Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 11 of 216
Found at i:3648603 original size:31 final size:31
Alignment explanation
Indices: 3648551--3648610 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3648541 GCTATGAAAT
* *
3648551 CAAATTCAGGTACCAATTTGAATAAAAAAAC
1 CAAATTCAGATACCAATTTGAACAAAAAAAC
*
3648582 CAAATTTAGATACCTAA-TTGAACAAAAAA
1 CAAATTCAGATACC-AATTTGAACAAAAAA
3648611 TAATCTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.23
Consensus pattern (31 bp):
CAAATTCAGATACCAATTTGAACAAAAAAAC
Found at i:3651785 original size:13 final size:13
Alignment explanation
Indices: 3651767--3651797 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3651757 GAAATTGAAC
3651767 TAATTTTTATTTA
1 TAATTTTTATTTA
3651780 TAA-TTTTATTTA
1 TAATTTTTATTTA
3651792 TAATTT
1 TAATTT
3651798 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTTATTTA
Found at i:3651946 original size:22 final size:22
Alignment explanation
Indices: 3651904--3651946 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3651894 AATTAGTTTC
**
3651904 TTTTAAAAATATTTATGAATAT
1 TTTTAAAAATATTTAAAAATAT
3651926 TTTTAAAAAT-TTTACAAAATA
1 TTTTAAAAATATTTA-AAAATA
3651947 ATATCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAAAATATTTAAAAATAT
Found at i:3660385 original size:26 final size:27
Alignment explanation
Indices: 3660336--3660387 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3660326 TTTTAAATTA
*
3660336 AAAAAGTTAAGGAATTAAATTTCTAAT
1 AAAAAGTTAAAGAATTAAATTTCTAAT
3660363 AAAAAGTGTAAAG-ATTAAA-TTCTAA
1 AAAAAGT-TAAAGAATTAAATTTCTAA
3660388 ATGTACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 13 0.57
28 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.31
Consensus pattern (27 bp):
AAAAAGTTAAAGAATTAAATTTCTAAT
Found at i:3672216 original size:21 final size:21
Alignment explanation
Indices: 3672192--3672234 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3672182 GTTTTGTTAC
3672192 TTAGTTTGATTTGAACTAAGT
1 TTAGTTTGATTTGAACTAAGT
3672213 TTAGTTTGATTTGAACTAAGT
1 TTAGTTTGATTTGAACTAAGT
3672234 T
1 T
3672235 GTCAATGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (21 bp):
TTAGTTTGATTTGAACTAAGT
Found at i:3676483 original size:28 final size:28
Alignment explanation
Indices: 3676412--3676467 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3676402 GTTGGTTCTA
*
3676412 CCGCTTGAATGATATATGATCGGCCTTG
1 CCGCTTGAATAATATATGATCGGCCTTG
3676440 CCGCTTGAATAATATATGATCGGCCTTG
1 CCGCTTGAATAATATATGATCGGCCTTG
3676468 TTGCCTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
CCGCTTGAATAATATATGATCGGCCTTG
Found at i:3678043 original size:26 final size:26
Alignment explanation
Indices: 3678007--3678061 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
3677997 CAAACATATC
*
3678007 CCATAGATACCACTTGATATCAAGCA
1 CCATAGATACCACTCGATATCAAGCA
3678033 CCATAGATACCACTCGATATCAAGCA
1 CCATAGATACCACTCGATATCAAGCA
3678059 CCA
1 CCA
3678062 CCATGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (26 bp):
CCATAGATACCACTCGATATCAAGCA
Found at i:3683827 original size:18 final size:19
Alignment explanation
Indices: 3683794--3683831 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3683784 AGACTCCAGG
*
3683794 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
3683813 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
3683831 T
1 T
3683832 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:3692028 original size:66 final size:66
Alignment explanation
Indices: 3691922--3692053 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
3691912 AGCTCGATTG
3691922 AGACTTGTAATTGTTTGTAGGTCATATTATAAATGAACTATAAATTGTTTTGTTGTTTCATTAAA
1 AGACTTGTAATTGTTTGTAGGTCATATTATAAATGAACTATAAATTGTTTTGTTGTTTCATTAAA
3691987 T
66 T
3691988 AGACTTGTAATTGTTTGTAGGTCATATTATAAATGAACTATAAATTGTTTTGTTGTTTCATTAAA
1 AGACTTGTAATTGTTTGTAGGTCATATTATAAATGAACTATAAATTGTTTTGTTGTTTCATTAAA
3692053 T
66 T
3692054 GTTAAAGTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (66 bp):
AGACTTGTAATTGTTTGTAGGTCATATTATAAATGAACTATAAATTGTTTTGTTGTTTCATTAAA
T
Found at i:3692034 original size:34 final size:34
Alignment explanation
Indices: 3691930--3692037 Score: 111
Period size: 34 Copynumber: 3.2 Consensus size: 34
3691920 TGAGACTTGT
3691930 AATTGTTTGTAGGTCATATTATAAATGAACTATA
1 AATTGTTTGTAGGTCATATTATAAATGAACTATA
* * *
3691964 AATTGTTTTGT-TGT--T-TCATTAAAT-AGACT-TGT
1 AATTG-TTTGTAGGTCATATTA-TAAATGA-ACTAT-A
3691996 AATTGTTTGTAGGTCATATTATAAATGAACTATA
1 AATTGTTTGTAGGTCATATTATAAATGAACTATA
3692030 AATTGTTT
1 AATTGTTT
3692038 TGTTGTTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
31 9 0.16
32 16 0.28
34 24 0.41
35 9 0.16
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (34 bp):
AATTGTTTGTAGGTCATATTATAAATGAACTATA
Found at i:3693472 original size:7 final size:7
Alignment explanation
Indices: 3693460--3693503 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
3693450 GTAAGTCATT
3693460 TAATCAA
1 TAATCAA
3693467 TAATCAA
1 TAATCAA
3693474 TAAT-AA
1 TAATCAA
3693480 TAATCAA
1 TAATCAA
3693487 TAATCAA
1 TAATCAA
3693494 TAATCAA
1 TAATCAA
3693501 TAA
1 TAA
3693504 GATAGTACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATCAA
Found at i:3693485 original size:20 final size:21
Alignment explanation
Indices: 3693460--3693503 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
3693450 GTAAGTCATT
3693460 TAATCAATAATCAATAAT-AA
1 TAATCAATAATCAATAATCAA
3693480 TAATCAATAATCAATAATCAA
1 TAATCAATAATCAATAATCAA
3693501 TAA
1 TAA
3693504 GATAGTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATCAATAATCAATAATCAA
Found at i:3706168 original size:20 final size:20
Alignment explanation
Indices: 3706143--3706184 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3706133 CTTTAAATAA
3706143 TTAAATAAAATTTTTATCAT
1 TTAAATAAAATTTTTATCAT
*
3706163 TTAAATAAATTTTTTATCAT
1 TTAAATAAAATTTTTATCAT
3706183 TT
1 TT
3706185 TTGAGATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATAAAATTTTTATCAT
Found at i:3708652 original size:14 final size:14
Alignment explanation
Indices: 3708633--3708665 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3708623 TGTTAGCATG
3708633 TTTAAAATAAATAT
1 TTTAAAATAAATAT
3708647 TTTAAAATAAATAT
1 TTTAAAATAAATAT
3708661 TTTAA
1 TTTAA
3708666 TTATTTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAAATAAATAT
Found at i:3712225 original size:26 final size:26
Alignment explanation
Indices: 3712187--3712241 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
3712177 CAAACATATC
* *
3712187 CCATAGATGCCACTTGATATCAAACA
1 CCATAGATACCACTCGATATCAAACA
*
3712213 CCATAGATACCACTCGATATCAAGCA
1 CCATAGATACCACTCGATATCAAACA
3712239 CCA
1 CCA
3712242 CCATGAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (26 bp):
CCATAGATACCACTCGATATCAAACA
Found at i:3720300 original size:9 final size:9
Alignment explanation
Indices: 3720284--3720329 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
3720274 TTAAGTTCTC
3720284 TATTTTTTT
1 TATTTTTTT
*
3720293 TGTTTTTTT
1 TATTTTTTT
*
3720302 TATTTATTT
1 TATTTTTTT
3720311 TATTTTTCTTT
1 TA-TTTT-TTT
3720322 TATTTTTT
1 TATTTTTT
3720330 CTCTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 19 0.61
10 7 0.23
11 5 0.16
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.85
Consensus pattern (9 bp):
TATTTTTTT
Found at i:3720329 original size:18 final size:17
Alignment explanation
Indices: 3720284--3720340 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
3720274 TTAAGTTCTC
*
3720284 TATTTTTTTTGTTTTTTT
1 TATTTTTTTT-TTTCTTT
3720302 TATTTATTTTATTTTTCTTT
1 TA-TT-TTTT-TTTTTCTTT
*
3720322 TATTTTTTCTCTTTCTTT
1 TATTTTTT-TTTTTCTTT
3720340 T
1 T
3720341 CGTTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.45
19 4 0.12
20 12 0.36
21 2 0.06
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (17 bp):
TATTTTTTTTTTTCTTT
Found at i:3720340 original size:29 final size:28
Alignment explanation
Indices: 3720286--3720340 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
3720276 AAGTTCTCTA
* *
3720286 TTTTTTTTGTTTTTTTTATTTATTTTAT
1 TTTTTTTTATTTTTTCTATTTATTTTAT
* *
3720314 TTTTCTTTTATTTTTTCTCTTTCTTTT
1 TTTT-TTTTATTTTTTCTATTTATTTT
3720341 CGTTTTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.18
29 18 0.82
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (28 bp):
TTTTTTTTATTTTTTCTATTTATTTTAT
Found at i:3721061 original size:2 final size:2
Alignment explanation
Indices: 3721056--3721082 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3721046 ATAATTTTTT
3721056 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3721083 GCACGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3727566 original size:41 final size:41
Alignment explanation
Indices: 3727509--3727591 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
3727499 CCCGTCAAAA
3727509 GTCTTTGCTTCATTCTCGTTACACGACAATGAGCAAAGAGG
1 GTCTTTGCTTCATTCTCGTTACACGACAATGAGCAAAGAGG
3727550 GTCTTTGCTTCATTCTCGTTACACGACAATGAGCAAAGAGG
1 GTCTTTGCTTCATTCTCGTTACACGACAATGAGCAAAGAGG
3727591 G
1 G
3727592 CAGCTGTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
GTCTTTGCTTCATTCTCGTTACACGACAATGAGCAAAGAGG
Found at i:3777223 original size:19 final size:19
Alignment explanation
Indices: 3777199--3777244 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3777189 TCTTGTCACT
3777199 ATATATTTTAGAAT-TAAAA
1 ATATATTTTA-AATGTAAAA
3777218 ATATA--TTAAATGTAAAA
1 ATATATTTTAAATGTAAAA
3777235 ATATGATTTT
1 ATAT-ATTTT
3777245 TTAATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 1 0.04
19 5 0.22
20 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (19 bp):
ATATATTTTAAATGTAAAA
Found at i:3777380 original size:17 final size:17
Alignment explanation
Indices: 3777338--3777384 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3777328 AATTCAATTT
3777338 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
3777354 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
3777372 TAATATAAATAAT
1 TAATATAAATAAT
3777385 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:3777548 original size:15 final size:16
Alignment explanation
Indices: 3777528--3777557 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3777518 GGGGAAAATA
3777528 AAAAGTTT-AGGGAAT
1 AAAAGTTTGAGGGAAT
3777543 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
3777558 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:3777847 original size:30 final size:31
Alignment explanation
Indices: 3777806--3777866 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
3777796 GGGTGGGGAG
* *
3777806 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
3777837 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
3777867 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:3793013 original size:45 final size:45
Alignment explanation
Indices: 3792929--3793095 Score: 142
Period size: 45 Copynumber: 3.7 Consensus size: 45
3792919 AGATCATATA
* * ** * *
3792929 AAATATTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGACAGC
* *
3792974 GAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGACAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGACAGC
** * * **
3793019 AAATCTGGTCTCCCT-ACAATTGCAGTGGAGCAGGTTGGAGTTA-C
1 AAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGGTTGAAGACAGC
* * *
3793063 AAGTCTTATCTCCCT-AACATTGTAGTGGAGCAG
1 AAATCTTATCTCCCTGAA-GTTGCAGTGGAGCAG
3793096 ACTAAAACCA
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
43 1 0.01
44 29 0.29
45 70 0.70
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (45 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGACAGC
Found at i:3803341 original size:13 final size:13
Alignment explanation
Indices: 3803323--3803353 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3803313 TTTATTTGTA
3803323 TAAATTTTAATTT
1 TAAATTTTAATTT
3803336 TAAATTTTAATTT
1 TAAATTTTAATTT
3803349 TAAAT
1 TAAAT
3803354 AATTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTTTAATTT
Found at i:3806579 original size:18 final size:19
Alignment explanation
Indices: 3806556--3806599 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
3806546 TTTTTATCAT
3806556 ATATTTTT-TGAA-TTTTAA
1 ATATTTTTAT-AATTTTTAA
3806574 ATATTTTTATAATTTTTAA
1 ATATTTTTATAATTTTTAA
3806593 ATTATTT
1 A-TATTT
3806600 GTTAGCGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATATTTTTATAATTTTTAA
Found at i:3812927 original size:59 final size:57
Alignment explanation
Indices: 3812828--3812951 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 57
3812818 CGTCGTCCTC
* * *
3812828 CTTGTTTTGCTCTATTTTTTAATGTCATCCTCTCGATTTAATAAT-CTCTTTTGGGGT
1 CTTGTTTTGCTCTATTTTTTAATATCATCCTCTCAATTTAAAAATCCT-TTTTGGGGT
* * * *
3812885 CTTGTCTTCTGCTCTATTTTTTGATATCCTTCTCTCAATTTAAAAATCCTTTTTGGGGGC
1 CTTGT-TT-TGCTCTATTTTTTAATATCATCCTCTCAATTTAAAAATCCTTTTT-GGGGT
3812945 CTTGTTT
1 CTTGTTT
3812952 GAGCTTTCGT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
57 5 0.09
58 2 0.04
59 38 0.68
60 11 0.20
ACGTcount: A:0.15, C:0.19, G:0.14, T:0.52
Consensus pattern (57 bp):
CTTGTTTTGCTCTATTTTTTAATATCATCCTCTCAATTTAAAAATCCTTTTTGGGGT
Found at i:3813556 original size:40 final size:39
Alignment explanation
Indices: 3813473--3813558 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
3813463 TAATTTTTAA
** *
3813473 TATTTTTTGTATTTTTAATAATTTTCTCTAACTTATTCG
1 TATTTTTTGTATTTTTAATAATTTTCTAAAACTTATGCG
*
3813512 TATTTCTTTGTATTTTTTAATAA-TTTCTAAAATTTTATGC-
1 TATTT-TTTGTA-TTTTTAATAATTTTCTAAAA-CTTATGCG
3813552 TATTTTT
1 TATTTTT
3813559 ATAATAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 7 0.17
40 18 0.45
41 15 0.38
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (39 bp):
TATTTTTTGTATTTTTAATAATTTTCTAAAACTTATGCG
Found at i:3814926 original size:40 final size:40
Alignment explanation
Indices: 3814860--3814935 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
3814850 ACTGTTCATG
* * *
3814860 CCACGTCAGCAAATCGCGTCCTCGTAGGCGCGATTTGTGT
1 CCACGTAAGCAAATCGCGTCCACGTAGACGCGATTTGTGT
**
3814900 CCACGTAAGCAAATCGCGTTGACGTAGACGCGATTT
1 CCACGTAAGCAAATCGCGTCCACGTAGACGCGATTT
3814936 TCTGACGCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (40 bp):
CCACGTAAGCAAATCGCGTCCACGTAGACGCGATTTGTGT
Found at i:3822643 original size:20 final size:21
Alignment explanation
Indices: 3822615--3822657 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3822605 TTAAATATAA
3822615 ATTAAAAATTCATAAA-AATT
1 ATTAAAAATTCATAAACAATT
* *
3822635 ATTATAAATTTATAAACAATT
1 ATTAAAAATTCATAAACAATT
3822656 AT
1 AT
3822658 AAGACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAAAAATTCATAAACAATT
Found at i:3824721 original size:25 final size:26
Alignment explanation
Indices: 3824683--3824736 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
3824673 TTGATTTGAT
*
3824683 TTCTACTTTCCTTTTTTTAATA-TAA
1 TTCTACTTTCCTTTATTTAATAGTAA
*
3824708 TTCTCACTTT-CTTTATTTGATAGTAA
1 TTCT-ACTTTCCTTTATTTAATAGTAA
3824734 TTC
1 TTC
3824737 ACCTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (26 bp):
TTCTACTTTCCTTTATTTAATAGTAA
Found at i:3824742 original size:25 final size:26
Alignment explanation
Indices: 3824687--3824742 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
3824677 TTTGATTTCT
* *
3824687 ACTTTCCTTTTTTTAATATAATTCTC
1 ACTTTCCTTTATTTAATATAATTCAC
*
3824713 ACTTT-CTTTATTTGATAGTAATTCAC
1 ACTTTCCTTTATTTAATA-TAATTCAC
3824739 -CTTT
1 ACTTT
3824743 TTATAACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.55
Consensus pattern (26 bp):
ACTTTCCTTTATTTAATATAATTCAC
Found at i:3831140 original size:22 final size:23
Alignment explanation
Indices: 3831115--3831169 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3831105 GATTTTTAGG
3831115 GAATCTGTTAAAATTTT-TTTCA
1 GAATCTGTTAAAATTTTATTTCA
*
3831137 GAATCTGTTTAAATTTTATTTCA
1 GAATCTGTTAAAATTTTATTTCA
* *
3831160 AAATCAGTTA
1 GAATCTGTTA
3831170 TATTTCTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
GAATCTGTTAAAATTTTATTTCA
Found at i:3831557 original size:46 final size:46
Alignment explanation
Indices: 3831504--3831598 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
3831494 TGAAACAAAG
3831504 TTTAAATGGCATTCGACGCAAGTCGGAAGTAATTCATATGGAATCA
1 TTTAAATGGCATTCGACGCAAGTCGGAAGTAATTCATATGGAATCA
*
3831550 TTTAAATGGCATTCGACGCAAGTCGGAAGTAATTCTTATGGAATCA
1 TTTAAATGGCATTCGACGCAAGTCGGAAGTAATTCATATGGAATCA
3831596 TTT
1 TTT
3831599 GACAGTTCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (46 bp):
TTTAAATGGCATTCGACGCAAGTCGGAAGTAATTCATATGGAATCA
Found at i:3832784 original size:20 final size:20
Alignment explanation
Indices: 3832759--3832799 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3832749 GTGGTAGTGC
*
3832759 CTAGGTTGTGTGGAGGTCTA
1 CTAGGTCGTGTGGAGGTCTA
*
3832779 CTAGGTCGTGTGGTGGTCTA
1 CTAGGTCGTGTGGAGGTCTA
3832799 C
1 C
3832800 ACGCCCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.39, T:0.34
Consensus pattern (20 bp):
CTAGGTCGTGTGGAGGTCTA
Found at i:3834414 original size:3 final size:3
Alignment explanation
Indices: 3834406--3834444 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3834396 TAAGCTTGTC
3834406 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3834445 ATAGTAAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3836133 original size:188 final size:188
Alignment explanation
Indices: 3835792--3836161 Score: 661
Period size: 188 Copynumber: 2.0 Consensus size: 188
3835782 TCGTGTAAAT
3835792 AATTAACCATAATTCACATTGCTAAAACCATTGTTGCTCGAGTAATCTGTTACCATACCTTTCTT
1 AATTAACCATAATTCACATTGCTAAAACCATTGTTGCTCGAGTAATCTGTTACCATACCTTTCTT
* * *
3835857 TTTTCTTGCTAAGCGGAACACTCTAGGAAATTCTTTTTTTTTTGTGGTTGATTACAACACCAAAT
66 TTTTCTTGATAAGCGAAAAACTCTAGGAAATTCTTTTTTTTTTGTGGTTGATTACAACACCAAAT
3835922 ATCCTCTCAAAACATCGCATCCTTCCATTCCCAACCATCCATCTAAAAGCTTCGTTAG
131 ATCCTCTCAAAACATCGCATCCTTCCATTCCCAACCATCCATCTAAAAGCTTCGTTAG
* * * *
3835980 AATTCACCGTAATTCATATTGCTGAAACCATTGTTGCTCGAGTAATCTGTTACCATACCTTTCTT
1 AATTAACCATAATTCACATTGCTAAAACCATTGTTGCTCGAGTAATCTGTTACCATACCTTTCTT
3836045 TTTTCTTGATAAGCGAAAAACTCTAGGAAATTC-TTTTTTTTTGTGGTTGATTACAACACCAAAT
66 TTTTCTTGATAAGCGAAAAACTCTAGGAAATTCTTTTTTTTTTGTGGTTGATTACAACACCAAAT
3836109 ATCCTCTCAAAACATCGCCATCCTTCCATTCCCAACCATCCATCTAAAAGCTT
131 ATCCTCTCAAAACATCG-CATCCTTCCATTCCCAACCATCCATCTAAAAGCTT
3836162 TGTTCCCCAC
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
187 48 0.28
188 126 0.72
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (188 bp):
AATTAACCATAATTCACATTGCTAAAACCATTGTTGCTCGAGTAATCTGTTACCATACCTTTCTT
TTTTCTTGATAAGCGAAAAACTCTAGGAAATTCTTTTTTTTTTGTGGTTGATTACAACACCAAAT
ATCCTCTCAAAACATCGCATCCTTCCATTCCCAACCATCCATCTAAAAGCTTCGTTAG
Found at i:3837661 original size:21 final size:20
Alignment explanation
Indices: 3837637--3837699 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
3837627 CGTTTAGCTC
3837637 TTTGAGCTTTAGTATAACCCT
1 TTTGAGCTTTAGT-TAACCCT
* * *
3837658 TTTGAGTTTTAGTTCAGCTCT
1 TTTGAGCTTTAGTT-AACCCT
*
3837679 TTTGAGCTTCAGTTTAACCCT
1 TTTGAGCTTTAG-TTAACCCT
3837700 CATGGGTTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (20 bp):
TTTGAGCTTTAGTTAACCCT
Found at i:3837719 original size:42 final size:42
Alignment explanation
Indices: 3837607--3837759 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
3837597 ACAAGTTACC
* *
3837607 GTTTAA-CCTTAATGGGTTTCCGTTTAGCTC-TTTGAGCTTTA
1 GTTTAACCCTT-ATGGGTTTCAGTTTAGCTCTTTTGAGCTTCA
* * * * *
3837648 GTATAACCCTTTTGAGTTTTAGTTCAGCTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCAGTTTAGCTCTTTTGAGCTTCA
* *
3837690 GTTTAACCCTCATGGGTTTCCA-TTTAGCTCTTATGAGCTTTC-
1 GTTTAACCCTTATGGGTTT-CAGTTTAGCTCTTTTGAGC-TTCA
*
3837732 GTTCAACCCTTATGGGTTTCAGTTTAGC
1 GTTTAACCCTTATGGGTTTCAGTTTAGC
3837760 ACTTATGTTC
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 21 0.23
42 66 0.73
43 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (42 bp):
GTTTAACCCTTATGGGTTTCAGTTTAGCTCTTTTGAGCTTCA
Found at i:3837764 original size:21 final size:21
Alignment explanation
Indices: 3837686--3837766 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
3837676 TCTTTTGAGC
*
3837686 TTCAGTTTAACCCTCATGGGT
1 TTCAGTTTAACCCTTATGGGT
* * *
3837707 TTCCA-TTTAGCTCTTATGAGCT
1 TT-CAGTTTAACCCTTATG-GGT
*
3837729 TTC-GTTCAACCCTTATGGGT
1 TTCAGTTTAACCCTTATGGGT
* *
3837749 TTCAGTTTAGCACTTATG
1 TTCAGTTTAACCCTTATG
3837767 TTCTTTCGTG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
20 5 0.11
21 34 0.76
22 6 0.13
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (21 bp):
TTCAGTTTAACCCTTATGGGT
Found at i:3837765 original size:42 final size:42
Alignment explanation
Indices: 3837613--3837781 Score: 157
Period size: 42 Copynumber: 4.0 Consensus size: 42
3837603 TACCGTTTAA
* *
3837613 CCTTAATGGGTTTCCGTTTAGCTCTT-TGAGCTTTAGTAT-AAC
1 CCTT-ATGGGTTTCAGTTTAGCTCTTATGAGCTTTCGT-TCAAC
* * * * * *
3837655 CCTTTTGAGTTTTAGTTCAGCTCTTTTGAGC-TTCAGTTTAAC
1 CCTTATGGGTTTCAGTTTAGCTCTTATGAGCTTTC-GTTCAAC
*
3837697 CCTCATGGGTTTCCA-TTTAGCTCTTATGAGCTTTCGTTCAAC
1 CCTTATGGGTTT-CAGTTTAGCTCTTATGAGCTTTCGTTCAAC
* ** *
3837739 CCTTATGGGTTTCAGTTTAGCACTTATGTTCTTTCGTGCAAC
1 CCTTATGGGTTTCAGTTTAGCTCTTATGAGCTTTCGTTCAAC
3837781 C
1 C
3837782 TTTGGGCTTT
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 21 0.20
42 78 0.76
43 4 0.04
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (42 bp):
CCTTATGGGTTTCAGTTTAGCTCTTATGAGCTTTCGTTCAAC
Found at i:3849955 original size:57 final size:57
Alignment explanation
Indices: 3849861--3849975 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3849851 GTGATAGTCA
* **
3849861 CTAAATTATTTATATCTTGTGCTACAGAACTTTAAATTAAGATCCACTTGATTTTAC
1 CTAAATTATTTATATCTTGCGCTACAGAACTCCAAATTAAGATCCACTTGATTTTAC
3849918 CTAAATTATTTATATCTTGCGCTACAGAACTCCAAATTAAGATCCACTTGATTTTAC
1 CTAAATTATTTATATCTTGCGCTACAGAACTCCAAATTAAGATCCACTTGATTTTAC
3849975 C
1 C
3849976 AAAACTAGAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (57 bp):
CTAAATTATTTATATCTTGCGCTACAGAACTCCAAATTAAGATCCACTTGATTTTAC
Found at i:3850995 original size:44 final size:43
Alignment explanation
Indices: 3850938--3851071 Score: 130
Period size: 42 Copynumber: 3.1 Consensus size: 43
3850928 TATCGTACAA
* *
3850938 ATGCC-ATGTCCCAGACATGGTCTTACATGGAAATCTCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACA-CGAAATCTCATATCG
* * *
3850981 ATGCCAATATCCCAG-CTATGGTATTACACGAAGTCTCATAACG
1 ATGCCAATATCCCAGAC-ATGGTCTTACACGAAATCTCATATCG
* * * * * *
3851024 ATG-CTATATCTCAGATATGGTCTTATACGAAATCTCAAATCA
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
3851066 ATGCCA
1 ATGCCA
3851072 GTGCCATCTC
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 32 0.44
43 22 0.31
44 18 0.25
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACACGAAATCTCATATCG
Found at i:3851214 original size:48 final size:48
Alignment explanation
Indices: 3851022--3851194 Score: 231
Period size: 48 Copynumber: 3.6 Consensus size: 48
3851012 AGTCTCATAA
* * **
3851022 CGATGCTATATCTCAGATATGGTCTTATACGAAATCTCAAATCAATGC
1 CGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATGC
* * * * *
3851070 C-AGTGCCATCTCCCAGATATGGTCTTATATGGGATCTCGAATCGATGT
1 CGA-TGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATGC
* *
3851118 CGATGTCATATCCCAGATATGGTCTTATACGGGATCTTAAATCAATGC
1 CGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATGC
3851166 CGATGCCATATCCCAGATATGGTCTTATA
1 CGATGCCATATCCCAGATATGGTCTTATA
3851195 GATTTTCTCA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
47 1 0.01
48 104 0.98
49 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (48 bp):
CGATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATCAATGC
Found at i:3851403 original size:32 final size:30
Alignment explanation
Indices: 3851362--3851447 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 30
3851352 ATCCAATGCT
3851362 CAAATCAATTCGGCAATATATATATACATAGA
1 CAAATCAATTCGGCAATATATATATACAT--A
*
3851394 CAAATCAATTCGACAATGTATATATATACATA
1 CAAATCAATTCGGCAA--TATATATATACATA
*
3851426 TAAATCAATTCGGCAATATATA
1 CAAATCAATTCGGCAATATATA
3851448 AAACATATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
30 6 0.12
32 30 0.61
34 13 0.27
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (30 bp):
CAAATCAATTCGGCAATATATATATACATA
Found at i:3855121 original size:44 final size:44
Alignment explanation
Indices: 3855058--3855147 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
3855048 AAAGTTGAAT
*
3855058 TGGCTTGGGTGATTGTGATATGTTTAGATGATGAATGCAAGAAA
1 TGGCTTGGATGATTGTGATATGTTTAGATGATGAATGCAAGAAA
*
3855102 TGGCTTGGATGATTGTGATATGTTTAGATGATGAATGCATGAAA
1 TGGCTTGGATGATTGTGATATGTTTAGATGATGAATGCAAGAAA
3855146 TG
1 TG
3855148 TTTAAGGGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
TGGCTTGGATGATTGTGATATGTTTAGATGATGAATGCAAGAAA
Found at i:3855134 original size:22 final size:22
Alignment explanation
Indices: 3855067--3855135 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
3855057 TTGGCTTGGG
3855067 TGATTGTGATATGTTTAGATGA
1 TGATTGTGATATGTTTAGATGA
* * * *
3855089 TGAATGCAAGAAATGGCTT-G--GA
1 TGATTG--TGATAT-GTTTAGATGA
3855111 TGATTGTGATATGTTTAGATGA
1 TGATTGTGATATGTTTAGATGA
3855133 TGA
1 TGA
3855136 ATGCATGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
22 17 0.52
24 5 0.15
25 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.29, T:0.38
Consensus pattern (22 bp):
TGATTGTGATATGTTTAGATGA
Found at i:3855149 original size:24 final size:24
Alignment explanation
Indices: 3855077--3855151 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 24
3855067 TGATTGTGAT
*
3855077 ATGTTTAGATGATGAATGCAAGAA
1 ATGTTTAGATGATGAATGCATGAA
* * *
3855101 ATGGCTT-G--GATGATTG--TGAT
1 AT-GTTTAGATGATGAATGCATGAA
3855121 ATGTTTAGATGATGAATGCATGAA
1 ATGTTTAGATGATGAATGCATGAA
3855145 ATGTTTA
1 ATGTTTA
3855152 AGGGCAAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
22 14 0.37
24 13 0.34
25 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (24 bp):
ATGTTTAGATGATGAATGCATGAA
Found at i:3856196 original size:5 final size:5
Alignment explanation
Indices: 3856186--3856252 Score: 72
Period size: 5 Copynumber: 13.8 Consensus size: 5
3856176 AATTATGTTT
3856186 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -T-TA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
3856233 TTAT- TATATTA TTATA TTAT
1 TTATA T-TA-TA TTATA TTAT
3856253 TATATATATG
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
3 4 0.07
4 5 0.09
5 36 0.67
6 8 0.15
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:3856200 original size:8 final size:8
Alignment explanation
Indices: 3856186--3856257 Score: 94
Period size: 8 Copynumber: 8.8 Consensus size: 8
3856176 AATTATGTTT
3856186 TTATATTA
1 TTATATTA
3856194 -TATTATTA
1 TTA-TATTA
3856202 TTA-ATATA
1 TTATAT-TA
3856210 TTATATTATA
1 TTATA-T-TA
3856220 TTATATTA
1 TTATATTA
3856228 TTATATTA
1 TTATATTA
3856236 TTATATTA
1 TTATATTA
3856244 TTATATTA
1 TTATATTA
3856252 TTATAT
1 TTATAT
3856258 ATATGACAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
7 4 0.07
8 42 0.71
9 4 0.07
10 9 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:3856202 original size:3 final size:3
Alignment explanation
Indices: 3856189--3856255 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
3856179 TATGTTTTTA
*
3856189 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3856231 TAT TAT TA- TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3856256 ATATATGACA
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
2 16 0.29
3 39 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3856218 original size:29 final size:27
Alignment explanation
Indices: 3856186--3856255 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 27
3856176 AATTATGTTT
3856186 TTATATTATATTATTATTAATATATTATA
1 TTATATTATATTATTATT-AT-TATTATA
3856215 TTATATTATATTATTA-TATTATTATA
1 TTATATTATATTATTATTATTATTATA
3856241 -T-TATTATATTATTAT
1 TTATATTATATTATTAT
3856256 ATATATGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
24 13 0.32
25 1 0.03
26 7 0.17
27 2 0.05
28 1 0.03
29 16 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATATTATATTATTATTATTATTATA
Found at i:3856224 original size:34 final size:35
Alignment explanation
Indices: 3856189--3856261 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 35
3856179 TATGTTTTTA
3856189 TATTATATTATTATTAATATATTATATTA-TATTATAT
1 TATTATATTATTA-T-AT-TATTATATTATTATTATAT
3856226 TATTATATTATTATATTATTATATTATTATATATAT
1 TATTATATTATTATATTATTATATTATTAT-TATAT
3856262 GACAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 10 0.29
35 5 0.15
36 6 0.18
37 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (35 bp):
TATTATATTATTATATTATTATATTATTATTATAT
Found at i:3856327 original size:40 final size:41
Alignment explanation
Indices: 3856271--3856350 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
3856261 TGACAAAGAA
3856271 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
*
3856312 AGAAAG-AAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
3856351 AAGGAAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 32 0.84
41 6 0.16
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (41 bp):
AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
Found at i:3857133 original size:29 final size:30
Alignment explanation
Indices: 3857074--3857131 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3857064 TCCGGGCCTT
*
3857074 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
3857104 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
3857132 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:3857361 original size:13 final size:13
Alignment explanation
Indices: 3857343--3857374 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3857333 TTTCCAGCAA
3857343 TTATGAATTTATT
1 TTATGAATTTATT
3857356 TTATGAATTTATT
1 TTATGAATTTATT
*
3857369 TGATGA
1 TTATGA
3857375 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3857582 original size:50 final size:50
Alignment explanation
Indices: 3857469--3857710 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
3857459 ATTTGGGTAA
* * *
3857469 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
3857525 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3857575 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3857625 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
3857675 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
3857711 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:3857658 original size:100 final size:103
Alignment explanation
Indices: 3857469--3857718 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
3857459 ATTTGGGTAA
3857469 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
3857534 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
3857575 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
3857637 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
3857675 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
3857719 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:3879657 original size:12 final size:13
Alignment explanation
Indices: 3879640--3879676 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3879630 GAACCGGACA
3879640 CGAACCGAA-CTC
1 CGAACCGAAGCTC
3879652 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
3879664 CGAACCGTAGCTC
1 CGAACCGAAGCTC
3879677 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:3908910 original size:29 final size:30
Alignment explanation
Indices: 3908877--3908933 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
3908867 CCTTTTTACT
*
3908877 TTTCCCTCAAAACTTTTACTCCT-TCCCAC
1 TTTCCCCCAAAACTTTTACTCCTCTCCCAC
3908906 TTTCCCCCAAAACTTTTACTCCTCTCCC
1 TTTCCCCCAAAACTTTTACTCCTCTCCC
3908934 CTCCCCACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTCCTCTCCCAC
Found at i:3909072 original size:30 final size:31
Alignment explanation
Indices: 3909038--3909097 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3909028 AAACCTTTTA
*
3909038 TTTTCCCCCAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
3909068 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
3909098 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:3909217 original size:17 final size:16
Alignment explanation
Indices: 3909183--3909213 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3909173 CCTATTTACT
*
3909183 TTCCCTCAAACTTTTA
1 TTCCCTAAAACTTTTA
3909199 TTCCCTAAAACTTTT
1 TTCCCTAAAACTTTT
3909214 TATTTTCCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTAAAACTTTTA
Found at i:3909239 original size:20 final size:21
Alignment explanation
Indices: 3909201--3909245 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3909191 AACTTTTATT
*
3909201 CCCTAAAACTTTTTATTTTCC
1 CCCTAAAACTTTTTATTTTCA
3909222 CCCT-AAAC-TTTTACTTTTCA
1 CCCTAAAACTTTTTA-TTTTCA
3909242 CCCT
1 CCCT
3909246 TTACTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (21 bp):
CCCTAAAACTTTTTATTTTCA
Found at i:3909377 original size:17 final size:17
Alignment explanation
Indices: 3909357--3909403 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3909347 CACATTTTAT
3909357 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
3909374 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
3909392 A-TATTTATATTA
1 ATTATTTATATTA
3909404 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:3909541 original size:19 final size:19
Alignment explanation
Indices: 3909497--3909542 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3909487 CTTTTATTAA
3909497 AAAATCATATTTTTACATTT
1 AAAAT-ATATTTTTACATTT
3909517 --AATATATTTTTA-ATTCT
1 AAAATATATTTTTACATT-T
3909534 AAAATATAT
1 AAAATATAT
3909543 AGTGACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 3 0.13
19 7 0.30
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATATTTTTACATTT
Found at i:3910375 original size:17 final size:17
Alignment explanation
Indices: 3910353--3910392 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3910343 ATTAGTGAAA
3910353 ACAAATTGTC-AATAGAT
1 ACAAATTGTCTAAT-GAT
3910370 ACAAATTGTCTAATGAT
1 ACAAATTGTCTAATGAT
3910387 ACAAAT
1 ACAAAT
3910393 CTAGGACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (17 bp):
ACAAATTGTCTAATGAT
Found at i:3912778 original size:13 final size:13
Alignment explanation
Indices: 3912760--3912786 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3912750 ACAACACCCA
3912760 ACTTATAACCACC
1 ACTTATAACCACC
3912773 ACTTATAACCACC
1 ACTTATAACCACC
3912786 A
1 A
3912787 TTAAAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (13 bp):
ACTTATAACCACC
Found at i:3913635 original size:25 final size:26
Alignment explanation
Indices: 3913604--3913655 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
3913594 AACACTTAAA
*
3913604 AATAATATATATCAAT-AT-AACTAAC
1 AATAATATAAAT-AATAATAAACTAAC
3913629 AATAATATAAATAATAATAAACTAAC
1 AATAATATAAATAATAATAAACTAAC
3913655 A
1 A
3913656 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 13 0.54
26 8 0.33
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATATAAATAATAATAAACTAAC
Found at i:3914521 original size:25 final size:24
Alignment explanation
Indices: 3914493--3914544 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
3914483 AATTTAACTC
3914493 TTTTTATTTTT-AAATTTTAATAT
1 TTTTTATTTTTAAAATTTTAATAT
3914516 ATTTTTATTTTTAAAATTTTAATAT
1 -TTTTTATTTTTAAAATTTTAATAT
3914541 TTTT
1 TTTT
3914545 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTATTTTTAAAATTTTAATAT
Found at i:3914527 original size:17 final size:16
Alignment explanation
Indices: 3914497--3914561 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
3914487 TAACTCTTTT
*
3914497 TATTTTTAAATTTTAATA
1 TATTTTT-ATTTTTAA-A
3914515 TATTTTTATTTTTAAA
1 TATTTTTATTTTTAAA
3914531 -ATTTTAATATTTTTAAA
1 TATTTT--TATTTTTAAA
*
3914548 AATTTTATATTTTT
1 TATTTT-TATTTTT
3914562 TTTATATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
15 5 0.12
16 1 0.02
17 25 0.58
18 12 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTATTTTTAAA
Found at i:3914549 original size:18 final size:16
Alignment explanation
Indices: 3914516--3914561 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
3914506 ATTTTAATAT
3914516 ATTTT-TATTTTTAAA
1 ATTTTATATTTTTAAA
3914531 ATTTTAATATTTTTAAAA
1 ATTTT-ATATTTTT-AAA
3914549 ATTTTATATTTTT
1 ATTTTATATTTTT
3914562 TTTATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.18
17 15 0.54
18 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTATATTTTTAAA
Found at i:3929350 original size:10 final size:10
Alignment explanation
Indices: 3929311--3929353 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
3929301 AAAATAGTGA
*
3929311 AAAAAATAACC
1 AAAAAAT-AGC
3929322 AAAAAATAGC
1 AAAAAATAGC
*
3929332 AAGAAAATAGT
1 AA-AAAATAGC
3929343 AAAAAATAGC
1 AAAAAATAGC
3929353 A
1 A
3929354 TTTTCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 12 0.43
11 16 0.57
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAAAATAGC
Found at i:3932356 original size:44 final size:44
Alignment explanation
Indices: 3932293--3932715 Score: 318
Period size: 44 Copynumber: 9.6 Consensus size: 44
3932283 TTTATTACCA
* * * *
3932293 TGAAGTTGCAATAGAGTAGATTCAAGCCATAAATCTTATCTCCT
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
* * * *
3932337 TGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCTT
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
* * * * * *
3932381 TGTAGTTGCAGTGGAACAGATTGAAA-ATAGCAAATCTTATCTCTT
1 TGAAGTTGCAGTAGAATAGATT-AAAGCTA-TAAATCTTATCTCCT
* * * *
3932426 TGAAGTTGTAGTAGATTAGATTAAAGCCATAAATCTTATCTCCC
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
* * * *
3932470 TGAAGTTGCAGTGGAATAGATTAAAACTATAAATCTTATTTCCC
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
* * * * * * *
3932514 TAAAGTTGCAGT-GCAACATATTGAAGATAGTATA-CTTGTCT-CT
1 TGAAGTTGCAGTAG-AATAGATTAAAGCTA-TAAATCTTATCTCCT
* * *
3932557 CTGAAGTTGCAGTAG-ATCAGATTGAAGCTACAAATCTTATCTCCC
1 -TGAAGTTGCAGTAGAAT-AGATTAAAGCTATAAATCTTATCTCCT
** * ** ** *
3932602 TGAAGTTGCAGTAGAGCAGATTAAAGATAGCAGCCATTATCTCCC
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATC-TTATCTCCT
* * * *
3932647 TGAAGTTGCAGTGGAACAGATTAATGCTACAAATCTTATCT-CT
1 TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
* *
3932690 CTGAAGTTGTAGTAGAGTAGATTAAA
1 -TGAAGTTGCAGTAGAATAGATTAAA
3932716 ATTACAATTC
Statistics
Matches: 300, Mismatches: 66, Indels: 26
0.77 0.17 0.07
Matches are distributed among these distances:
43 6 0.02
44 217 0.72
45 77 0.26
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (44 bp):
TGAAGTTGCAGTAGAATAGATTAAAGCTATAAATCTTATCTCCT
Found at i:3932446 original size:89 final size:87
Alignment explanation
Indices: 3932323--3932715 Score: 362
Period size: 89 Copynumber: 4.4 Consensus size: 87
3932313 TTCAAGCCAT
* ** *
3932323 AAATCTTATCTCCTTGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCTTTGTAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTT
3932388 GCAGTGGAACAGATTGAAAATAGC
66 GCAGTGGAACAGATT-AAAATA-C
** * * *
3932412 AAATCTTATCTCTTTGAAGTTGTAGTAGATTAGATTAAAGCCATAAATCTTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTT
* *
3932477 GCAGTGGAATAGATTAAAACTAT
66 GCAGTGGAACAGATTAAAA-TAC
* * ** * * * * * *
3932500 AAATCTTATTTCCCTAAAGTTGCAGT-GCAACATATTGAAG--ATAGTATACTTGTCTCTCTGAA
1 AAATCTTATCTCCCTGAAGTTGCAGTAG-AGTAGATTAAAGCCACA-AAT-CTTATCTCCCTGAA
* * **
3932562 GTTGCAGTAGATCAGATTGAAGCTAC
63 GTTGCAGTGGAACAGATT-AAAATAC
* ** **
3932588 AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGATAGC-AGCCATTATCTCCCTGAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCCA-CAAATC-TTATCTCCCTGAAG
**
3932652 TTGCAGTGGAACAGATTAATGCTAC
64 TTGCAGTGGAACAGATTAA-AATAC
* *
3932677 AAATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAA
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAA
3932716 ATTACAATTC
Statistics
Matches: 250, Mismatches: 43, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
86 3 0.01
87 3 0.01
88 98 0.39
89 145 0.58
90 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (87 bp):
AAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTT
GCAGTGGAACAGATTAAAATAC
Found at i:3932537 original size:133 final size:133
Alignment explanation
Indices: 3932293--3932715 Score: 489
Period size: 133 Copynumber: 3.2 Consensus size: 133
3932283 TTTATTACCA
* * *
3932293 TGAAGTTGCAATAGAGTAGATTCAAGCCATAAATCTTATCTCCTTGAAGTTGCAGTAGAGTAGAT
1 TGAAGTTGCAGTAGAGTAGATTAAAGCCATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGAT
* * ** * *
3932358 TAAAGCCACAAATCTTATCTCTTTGTAGTTGCAGTGGAACAGATTGAAAATAGCAAATCTTATCT
66 TAAAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCT
*
3932423 CTT
131 CTC
* * * *
3932426 TGAAGTTGTAGTAGATTAGATTAAAGCCATAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAT
1 TGAAGTTGCAGTAGAGTAGATTAAAGCCATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGAT
* * * * * * * *
3932491 TAAAACTATAAATCTTATTTCCCTAAAGTTGCAGTGCAACATATTGAAGATAGTATA-CTTGTCT
66 TAAAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCT
3932555 CTC
131 CTC
* * * *
3932558 TGAAGTTGCAGTAGA-TCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
1 TGAAGTTGCAGTAGAGT-AGATTAAAGCCATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA
** *
3932622 TTAAAGA-TAGC-AGCCATTATCTCCCTGAAGTTGCAGTGGAACAGATT-AATGCTA-CAAATCT
65 TTAAA-ACTA-CAAATC-TTATCTCCCTGAAGTTGCAGTGGAACAGATTGAA-GATAGCAAATCT
3932683 TATCTCTC
126 TATCTCTC
*
3932691 TGAAGTTGTAGTAGAGTAGATTAAA
1 TGAAGTTGCAGTAGAGTAGATTAAA
3932716 ATTACAATTC
Statistics
Matches: 241, Mismatches: 42, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
131 1 0.00
132 76 0.32
133 163 0.68
134 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (133 bp):
TGAAGTTGCAGTAGAGTAGATTAAAGCCATAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGAT
TAAAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCT
CTC
Found at i:3932747 original size:221 final size:221
Alignment explanation
Indices: 3932337--3932747 Score: 504
Period size: 221 Copynumber: 1.9 Consensus size: 221
3932327 CTTATCTCCT
** * *
3932337 TGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCTTTGTAGTTGCAGTGGAACAGAT
1 TGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAGAT
* ** * ** *
3932402 TGAAAATAGCAAATCTTATCTCTTTGAAGTTGTAGTAGATTAGATTAAAGCCATAAATCTTATCT
66 TGAAAATAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCCACAAATCTTATCT
* * * ** *
3932467 CCCTGAAGTTGCAGTGGAATAGATTAAAACTATAAATCTTATTTCCCTAAAGTTGCAGTGCAACA
131 CCCTGAAGTTGCAGTAGAATAGATTAAAACTACAAATCCTATACCCCTAAAGCTGCAGTGCAACA
3932532 TATTGAAGATAGTATACTTGTCTCTC
196 TATTGAAGATAGTATACTTGTCTCTC
* * *
3932558 TGAAGTTGCAGTAGA-TCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
1 TGAAGTTGCAGTAGAGT-AGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAGA
* * * *
3932622 TT-AAAGATAGC-AGCCATTATCTCCCTGAAGTTGCAGTGGAACAGATTAATGCTACAAATCTTA
65 TTGAAA-ATAGCAAACC-TTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCCACAAATCTTA
* * * * * *
3932685 TCTCTCTGAAGTTGTAGTAGAGTAGATTAAAATTACAATTCCTATACCCCTGAAGCTGCAGTG
128 TCTCCCTGAAGTTGCAGTAGAATAGATTAAAACTACAAATCCTATACCCCTAAAGCTGCAGTG
3932748 GGTTAGAATA
Statistics
Matches: 157, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
220 6 0.04
221 151 0.96
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (221 bp):
TGAAGTTGCAGTAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAGAT
TGAAAATAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAGCCACAAATCTTATCT
CCCTGAAGTTGCAGTAGAATAGATTAAAACTACAAATCCTATACCCCTAAAGCTGCAGTGCAACA
TATTGAAGATAGTATACTTGTCTCTC
Found at i:3938945 original size:18 final size:18
Alignment explanation
Indices: 3938920--3939012 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
3938910 ACCGTTTACG
3938920 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
* *
3938938 GCACTATTTACGTATACA
1 GTACTATTCACGTATACA
*
3938956 GTACTATTCACGTATACG
1 GTACTATTCACGTATACA
*
3938974 GTACTATTCACGTATACG
1 GTACTATTCACGTATACA
*
3938992 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
3939010 GTA
1 GTA
3939013 GTTGGGATTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:3956942 original size:69 final size:69
Alignment explanation
Indices: 3956860--3957004 Score: 263
Period size: 69 Copynumber: 2.1 Consensus size: 69
3956850 AACTCGAATA
*
3956860 TGAATTACACAATTCATATTCGAGTTGAACCAAAAAACTTAATTTTTTATTTGAGTTTATCTTAA
1 TGAATTACACAATTCATATTCGAGTTAAACCAAAAAACTTAATTTTTTATTTGAGTTTATCTTAA
3956925 TAAT
66 TAAT
*
3956929 TGAATTACACAATTCATATTCGAGTTAAACCAAAAAATTTAATTTTTTATTTGAGTTTATCTTAA
1 TGAATTACACAATTCATATTCGAGTTAAACCAAAAAACTTAATTTTTTATTTGAGTTTATCTTAA
3956994 TAAT
66 TAAT
*
3956998 TAAATTA
1 TGAATTA
3957005 ACTTAAATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (69 bp):
TGAATTACACAATTCATATTCGAGTTAAACCAAAAAACTTAATTTTTTATTTGAGTTTATCTTAA
TAAT
Found at i:3963489 original size:6 final size:6
Alignment explanation
Indices: 3963468--3963526 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
3963458 AAAATATATA
* * *
3963468 AAAAAG AGAGAG AAAAAG AAAATAG --AAAG AAAAAG AAGAAA- AGAAAG
1 AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AA-AAAG AAAAAG
3963515 AAAAAG AAAAAG
1 AAAAAG AAAAAG
3963527 GAGAGGCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
4 2 0.05
5 5 0.12
6 30 0.71
7 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:3963501 original size:18 final size:17
Alignment explanation
Indices: 3963467--3963525 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 17
3963457 AAAAATATAT
3963467 AAAAAAGAGAGAGAAAAAG
1 AAAAAAGA-A-AGAAAAAG
*
3963486 AAAATAGAAAGAAAAAG
1 AAAAAAGAAAGAAAAAG
3963503 AAGAAAAGAAAGAAAAAG
1 AA-AAAAGAAAGAAAAAG
3963521 AAAAA
1 AAAAA
3963526 GGAGAGGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.35
18 17 0.46
19 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAG
Found at i:3963519 original size:10 final size:10
Alignment explanation
Indices: 3963482--3963523 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
3963472 AGAGAGAGAA
3963482 AAAGAAAATAG
1 AAAGAAAA-AG
3963493 AAAGAAAAAG
1 AAAGAAAAAG
3963503 -AAG-AAAAG
1 AAAGAAAAAG
3963511 AAAGAAAAAG
1 AAAGAAAAAG
3963521 AAA
1 AAA
3963524 AAGGAGAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.17
9 6 0.21
10 10 0.34
11 8 0.28
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:3963588 original size:22 final size:22
Alignment explanation
Indices: 3963560--3963603 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3963550 AAAGGGCACC
3963560 TTGAGACCAAAGAGGATTTAAG
1 TTGAGACCAAAGAGGATTTAAG
*
3963582 TTGAGACCAAAGGGGATTTAAG
1 TTGAGACCAAAGAGGATTTAAG
3963604 ATGAAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (22 bp):
TTGAGACCAAAGAGGATTTAAG
Found at i:3964765 original size:25 final size:26
Alignment explanation
Indices: 3964734--3964785 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
3964724 AACACTTAAA
*
3964734 AATAATATATATCAAT-AT-AACTAAC
1 AATAATATAAAT-AATAATAAACTAAC
3964759 AATAATATAAATAATAATAAACTAAC
1 AATAATATAAATAATAATAAACTAAC
3964785 A
1 A
3964786 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 13 0.54
26 8 0.33
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATATAAATAATAATAAACTAAC
Found at i:3965650 original size:25 final size:26
Alignment explanation
Indices: 3965622--3965670 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
3965612 TAATTTAACT
3965622 TTTTTTATTTTT-AAATTTTAATACA
1 TTTTTTATTTTTAAAATTTTAATACA
3965647 TTTTTTATTTTTAAAATTTTAATA
1 TTTTTTATTTTTAAAATTTTAATA
3965671 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTTTATTTTTAAAATTTTAATACA
Found at i:3965658 original size:26 final size:25
Alignment explanation
Indices: 3965622--3965670 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3965612 TAATTTAACT
*
3965622 TTTTTTATTTTTAAATTTTAATACA
1 TTTTTTATTTTAAAATTTTAATACA
3965647 TTTTTTATTTTTAAAATTTTAATA
1 TTTTTTA-TTTTAAAATTTTAATA
3965671 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTTATTTTAAAATTTTAATACA
Found at i:3965672 original size:17 final size:17
Alignment explanation
Indices: 3965646--3965692 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
3965636 ATTTTAATAC
*
3965646 ATTTTTTATTTTT-AAA
1 ATTTTATATTTTTAAAA
3965662 ATTTTAATATTTTTAAAA
1 ATTTT-ATATTTTTAAAA
3965680 ATTTTATATTTTT
1 ATTTTATATTTTT
3965693 TATATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.18
17 15 0.54
18 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTATATTTTTAAAA
Found at i:3965675 original size:25 final size:25
Alignment explanation
Indices: 3965619--3965675 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3965609 CTTTAATTTA
3965619 ACTTTTTTTATTTTTAAATTTTAAT
1 ACTTTTTTTATTTTTAAATTTTAAT
*
3965644 ACATTTTTTATTTTTAAAATTTTAAT
1 ACTTTTTTTATTTTT-AAATTTTAAT
3965670 A-TTTTT
1 ACTTTTT
3965676 AAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
ACTTTTTTTATTTTTAAATTTTAAT
Found at i:3965701 original size:18 final size:17
Alignment explanation
Indices: 3965654--3965702 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3965644 ACATTTTTTA
3965654 TTTTTA-AAATTTTAAT
1 TTTTTATAAATTTTAAT
*
3965670 ATTTTTAAAAATTTTATAT
1 -TTTTTATAAATTTTA-AT
*
3965689 TTTTTATATATTTT
1 TTTTTATAAATTTT
3965703 TTAAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 20 0.71
19 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATAAATTTTAAT
Found at i:3966331 original size:123 final size:123
Alignment explanation
Indices: 3966175--3966419 Score: 359
Period size: 123 Copynumber: 2.0 Consensus size: 123
3966165 TATTTGAATT
* * * *
3966175 TTAGTCTTCATAATCTTATTTTTAGAAATTTAATCAACTTCTTTTCGGATTTAAAAATTCAGGAT
1 TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
* * *
3966240 CTATTATTACCACTGTTAATATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
66 CCATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
* * *
3966298 TTAGT-TTCCATACTCTTA-TTTTAAATAATTTAATTATCTACTTTTCAGATTTAAAAATTCAGG
1 TTAGTCTT-CATAATCTTATTTTTAAA-AATTTAATCAACTACTTTTCAGATTTAAAAATTCAGG
*
3966361 ACCCATTATTATCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAA
64 ACCCATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAA
3966420 TTTAAAATAT
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 8 0.07
123 101 0.93
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (123 bp):
TTAGTCTTCATAATCTTATTTTTAAAAATTTAATCAACTACTTTTCAGATTTAAAAATTCAGGAC
CCATTATTACCACCGTTAAAATTCTTCTATTAAATTCATTGGTGTGACGTTTTGGAAC
Found at i:3971854 original size:35 final size:35
Alignment explanation
Indices: 3971813--3971882 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
3971803 TTTAATGAAT
3971813 TTAATATTAAATTAAATTTAATATTTACCTAGATA
1 TTAATATTAAATTAAATTTAATATTTACCTAGATA
* * * *
3971848 TTAATATTATATTTAATTTAGTATTTATCTAGATA
1 TTAATATTAAATTAAATTTAATATTTACCTAGATA
3971883 ATATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (35 bp):
TTAATATTAAATTAAATTTAATATTTACCTAGATA
Found at i:3972468 original size:38 final size:38
Alignment explanation
Indices: 3972409--3972523 Score: 135
Period size: 38 Copynumber: 3.0 Consensus size: 38
3972399 ACCTCGAAGA
* * * *
3972409 TTTGAAATGTTGA-ACAGATCTTCCCTCTATCTTGATGC
1 TTTGAAGTGTTGAGAGA-ATCTTCCCACCATCTTGATGC
* *
3972447 TTTGAAGTGTT-AGGAGAATCTTGCCACCATCTTGAAGC
1 TTTGAAGTGTTGA-GAGAATCTTCCCACCATCTTGATGC
*
3972485 TTTGAAGTGTTGAGCGAATCTTCCCACCATCTTGATGC
1 TTTGAAGTGTTGAGAGAATCTTCCCACCATCTTGATGC
3972523 T
1 T
3972524 ACTAAGGGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 61 0.94
39 3 0.05
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (38 bp):
TTTGAAGTGTTGAGAGAATCTTCCCACCATCTTGATGC
Found at i:3972535 original size:38 final size:38
Alignment explanation
Indices: 3972462--3972574 Score: 106
Period size: 38 Copynumber: 3.0 Consensus size: 38
3972452 AGTGTTAGGA
* * * *
3972462 GAATCTTGCCACCATCTTGAAGCT-TTGAAGTGTTGAGC
1 GAATCTTCCCACCATCTTGATGCTACT-AAGAGTTGAGC
*
3972500 GAATCTTCCCACCATCTTGATGCTACTAAGGGTTGA-C
1 GAATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
* * * *
3972537 TAGA-CTTCCCACCTTATTGATGCTACAAAGAGTTGAGC
1 GA-ATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
3972575 AAATTTCTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
37 30 0.48
38 32 0.51
39 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (38 bp):
GAATCTTCCCACCATCTTGATGCTACTAAGAGTTGAGC
Found at i:3978131 original size:33 final size:33
Alignment explanation
Indices: 3978094--3978161 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3978084 CATGGAAAGT
3978094 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
1 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
3978127 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
1 CTCCATATGAGATGTTGTACAAATCTGTGCTTG
3978160 CT
1 CT
3978162 TACATGTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (33 bp):
CTCCATATGAGATGTTGTACAAATCTGTGCTTG
Found at i:3980354 original size:20 final size:18
Alignment explanation
Indices: 3980326--3980374 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3980316 GATTTTAAAA
*
3980326 TAGTAGTTAACAGTTATAGT
1 TAGTTGTTAACAG-T-TAGT
*
3980346 TAGTTGTTAGCAGTTAGT
1 TAGTTGTTAACAGTTAGT
*
3980364 TAGTTGATAAC
1 TAGTTGTTAAC
3980375 TGGTACTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 13 0.52
19 1 0.04
20 11 0.44
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (18 bp):
TAGTTGTTAACAGTTAGT
Found at i:3982069 original size:35 final size:36
Alignment explanation
Indices: 3981990--3982070 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
3981980 ATATATGTGG
*
3981990 ATATATATG--TATGTGAATTATAAAATATACGAAAA
1 ATATATATGTATATATGAATTATAAAATATAC-AAAA
* *
3982025 ATATGTATGTATATATGAATTATGAAATATA-AAAA
1 ATATATATGTATATATGAATTATAAAATATACAAAA
*
3982060 CTATATATGTA
1 ATATATATGTA
3982071 AAAGAGGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 21 0.54
37 18 0.46
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37
Consensus pattern (36 bp):
ATATATATGTATATATGAATTATAAAATATACAAAA
Found at i:3982314 original size:5 final size:5
Alignment explanation
Indices: 3982306--3982354 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
3982296 AAAAATAAAA
* *
3982306 ATAAT ATAAT ATAAT ATAAT ATAAGCA ATTAT ATAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT -ATAAT ATAAT
3982354 A
1 A
3982355 AGATACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 29 0.78
6 5 0.14
7 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:3982411 original size:3 final size:3
Alignment explanation
Indices: 3982405--3982438 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3982395 AAATATGATG
*
3982405 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3982439 CAATCACAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3982419 original size:9 final size:9
Alignment explanation
Indices: 3982405--3982442 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3982395 AAATATGATG
3982405 ATAATAACA
1 ATAATAACA
*
3982414 ATAATAATA
1 ATAATAACA
*
3982423 ATAATAATA
1 ATAATAACA
3982432 ATAATAACA
1 ATAATAACA
3982441 AT
1 AT
3982443 CACAGGACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAATAACA
Found at i:3983005 original size:17 final size:18
Alignment explanation
Indices: 3982983--3983022 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
3982973 TTGAAATAAA
3982983 AATAAAATAAA-ATAAT-G
1 AATAAAATAAACA-AATCG
3983000 AAT-AAATAAACAAATCG
1 AATAAAATAAACAAATCG
3983017 AATAAA
1 AATAAA
3983023 GGACCTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.50
17 8 0.40
18 2 0.10
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (18 bp):
AATAAAATAAACAAATCG
Found at i:3984485 original size:42 final size:41
Alignment explanation
Indices: 3984414--3984498 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 41
3984404 ATAAAATTTT
* *
3984414 AATCAATATTTTCATTAGAAATAACAATTCAACTCTTTTTGA
1 AATCAATATTTTCATCAGAAACAACAATTCAACT-TTTTTGA
* *
3984456 AATCAATATTTTCATCAGAAGCAATAATTCAACTTTTTTGA
1 AATCAATATTTTCATCAGAAACAACAATTCAACTTTTTTGA
3984497 AA
1 AA
3984499 GCTTGAGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 9 0.23
42 30 0.77
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (41 bp):
AATCAATATTTTCATCAGAAACAACAATTCAACTTTTTTGA
Found at i:3987306 original size:28 final size:28
Alignment explanation
Indices: 3987271--3987326 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3987261 GGGGAATAAT
3987271 TTGAAATTATTCAAATTTCCTTAAATTA
1 TTGAAATTATTCAAATTTCCTTAAATTA
*
3987299 TTGAAATTATTTAAATTTCCTTAAATTA
1 TTGAAATTATTCAAATTTCCTTAAATTA
3987327 ACTGAGTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (28 bp):
TTGAAATTATTCAAATTTCCTTAAATTA
Found at i:3988447 original size:21 final size:21
Alignment explanation
Indices: 3988420--3988463 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3988410 AATTTTTATT
* *
3988420 GTAAAAAAGAAAATTACCCATA
1 GTAAAAAA-AAAAATACCAATA
3988442 GTAAAAAAAAAAATACCAATA
1 GTAAAAAAAAAAATACCAATA
3988463 G
1 G
3988464 CAGTCCCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (21 bp):
GTAAAAAAAAAAATACCAATA
Found at i:3996755 original size:6 final size:6
Alignment explanation
Indices: 3996746--3996780 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3996736 TGTTGTTTCT
* *
3996746 TTGTCG TTGTCG TTGTCG TTGTCT TTGTCT TTGTC
1 TTGTCG TTGTCG TTGTCG TTGTCG TTGTCG TTGTC
3996781 TGTCTTTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.26, T:0.57
Consensus pattern (6 bp):
TTGTCG
Found at i:3996773 original size:18 final size:18
Alignment explanation
Indices: 3996734--3996781 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3996724 ACAGCGATGT
*
3996734 GTTGTTGTT-TCTTTGTC
1 GTTGTCGTTGTCTTTGTC
*
3996751 GTTGTCGTTGTCGTTGTC
1 GTTGTCGTTGTCTTTGTC
* *
3996769 TTTGTCTTTGTCT
1 GTTGTCGTTGTCT
3996782 GTCTTTCACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.00, C:0.15, G:0.25, T:0.60
Consensus pattern (18 bp):
GTTGTCGTTGTCTTTGTC
Found at i:3996781 original size:6 final size:6
Alignment explanation
Indices: 3996743--3996781 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3996733 TGTTGTTGTT
* * *
3996743 TCTTTG TCGTTG TCGTTG TCGTTG TCTTTG TCTTTG TCT
1 TCTTTG TCTTTG TCTTTG TCTTTG TCTTTG TCTTTG TCT
3996782 GTCTTTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.23, T:0.59
Consensus pattern (6 bp):
TCTTTG
Found at i:3996781 original size:12 final size:12
Alignment explanation
Indices: 3996743--3996781 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3996733 TGTTGTTGTT
3996743 TCTTTGTCGTTG
1 TCTTTGTCGTTG
*
3996755 TCGTTGTCGTTG
1 TCTTTGTCGTTG
*
3996767 TCTTTGTCTTTG
1 TCTTTGTCGTTG
3996779 TCT
1 TCT
3996782 GTCTTTCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.23, T:0.59
Consensus pattern (12 bp):
TCTTTGTCGTTG
Found at i:3997048 original size:30 final size:31
Alignment explanation
Indices: 3997014--3997084 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
3997004 TAAATTTTGT
* * *
3997014 TTAAATTTTAATTTTATGT-AATTTTATATA
1 TTAAATATTAATTTAATGTAAATTTTATAAA
* *
3997044 TTAAATATTAGTTTAATTTAAATTTTATAAA
1 TTAAATATTAATTTAATGTAAATTTTATAAA
3997075 TT--ATATTAAT
1 TTAAATATTAAT
3997085 AACCTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 7 0.21
30 15 0.44
31 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TTAAATATTAATTTAATGTAAATTTTATAAA
Found at i:3997899 original size:15 final size:15
Alignment explanation
Indices: 3997879--3997909 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3997869 ATATGACTCG
3997879 AATAATTTAGATGAA
1 AATAATTTAGATGAA
3997894 AATAATTTAGATGAA
1 AATAATTTAGATGAA
3997909 A
1 A
3997910 TCAAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (15 bp):
AATAATTTAGATGAA
Found at i:3998454 original size:31 final size:31
Alignment explanation
Indices: 3998412--3998499 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
3998402 TTTTTTAATG
3998412 TGTATAATTAAATCAAAATTAAAATTTTAT-
1 TGTATAATTAAATCAAAATTAAAATTTTATA
* *
3998442 T-TATAAATTTAAATCATAATCAAAATTTTATA
1 TGTAT-AA-TTAAATCAAAATTAAAATTTTATA
*
3998474 TGTATAATTATATC-AAATTAAAATTT
1 TGTATAATTAAATCAAAATTAAAATTT
3998500 ATGTATCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 3 0.06
30 13 0.27
31 27 0.55
32 3 0.06
33 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
TGTATAATTAAATCAAAATTAAAATTTTATA
Found at i:3998889 original size:9 final size:11
Alignment explanation
Indices: 3998848--3998886 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3998838 TTCACATATT
3998848 ATTTCT-TCAA
1 ATTTCTCTCAA
*
3998858 TTTTCTCTCAA
1 ATTTCTCTCAA
3998869 ATTTCTCTCAA
1 ATTTCTCTCAA
3998880 ATTTCTC
1 ATTTCTC
3998887 AAAGCTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTCTCTCAA
Found at i:4000061 original size:7 final size:7
Alignment explanation
Indices: 4000045--4000080 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
4000035 AAATAGTCGT
4000045 TTTA-TA
1 TTTAGTA
4000051 TTTAGTA
1 TTTAGTA
4000058 TTTAGTA
1 TTTAGTA
4000065 TTTAGTA
1 TTTAGTA
4000072 TTTAGTA
1 TTTAGTA
4000079 TT
1 TT
4000081 ATGTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTTAGTA
Found at i:4000629 original size:18 final size:18
Alignment explanation
Indices: 4000606--4000648 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4000596 TGCCAGGTGC
*
4000606 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
4000624 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
4000642 GTTTCCT
1 GTATCCT
4000649 TTTTCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:4001994 original size:23 final size:23
Alignment explanation
Indices: 4001935--4002008 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
4001925 TTTGGCCCCT
*
4001935 TAAAATTATAAAGATATAGACTA
1 TAAAAATATAAAGATATAGACTA
4001958 TAAAAA-AT-----TATAGACTA
1 TAAAAATATAAAGATATAGACTA
4001975 TAAAAATATAAAGATATAGACTA
1 TAAAAATATAAAGATATAGACTA
4001998 TAAAAAT-TAAA
1 TAAAAATATAAA
4002009 ATTTCATTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 15 0.34
18 2 0.05
22 6 0.14
23 21 0.48
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (23 bp):
TAAAAATATAAAGATATAGACTA
Found at i:4002001 original size:15 final size:15
Alignment explanation
Indices: 4001941--4001984 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 15
4001931 CCCTTAAAAT
*
4001941 TATAAAGATATAGAC
1 TATAAAAATATAGAC
4001956 TATAAAAAATTATAGAC
1 TAT-AAAAA-TATAGAC
4001973 TATAAAAATATA
1 TATAAAAATATA
4001985 AAGATATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 7 0.27
16 9 0.35
17 10 0.38
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (15 bp):
TATAAAAATATAGAC
Found at i:4002348 original size:15 final size:15
Alignment explanation
Indices: 4002328--4002365 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4002318 TACTGGGGAC
* *
4002328 AATACTAGGGTGGAT
1 AATACTAGGGTGAAG
4002343 AATACTAGGGTGAAG
1 AATACTAGGGTGAAG
4002358 AATACTAG
1 AATACTAG
4002366 TAATATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (15 bp):
AATACTAGGGTGAAG
Found at i:4003072 original size:97 final size:97
Alignment explanation
Indices: 4002906--4003100 Score: 273
Period size: 97 Copynumber: 2.0 Consensus size: 97
4002896 TATGCGGGTG
* ** ** * *
4002906 ACAAGTAATGCTCGTTCCATCAATATAAATTACTTGTTCAAAAGTAGTGGTTCATGTGTTCTCTA
1 ACAAGTAATGCTCGTTCCATCAATATAAATTACCTACTCAAAAGTAGCAGCTCACGTGTTCTCTA
*
4002971 GGTATTAGTTGAATAGTACTATTAATGGAGGT
66 GGTATTAGTTGAATAGTACTATTAACGGAGGT
* *
4003003 ACAAGTAATGCTCGTTCCATCAATATAAATTGCCTACTCAAAAGTAGCAGCTCACGTGTTCTTTA
1 ACAAGTAATGCTCGTTCCATCAATATAAATTACCTACTCAAAAGTAGCAGCTCACGTGTTCTCTA
* * *
4003068 GGTATTGGTTGAATAGTTCTATTAGCGGAGGT
66 GGTATTAGTTGAATAGTACTATTAACGGAGGT
4003100 A
1 A
4003101 TGTTGATGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (97 bp):
ACAAGTAATGCTCGTTCCATCAATATAAATTACCTACTCAAAAGTAGCAGCTCACGTGTTCTCTA
GGTATTAGTTGAATAGTACTATTAACGGAGGT
Found at i:4007059 original size:14 final size:14
Alignment explanation
Indices: 4007040--4007075 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
4007030 TAAGTGACTA
4007040 AAACATAATATTTC
1 AAACATAATATTTC
4007054 AAACATAATATTTC
1 AAACATAATATTTC
4007068 AAACATAA
1 AAACATAA
4007076 GTAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (14 bp):
AAACATAATATTTC
Found at i:4007864 original size:6 final size:6
Alignment explanation
Indices: 4007853--4007881 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4007843 ACATCTTACC
4007853 ACACAG ACACAG ACACAG ACACAG ACACA
1 ACACAG ACACAG ACACAG ACACAG ACACA
4007882 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.34, G:0.14, T:0.00
Consensus pattern (6 bp):
ACACAG
Found at i:4008927 original size:30 final size:30
Alignment explanation
Indices: 4008893--4008955 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4008883 ACTTAACAAG
4008893 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
4008923 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
4008953 CAA
1 CAA
4008956 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Done.