406 TTAAAATTACATTA
1 TTAAAA-TACATTA
3786420 TTAAAA-ACA-TA
1 TTAAAATACATTA
3786431 TTAAAAATACATTA
1 TT-AAAATACATTA
3786445 TT
1 TT
3786447 GATAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 3 0.12
14 10 0.42
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (13 bp):
TTAAAATACATTA
Found at i:3787752 original size:7 final size:7
Alignment explanation
Indices: 3787740--3787839 Score: 74
Period size: 7 Copynumber: 14.1 Consensus size: 7
3787730 CTTTATAATG
3787740 AACCCTA
1 AACCCTA
3787747 AACCCTA
1 AACCCTA
***
3787754 AAAATTA
1 AACCCTA
*
3787761 AATCCTA
1 AACCCTA
*
3787768 AACTCTA
1 AACCCTA
*
3787775 ATCCCTA
1 AACCCTA
3787782 AACCCTAA
1 AACCCT-A
**
3787790 AATGCTA
1 AACCCTA
*
3787797 AACACTA
1 AACCCTA
*
3787804 AACCTTA
1 AACCCTA
*
3787811 AATCCTA
1 AACCCTA
3787818 AACCCTA
1 AACCCTA
*
3787825 AACACTA
1 AACCCTA
*
3787832 ACCCCTA
1 AACCCTA
3787839 A
1 A
3787840 GCACTTAATC
Statistics
Matches: 69, Mismatches: 23, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
7 64 0.93
8 5 0.07
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:3788908 original size:16 final size:17
Alignment explanation
Indices: 3788879--3788918 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3788869 GATCATATTC
*
3788879 AATTTAAACTAAACCTA
1 AATTAAAACTAAACCTA
3788896 AATTAAAAC-AAACCTA
1 AATTAAAACTAAACCTA
*
3788912 AAATAAA
1 AATTAAA
3788919 TATTCAGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (17 bp):
AATTAAAACTAAACCTA
Found at i:3791422 original size:37 final size:36
Alignment explanation
Indices: 3791356--3791430 Score: 114
Period size: 37 Copynumber: 2.1 Consensus size: 36
3791346 AAGGAAAATA
*
3791356 TTGTCATCTTGTATAAATTTGGATATGTTGTCATAT
1 TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
* *
3791392 TTGTCATCTTTTTATAAATTTAGATGTGTTGTCATAT
1 TTGTCATC-TTGTATAAATTTAGATATGTTGTCATAT
3791429 TT
1 TT
3791431 TGTAAACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (36 bp):
TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
Found at i:3801470 original size:23 final size:23
Alignment explanation
Indices: 3801439--3801504 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
3801429 CCTTATATGA
3801439 CACTTCGGTGCATTTCTACGCGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
3801462 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
*
3801485 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
3801505 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.30
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:3805282 original size:22 final size:22
Alignment explanation
Indices: 3805256--3805321 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
3805246 CATGTGAAAT
*
3805256 ATGTCCCGAAAGACCTCTGTAA
1 ATGTCCCGAAAGACCTATGTAA
* * * *
3805278 ATGTCTCGAATGACCTATGCAT
1 ATGTCCCGAAAGACCTATGTAA
*
3805300 ATGTCCCGAAGGACCTATGTAA
1 ATGTCCCGAAAGACCTATGTAA
3805322 CCCTTGACTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (22 bp):
ATGTCCCGAAAGACCTATGTAA
Found at i:3812722 original size:3 final size:3
Alignment explanation
Indices: 3812714--3812814 Score: 195
Period size: 3 Copynumber: 34.0 Consensus size: 3
3812704 AATATGTATG
3812714 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3812762 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3812809 ATA ATA
1 ATA ATA
3812815 TGTATATGTA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3812821 original size:6 final size:6
Alignment explanation
Indices: 3812812--3812848 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3812802 AATAATAATA
3812812 ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT ATA
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA
3812849 ATATGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:3812840 original size:10 final size:10
Alignment explanation
Indices: 3812813--3812857 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
3812803 ATAATAATAA
3812813 TATGTATATG
1 TATGTATATG
3812823 TATATGTATATG
1 --TATGTATATG
3812835 TATGTATATG
1 TATGTATATG
*
3812845 TAT-AATATG
1 TATGTATATG
3812854 TATG
1 TATG
3812858 ATGATTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 8 0.26
10 13 0.42
12 10 0.32
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (10 bp):
TATGTATATG
Found at i:3812968 original size:15 final size:15
Alignment explanation
Indices: 3812912--3812968 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 15
3812902 TATAAGTATT
3812912 AAACTACATAATATA
1 AAACTACATAATATA
*
3812927 AAACTTATATAACTATA
1 AAAC-TACATAA-TATA
3812944 TTTTAAACTACATAATATA
1 ----AAACTACATAATATA
3812963 AAACTA
1 AAACTA
3812969 TAAAACCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 10 0.29
16 6 0.18
17 4 0.12
19 4 0.12
20 6 0.18
21 4 0.12
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
AAACTACATAATATA
Found at i:3815979 original size:14 final size:14
Alignment explanation
Indices: 3815960--3815986 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3815950 AATCATTTTT
3815960 AAAATAATTTTAAG
1 AAAATAATTTTAAG
3815974 AAAATAATTTTAA
1 AAAATAATTTTAA
3815987 AAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:3819592 original size:45 final size:45
Alignment explanation
Indices: 3819528--3820322 Score: 1248
Period size: 45 Copynumber: 17.7 Consensus size: 45
3819518 GAAAAGGATA
* * *
3819528 TAAAGGCATGAAAAGATGCCATACATGAAATACATAACGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
3819573 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
*
3819618 TAAAGGCATGAAAGGATTCCATAAATGAAATGCATAACGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
3819663 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
*
3819708 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * *
3819753 TAAAGGCATGATAGGATGCAATAAATGAAATGCATAACAGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * *
3819798 TAAAGGCATGAAAGGATGCAATAAATGAAATGCATAAGGGTACAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* *
3819843 TAAAGGCATGAAAGGATACCATAAATGAAATGCATAATGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * *
3819888 TAAAGGCATGAAAGAATACCATAAATGAAATGCATAATGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * *
3819933 TAAAGACATGAAAGGATGCCATAAATGAAATGTATAATGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * * * * *
3819978 TAAAGACACGAAAGGATTCTATAAATGAAATACATAACAGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
*
3820023 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* * *
3820068 TAAAGGCATAAAAGGATGCCATAAATGAAATGCATAATGGTACAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* **
3820113 TAAAGGCATGAGAGGATGCCATAAATGAAATGCATAACAATGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* *
3820158 TAAAGGCATGAAAGGATGCCACAAATGAAATGCATAACGGTGCAC
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
*
3820203 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
*
3820248 TAAAGGCATGAAAGGATGCCATAAATGAAATGCGTAACGGTGCAT
1 TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
* *
3820293 TAAAGGCATGCAATGATGCCATAAATGAAA
1 TAAAGGCATGAAAGGATGCCATAAATGAAA
3820323 ATAACAAATA
Statistics
Matches: 695, Mismatches: 55, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 695 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
TAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCAT
Found at i:3819867 original size:21 final size:21
Alignment explanation
Indices: 3819798--3819867 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
3819788 AACAGTGCAT
* *
3819798 TAAAGGCATGAAAGGATGCAA
1 TAAAGGCATGAAAGGATACCA
** *
3819819 TAAATGAAATGCATAAGGGTA-CA
1 TAAA-GGCATG-A-AAGGATACCA
3819842 TTAAAGGCATGAAAGGATACCA
1 -TAAAGGCATGAAAGGATACCA
3819864 TAAA
1 TAAA
3819868 TGAAATGCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 14 0.39
22 7 0.19
23 6 0.17
24 9 0.25
ACGTcount: A:0.49, C:0.10, G:0.23, T:0.19
Consensus pattern (21 bp):
TAAAGGCATGAAAGGATACCA
Found at i:3826405 original size:37 final size:37
Alignment explanation
Indices: 3826355--3826485 Score: 110
Period size: 37 Copynumber: 3.4 Consensus size: 37
3826345 TTATAAAATA
3826355 ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
*
3826392 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAAATTA--TT--ATAA---A--A-TATGGATTG
* *
3826439 ATTTATTTT-AAAT-AA-T-TTAT-TAGTATGGATTG
1 ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
3826471 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
3826486 TGGATTGATT
Statistics
Matches: 78, Mismatches: 4, Indels: 27
0.72 0.04 0.25
Matches are distributed among these distances:
32 18 0.23
33 4 0.05
35 1 0.01
37 19 0.24
39 4 0.05
41 6 0.08
44 2 0.03
45 1 0.01
46 5 0.06
47 18 0.23
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.51
Consensus pattern (37 bp):
ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
Found at i:3826421 original size:14 final size:15
Alignment explanation
Indices: 3826280--3826427 Score: 190
Period size: 15 Copynumber: 9.5 Consensus size: 15
3826270 TAATAAGGTT
3826280 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
3826295 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3826310 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
3826325 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3826340 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
3826355 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
3826370 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
3826389 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
3826407 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
3826421 ATTTATT
1 ATTTATT
3826428 AGTATGGATT
Statistics
Matches: 118, Mismatches: 8, Indels: 15
0.84 0.06 0.11
Matches are distributed among these distances:
14 12 0.10
15 86 0.73
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:3826445 original size:32 final size:32
Alignment explanation
Indices: 3826407--3826536 Score: 190
Period size: 32 Copynumber: 4.4 Consensus size: 32
3826397 TTTTAAAATA
3826407 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3826439 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3826471 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3826493 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
3826525 ATTTATTTTAAA
1 ATTTATTTTAAA
3826537 ATATAGATTT
Statistics
Matches: 88, Mismatches: 0, Indels: 20
0.81 0.00 0.19
Matches are distributed among these distances:
22 14 0.16
23 4 0.05
25 1 0.01
26 3 0.03
28 3 0.03
29 1 0.01
31 4 0.05
32 58 0.66
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:3826487 original size:22 final size:22
Alignment explanation
Indices: 3826462--3826504 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3826452 AATTTATTAG
3826462 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3826484 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
3826505 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Done.