Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1356
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: 78840
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:1971 original size:20 final size:22
Alignment explanation
Indices: 1926--1971 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1916 AAAATTCAAA
1926 AACTAAAATAAAGTCTTATCTC
1 AACTAAAATAAAGTCTTATCTC
*
1948 --CTAAAAT-AAGT-TTTTCTC
1 AACTAAAATAAAGTCTTATCTC
1966 AACTAA
1 AACTAA
1972 GCCAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.35
Consensus pattern (22 bp):
AACTAAAATAAAGTCTTATCTC
Found at i:5007 original size:29 final size:29
Alignment explanation
Indices: 4893--5041 Score: 126
Period size: 29 Copynumber: 5.2 Consensus size: 29
4883 ATGGGCCTGA
* * **
4893 AAAGGGTGCCACTTACTTGTGGGCTTAGG
1 AAAGGGTGCCACTAACTTGTGGACTTTTG
* * * *
4922 AGAGGATGCCATTAACTTATGGAAC-TTTG
1 AAAGGGTGCCACTAACTTGTGG-ACTTTTG
** * *
4951 AAAGGGCACCACTAACTTATGGACTTTTA
1 AAAGGGTGCCACTAACTTGTGGACTTTTG
4980 AAAGGGTGCCACTAACTTGTGGACTTTTGG
1 AAAGGGTGCCACTAACTTGTGGACTTTT-G
*
5010 AAA-GGTGCCACTGACTTGT-GAGC-TTTG
1 AAAGGGTGCCACTAACTTGTGGA-CTTTTG
5037 AAAGG
1 AAAGG
5042 ATTTAACTTG
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
27 4 0.04
28 8 0.08
29 80 0.83
30 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
AAAGGGTGCCACTAACTTGTGGACTTTTG
Found at i:5181 original size:27 final size:29
Alignment explanation
Indices: 5151--5205 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
5141 TAACTCATAG
5151 GCTTT-AAAAG-GTGCCACTGACTTGTAC
1 GCTTTGAAAAGAGTGCCACTGACTTGTAC
*
5178 GCTTTGAAAAGAGTGCCATTGACTTGTA
1 GCTTTGAAAAGAGTGCCACTGACTTGTA
5206 TGGACCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 5 0.20
29 15 0.60
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (29 bp):
GCTTTGAAAAGAGTGCCACTGACTTGTAC
Found at i:5338 original size:31 final size:31
Alignment explanation
Indices: 5231--5349 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 31
5221 TTTTAAAGGG
* *
5231 CTTTGAAAAGGTTGCCACCAACTCATG-CAA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTCGA
* * *
5261 CCTTTG-AAAGGTTGTCACC-ACTTGTGTTGA
1 -CTTTGAAAAGGTTGCCACCAACTCGTGTCGA
** * * *
5291 CTTTGATTAGGGTGCCACCAACTTGTGTGGA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTCGA
* *
5322 CTTTGAAAATGTTGCCATCAACTCGTGT
1 CTTTGAAAAGGTTGCCACCAACTCGTGT
5350 AGAGTGCTAC
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
29 10 0.14
30 22 0.32
31 37 0.54
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (31 bp):
CTTTGAAAAGGTTGCCACCAACTCGTGTCGA
Found at i:5405 original size:34 final size:34
Alignment explanation
Indices: 5353--5420 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
5343 CTCGTGTAGA
* *
5353 GTGCTACTAACTTGTGTGGACTTTAAAAAAGATT
1 GTGCCACTAACTTATGTGGACTTTAAAAAAGATT
*
5387 GTGCCACTAACTTATGTGGACTTTAAAAATGATT
1 GTGCCACTAACTTATGTGGACTTTAAAAAAGATT
5421 TAGATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (34 bp):
GTGCCACTAACTTATGTGGACTTTAAAAAAGATT
Found at i:7439 original size:78 final size:79
Alignment explanation
Indices: 7329--7681 Score: 322
Period size: 78 Copynumber: 4.5 Consensus size: 79
7319 TAGAGTACAT
* * ** *
7329 TCCCCAATGGTGGAAAATTAATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTTTCAGAAATA
1 TCCCCGATTGTGGAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCAGAAATA
*
7394 ATGGGGTTGGAGTA
66 ATGGGGTTAGAGTA
* * * * ** *
7408 TCCCCGATTATGGAAAA-CAATGTTTTAGAAATAAAGTCGGGGTTCTAGCAT-CTCCTCAGAAAT
1 TCCCCGATTGTGGAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCT-CTCAGAAAT
*
7471 AATGGGGCTAGAGTA
65 AATGGGGTTAGAGTA
** * * * * * * * *
7486 TCTTCGATTTTGAAAAATTGGTGTTTTAGAAATAAAAAATCAGGGTTGGAGTATCCCCT-TGAAA
1 TCCCCGATTGTGGAAAATCGATGTTTTGGAAAT--AAAATCGGGGTTGGAGTATCCTCTCAG-AA
* *
7550 ATATTGGGGTTAGAATA
63 ATAATGGGGTTAGAGTA
* *
7567 TCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAA-CTGGGGTTGGAGTATCCTCTC-GAAAA
1 TCCCCGATTGTGGAAAATCGATGTTTTGGAAATAAAATC-GGGGTTGGAGTATCCTCTCAG-AAA
*
7630 TAAAGGGGTT-GAGTA
64 TAATGGGGTTAGAGTA
* * *
7645 TCCTCGATTGTAGAAAATCGGTGTTTTGGAAATAAAA
1 TCCCCGATTGTGGAAAATCGATGTTTTGGAAATAAAA
7682 CTGAGGTTGA
Statistics
Matches: 220, Mismatches: 46, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
77 2 0.01
78 99 0.45
79 59 0.27
80 1 0.00
81 58 0.26
82 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (79 bp):
TCCCCGATTGTGGAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCAGAAATA
ATGGGGTTAGAGTA
Found at i:7558 original size:81 final size:79
Alignment explanation
Indices: 7467--7681 Score: 245
Period size: 81 Copynumber: 2.7 Consensus size: 79
7457 ATCTCCTCAG
* * * *
7467 AAATAATGGGGCTAGAGTATCTTCGATTTTGAAAAATTGGTGTTTTAGAAATAAAAAATCAGGGT
1 AAATAATGGGG-TAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTGGAAATAAAAAAT-AGGGT
*
7532 TGGAGTATCCCCTTGA
64 TGGAGTATCCCCTCGA
* * * * * * *
7548 AAATATTGGGGTTAGAATATCCCCGATGGTGAAAAATCGATGTTTTGGAAAT-AAAACTGGGGTT
1 AAATAATGGGG-TAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTGGAAATAAAAAATAGGGTT
*
7612 GGAGTATCCTCTCGA
65 GGAGTATCCCCTCGA
* *
7627 AAATAAAGGGGTTGAGTATCCTCGATTGT-AGAAAATCGGTGTTTTGGAAATAAAA
1 AAATAATGGGGTAGAGTATCCTCGATTGTGA-AAAATCGGTGTTTTGGAAATAAAA
7682 CTGAGGTTGA
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
77 1 0.01
78 33 0.30
79 30 0.27
80 5 0.05
81 42 0.38
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (79 bp):
AAATAATGGGGTAGAGTATCCTCGATTGTGAAAAATCGGTGTTTTGGAAATAAAAAATAGGGTTG
GAGTATCCCCTCGA
Found at i:7644 original size:159 final size:159
Alignment explanation
Indices: 7350--7681 Score: 365
Period size: 159 Copynumber: 2.1 Consensus size: 159
7340 GGAAAATTAA
* * * *
7350 TGTTTTGGAAAT--AAAATCGGGGTTGGAGTATCCTTTCAGAAATAATGGGGTTGGAGTATCCCC
1 TGTTTTGGAAATAAAAAATCAGGGTTGGAGTATCCCTTCAGAAATAATGGGGTTAGAATATCCCC
* * * * *
7413 GATTATGGAAAACAATGTTTTAGAAATAAAGTCGGGGTTCTAGCATCTCCTCAGAAATAATGGGG
66 GATGATGAAAAACAATGTTTTAGAAATAAACTCGGGGTTCGAGCATCTCCTCAGAAATAAAGGGG
* * *
7478 CTAGAGTATCTTCGATT-TTGAAAAATTGG
131 CTAGAGTATCCTCGATTGTAG-AAAATCGG
* * *
7507 TGTTTTAGAAATAAAAAATCAGGGTTGGAGTATCCCCTTGA-AAATATTGGGGTTAGAATATCCC
1 TGTTTTGGAAATAAAAAATCAGGGTTGGAGTAT-CCCTTCAGAAATAATGGGGTTAGAATATCCC
* * * * *
7571 CGATGGTGAAAAATCGATGTTTTGGAAATAAAACT-GGGGTTGGAGTATC-CTCTC-GAAAATAA
65 CGATGATGAAAAA-CAATGTTTTAGAAAT-AAACTCGGGGTTCGAGCATCTC-CTCAG-AAATAA
*
7633 AGGGG-TTGAGTATCCTCGATTGTAGAAAATCGG
126 AGGGGCTAGAGTATCCTCGATTGTAGAAAATCGG
7666 TGTTTTGGAAATAAAA
1 TGTTTTGGAAATAAAA
7682 CTGAGGTTGA
Statistics
Matches: 145, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
157 11 0.08
159 86 0.59
160 44 0.30
161 4 0.03
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (159 bp):
TGTTTTGGAAATAAAAAATCAGGGTTGGAGTATCCCTTCAGAAATAATGGGGTTAGAATATCCCC
GATGATGAAAAACAATGTTTTAGAAATAAACTCGGGGTTCGAGCATCTCCTCAGAAATAAAGGGG
CTAGAGTATCCTCGATTGTAGAAAATCGG
Found at i:7709 original size:78 final size:77
Alignment explanation
Indices: 7350--7726 Score: 239
Period size: 78 Copynumber: 4.8 Consensus size: 77
7340 GGAAAATTAA
* * * *
7350 TGTTTTGGAAATAAAA-TCGGGGTTGGAGTA-TCCTTTCAGAAATAATGGGGTTGGAGTATCCCC
1 TGTTTTGGAAATAAAACT-GAGGTTGGAGTATTCC-TTGA-AAATAAAGGGGTT-GAGTATCCTC
* * **
7413 GATTATGGAAAA-CAA
62 GATTGTGAAAAATCGG
* * * ** * * * * *
7428 TGTTTTAGAAAT-AAAGTCGGGGTTCTAGCATCTCC-TCAGAAATAATGGGGCTAGAGTATCTTC
1 TGTTTTGGAAATAAAACT-GAGGTTGGAGTAT-TCCTTGA-AAATAAAGGGG-TTGAGTATCCTC
* *
7491 GATTTTGAAAAATTGG
62 GATTGTGAAAAATCGG
* * * * ** * *
7507 TGTTTTAGAAATAAAAAATCAGGGTTGGAGTATCCCCTTGAAAATATTGGGGTTAGAATATCCCC
1 TGTTTTGGAAAT-AAAACTGA-GGTTGGAGTAT-TCCTTGAAAATAAAGGGGTT-GAGTATCCTC
* *
7572 GATGGTGAAAAATCGA
62 GATTGTGAAAAATCGG
*
7588 TGTTTTGGAAATAAAACTGGGGTTGGAGTA-TCCTCTCGAAAATAAAGGGGTTGAGTATCCTCGA
1 TGTTTTGGAAATAAAACTGAGGTTGGAGTATTCCT-T-GAAAATAAAGGGGTTGAGTATCCTCGA
7652 TTGT-AGAAAATCGG
64 TTGTGA-AAAATCGG
* *
7666 TGTTTTGGAAATAAAACTGAGGTTGAAGTAGTTCCTTGGAAATAACA-GGGTTGTAGTATCC
1 TGTTTTGGAAATAAAACTGAGGTTGGAGTA-TTCCTTGAAAATAA-AGGGGTTG-AGTATCC
7727 CCTCAAAAAT
Statistics
Matches: 239, Mismatches: 43, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
77 7 0.03
78 117 0.49
79 45 0.19
80 13 0.05
81 55 0.23
82 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (77 bp):
TGTTTTGGAAATAAAACTGAGGTTGGAGTATTCCTTGAAAATAAAGGGGTTGAGTATCCTCGATT
GTGAAAAATCGG
Found at i:7717 original size:106 final size:107
Alignment explanation
Indices: 7607--7802 Score: 279
Period size: 107 Copynumber: 1.8 Consensus size: 107
7597 AATAAAACTG
* * * *
7607 GGGTTGGAGTATCCTCTCGAAAATAAAGGGGTT-GAGTA-TCCTCGATTGTAGAAAATCGGTGTT
1 GGGTTGGAGTATCCCCTCAAAAATAAAGAGGTTGGAGTATTCC-CGATTGTACAAAATCGGTGTT
*
7670 TTGGAAATAAAACTGAGGTTGAAGTAGTTCCTTGGAAATAACA
65 TTGAAAATAAAACTGAGGTTGAAGTAGTTCCTTGGAAATAACA
* * *
7713 GGGTTGTAGTATCCCCTCAAAAATAACGAGGTTGGAGTATTCCCGATTGTACAAAATTGGTGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAAAGAGGTTGGAGTATTCCCGATTGTACAAAATCGGTGTTT
* *
7778 TGAAAATAAAATTGAGGTTGGAGTA
66 TGAAAATAAAACTGAGGTTGAAGTA
7803 TCCCTGATTG
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
106 28 0.36
107 47 0.60
108 3 0.04
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (107 bp):
GGGTTGGAGTATCCCCTCAAAAATAAAGAGGTTGGAGTATTCCCGATTGTACAAAATCGGTGTTT
TGAAAATAAAACTGAGGTTGAAGTAGTTCCTTGGAAATAACA
Found at i:7797 original size:51 final size:51
Alignment explanation
Indices: 7740--7839 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
7730 CAAAAATAAC
* * *
7740 GAGGTTGGAGTATTCCC-GATT-GTACAAAATTGGTGTTTTGAAAATAAAATT
1 GAGGTTGGAGTA-TCCCTGATTGGGA-AAAATCGATGTTTTGAAAATAAAATT
*
7791 GAGGTTGGAGTATCCCTGATTGGGAAAAATCGATGTTTTGGAAATAAAA
1 GAGGTTGGAGTATCCCTGATTGGGAAAAATCGATGTTTTGAAAATAAAA
7840 CCGAAATTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 4 0.09
51 37 0.86
52 2 0.05
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (51 bp):
GAGGTTGGAGTATCCCTGATTGGGAAAAATCGATGTTTTGAAAATAAAATT
Found at i:7873 original size:79 final size:78
Alignment explanation
Indices: 7790--7937 Score: 219
Period size: 79 Copynumber: 1.9 Consensus size: 78
7780 AAAATAAAAT
* * * *
7790 TGAGGTTGGAGTATCCCTGATTGG-GAAAAATCGATGTTTTGGAAATAAAACCGAAA-TTGGAGT
1 TGAGGTTGGAATATCCCGGA-TGGTGAAAAATCAATGTTTTGAAAAT-AAACC-AAAGTTGGAGT
7853 ATCTCCTCGAAAATAA
63 ATCTCCTCGAAAATAA
7869 TGAGGTTGGAATATCCCGGATGGTGAAAAATCAATGTTTTGAAAATAAACCAAAGTTGGAGTATC
1 TGAGGTTGGAATATCCCGGATGGTGAAAAATCAATGTTTTGAAAATAAACCAAAGTTGGAGTATC
7934 TCCT
66 TCCT
7938 TCAAATAACA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
77 3 0.05
78 22 0.35
79 38 0.60
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (78 bp):
TGAGGTTGGAATATCCCGGATGGTGAAAAATCAATGTTTTGAAAATAAACCAAAGTTGGAGTATC
TCCTCGAAAATAA
Found at i:7970 original size:77 final size:78
Alignment explanation
Indices: 7794--7974 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 78
7784 TAAAATTGAG
* * *
7794 GTTGGAGTATCCCTGATTGG-GAAAAATCGATGTTTTGGAAATAAAACCGAAATTGGAGTATCTC
1 GTTGGAGTATCCCGGA-TGGTGAAAAATCAATGTTTTGAAAATAAAACCGAAATTGGAGTATCTC
7858 CTCGAAAATAATGA
65 CTCGAAAATAATGA
*
7872 GGTTGGAATATCCCGGATGGTGAAAAATCAATGTTTTGAAAAT-AAACC-AAAGTTGGAGTATCT
1 -GTTGGAGTATCCCGGATGGTGAAAAATCAATGTTTTGAAAATAAAACCGAAA-TTGGAGTATCT
7935 CCTTC--AAATAACATGA
64 CC-TCGAAAAT-A-ATGA
7951 -TTGGAGTATCCTC-GATGGTGAAAA
1 GTTGGAGTATCC-CGGATGGTGAAAA
7975 TCGGTATTAT
Statistics
Matches: 91, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
77 28 0.31
78 23 0.25
79 40 0.44
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (78 bp):
GTTGGAGTATCCCGGATGGTGAAAAATCAATGTTTTGAAAATAAAACCGAAATTGGAGTATCTCC
TCGAAAATAATGA
Found at i:9623 original size:13 final size:13
Alignment explanation
Indices: 9605--9631 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9595 ACATTATGCT
9605 TTGTATCGATACA
1 TTGTATCGATACA
9618 TTGTATCGATACA
1 TTGTATCGATACA
9631 T
1 T
9632 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:9628 original size:33 final size:32
Alignment explanation
Indices: 9586--9649 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
9576 CACATCCAAA
*
9586 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
9619 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
9650 CATTCAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:9640 original size:19 final size:19
Alignment explanation
Indices: 9616--9671 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
9606 TGTATCGATA
9616 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
**
9635 CATTGTATCGATACACATT
1 CATTGTATCGATACATGTT
9654 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
9672 AATTGTAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:13483 original size:22 final size:23
Alignment explanation
Indices: 13455--13510 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
13445 TGGACATGTT
13455 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
13477 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
13500 AAAAATGCATG
1 AAAAATGCATG
13511 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:14468 original size:20 final size:20
Alignment explanation
Indices: 14421--14495 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
14411 AAAAAGACAT
*
14421 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
14440 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
14461 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
14481 AATGCATCGATACAT
1 AATGTATCGATACAT
14496 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:14490 original size:40 final size:39
Alignment explanation
Indices: 14418--14495 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
14408 GGTAAAAAGA
* * *
14418 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
14457 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
14496 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:15066 original size:28 final size:28
Alignment explanation
Indices: 14984--16497 Score: 1996
Period size: 29 Copynumber: 52.9 Consensus size: 28
14974 TGAAAAGGGT
* * *
14984 TGCCATTGACTTGCATGGGCTTTAAAAGGG
1 TGCCACTGACTTG--TGGGCTTTGAAAGAG
* *
15014 TGCCACTGACGTGCGTGGGCTTTGAAAGAA
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGAG
* *
15044 TGCCACTAACTCGTGGGCTTTGAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
15071 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAGAG
15100 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
* * *
15128 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAA-GAG
* *
15159 TGCCACTGACTTGTGTGAGCTTTAAAAGGG
1 TGCCACTGACTTGTG-G-GCTTTGAAAGAG
15189 TGCCACTGACTTGTGGGCTTTGAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15217 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
15245 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
15273 TGCCACTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
15301 TGCCA-TAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
15328 TGCCACTGACTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
15357 CGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
15386 TGCCACTGACTTATGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
15415 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15443 TGCCATTGACTTGTGGTCTTTGAAAATAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
15472 TGCCACTAATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
15501 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
15530 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15558 TGCCACTAACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
15586 TGCCACTGAGTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
15614 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
15643 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
15672 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
15701 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15729 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
15757 TGCCACTGACTTGTGGGCTTCGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
15785 TGCCACTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
15813 TGCCACTGACTTGTGGGCTCTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15841 TGCCACTAATTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
15869 TGCCACTGACTTGTGGGCTTTAAAAAGAG
1 TGCCACTGACTTGTGGGCTTT-GAAAGAG
*
15898 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
* *
15927 TGCCACTGACTTGTGGGCTTTTAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
15955 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
15984 TGCCACTGATTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
16013 TGCCACTGACTTGTGGGCTTTGAAAGGAA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
16042 TGCCACTGACTTGTGGGCTTTGAAAGGAA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
16071 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
16099 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
16128 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
16157 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
16186 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
16214 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
16243 TGCCACTGATTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTG-AAAGAG
*
16272 TGCCACTGACTTGTGGGCTTTGAAAGGAA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
16301 TGCCACTGACTTGTGGGCTTTGAAAGGAA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
16330 TGCCACTGACTTGTGGGCTTTGAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
*
16358 TGCCACTGACTTGTGGGCTTTGAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
*
16387 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGAG
* *
16415 TGCCACTAACTTGTAGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAG
16444 TGCCACTGACTTGTGGGCTTTGAAA-AGG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-G
16472 TGCCACTGACTTGTGGGCTTTGAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAG
16498 GGATGAACAT
Statistics
Matches: 1343, Mismatches: 108, Indels: 67
0.88 0.07 0.04
Matches are distributed among these distances:
27 33 0.02
28 581 0.43
29 647 0.48
30 58 0.04
31 22 0.02
32 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGAG
Found at i:15453 original size:115 final size:114
Alignment explanation
Indices: 14984--16496 Score: 2082
Period size: 115 Copynumber: 13.2 Consensus size: 114
14974 TGAAAAGGGT
* * * *
14984 TGCCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACGTGCGTGGGCTTTGAAAGAATGCC
1 TGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCC
* *
15048 ACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAG
62 ACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15100 TGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCA
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCA
*
15164 CTGACTTGTGTGAGCTTTAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGAG
63 CTGACTTGTG-G-GCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * * *
15217 TGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* * *
15281 ACTTGTGGGCTCTGAAAGG-GTGCCA-TAACTTGTGGGCTTTGAAAGGG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
15328 TGCCACTGACTTATGGGCTTTGAAAAGAGCGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACT
* *
15393 GACTTATGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
65 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
15443 TGCCATTGACTTGTGGTCTTTGAAAATAGTGCCACTAATTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACT
*
15508 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
65 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
15558 TGCCACTAACTTGTGGGCTCTG-AAAGGGTGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
15622 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA-GAG
* * *
15672 TGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* * * * * *
15737 AATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * * * *
15785 TGCCACTGACTTGTGGGCTCTG-AAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* *
15849 ATTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTAAAAAGAG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT-GAAAGAG
* * * * *
15898 TGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTTAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
* * *
15963 ACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATGGGCTTTGAAAAGAG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAG
* * *
16013 TGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACT
16078 GACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAG
65 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAG
* *
16128 TGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACT
*
16193 GACTTGTGGGCTTTGAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAAGAG
65 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAG
* * *
16243 TGCCACTGATTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACT
*
16308 GACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTGAAAGAG
65 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * * *
16358 TGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
*
16423 ACTTGTAGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA-AGG
66 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGA-G
16472 TGCCACTGACTTGTGGGCTTTGAAA
1 TGCCACTGACTTGTGGGCTTTGAAA
16497 GGGATGAACA
Statistics
Matches: 1265, Mismatches: 112, Indels: 42
0.89 0.08 0.03
Matches are distributed among these distances:
111 42 0.03
112 109 0.09
113 139 0.11
114 257 0.20
115 585 0.46
116 60 0.05
117 73 0.06
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (114 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
Found at i:17725 original size:1 final size:1
Alignment explanation
Indices: 17719--17792 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
17709 GACCCTTCTA
** * * * * * * * *
17719 TTTTTTTTTTGCTATTTTTTCTTTTTTTGTTTTTTGTTTTGTTTTTTTTTGTGTTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17784 TTTTTTTTT
1 TTTTTTTTT
17793 GGGTGTAAAG
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.86
Consensus pattern (1 bp):
T
Found at i:17744 original size:22 final size:20
Alignment explanation
Indices: 17714--17790 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
17704 ATCTAGACCC
17714 TTCTATTTTTTTTTTGCTATTTT
1 TTCT-TTTTTTTTTTG-T-TTTT
*
17737 TTCTTTTTTTGTTTT-TTGTT
1 TTCTTTTTTT-TTTTGTTTTT
* *
17757 TTGTTTTTTTTTGTGTTTTT
1 TTCTTTTTTTTTTTGTTTTT
17777 TT-TTGTTTTTTTTT
1 TTCTT-TTTTTTTTT
17791 TTGGGTGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.11
20 26 0.57
21 1 0.02
22 6 0.13
23 8 0.17
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.84
Consensus pattern (20 bp):
TTCTTTTTTTTTTTGTTTTT
Found at i:17760 original size:12 final size:11
Alignment explanation
Indices: 17740--17791 Score: 79
Period size: 11 Copynumber: 4.6 Consensus size: 11
17730 CTATTTTTTC
17740 TTTTTTTGTTT
1 TTTTTTTGTTT
17751 TTTGTTTTG-TT
1 TTT-TTTTGTTT
17762 TTTTTTTGTGTT
1 TTTTTTTGT-TT
17774 TTTTTTTGTTT
1 TTTTTTTGTTT
17785 TTTTTTT
1 TTTTTTT
17792 TGGGTGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.13
11 17 0.45
12 16 0.42
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:17792 original size:12 final size:12
Alignment explanation
Indices: 17735--17793 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
17725 TTTTGCTATT
17735 TTTTCTTTTTTTG
1 TTTT-TTTTTTTG
*
17748 TTTTTTGTTTTG
1 TTTTTTTTTTTG
17760 --TTTTTTTTTG
1 TTTTTTTTTTTG
*
17770 TGTTTTTTTTTG
1 TTTTTTTTTTTG
17782 TTTTTTTTTTTG
1 TTTTTTTTTTTG
17794 GGTGTAAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.22
12 28 0.68
13 4 0.10
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:17798 original size:26 final size:27
Alignment explanation
Indices: 17748--17798 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
17738 TCTTTTTTTG
**
17748 TTTTTTGTTTTGTTTTTTTTTGTGTTT
1 TTTTTTGTTTTGTTTTTTTGGGTGTTT
17775 TTTTTTGTTTT-TTTTTTTGGGTGT
1 TTTTTTGTTTTGTTTTTTTGGGTGT
17799 AAAGGACGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (27 bp):
TTTTTTGTTTTGTTTTTTTGGGTGTTT
Found at i:30883 original size:22 final size:23
Alignment explanation
Indices: 30855--30910 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
30845 TGGACATGTT
30855 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
30877 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
30900 AAAAATGCATG
1 AAAAATGCATG
30911 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:31868 original size:20 final size:20
Alignment explanation
Indices: 31821--31895 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
31811 AAAAAGACAT
*
31821 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
31840 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
31861 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
31881 AATGCATCGATACAT
1 AATGTATCGATACAT
31896 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:31890 original size:40 final size:39
Alignment explanation
Indices: 31818--31895 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
31808 GGTAAAAAGA
* * *
31818 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
31857 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
31896 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:33550 original size:130 final size:130
Alignment explanation
Indices: 33316--33573 Score: 444
Period size: 130 Copynumber: 2.0 Consensus size: 130
33306 AAAGGCTTGA
* * **
33316 GTCAAGTATGATAAAGGATATATTGCAGCTTAATTCACCCATTGGTAACTTTCTTTATTGAGGAT
1 GTCAAGTATGATAAAAGATATATTGCAGCTTAATTCACCCATTGGCAACTTTCTTTATTGAAAAT
* *
33381 CTTTTGAAGAGTATTTACAACTATTTTGAGACATGTATCCTTCTTTTTCATGACATTTTCTTTGG
66 CTTTTGAAGAGTATTTACAACTATTTTGAGACATATATCCATCTTTTTCATGACATTTTCTTTGG
* *
33446 GTCAAGTATGATAAAAGATATATTTCAGCTTAATTCATCCATTGGCAACTTTCTTTATTGAAAAT
1 GTCAAGTATGATAAAAGATATATTGCAGCTTAATTCACCCATTGGCAACTTTCTTTATTGAAAAT
33511 CTTTTGAAGAGTATTTACAACTATTTTGAGACATATATCCATCTTTTTCATGACATTTTCTTT
66 CTTTTGAAGAGTATTTACAACTATTTTGAGACATATATCCATCTTTTTCATGACATTTTCTTT
33574 TTCATGCCAC
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 120 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.43
Consensus pattern (130 bp):
GTCAAGTATGATAAAAGATATATTGCAGCTTAATTCACCCATTGGCAACTTTCTTTATTGAAAAT
CTTTTGAAGAGTATTTACAACTATTTTGAGACATATATCCATCTTTTTCATGACATTTTCTTTGG
Found at i:40942 original size:15 final size:15
Alignment explanation
Indices: 40922--40952 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40912 AGATTATAGC
40922 TATTTGAATAAAGGT
1 TATTTGAATAAAGGT
40937 TATTTGAATAAAGGT
1 TATTTGAATAAAGGT
40952 T
1 T
40953 GTTGATGCCA
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:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (15 bp):
TATTTGAATAAAGGT
Found at i:44243 original size:21 final size:22
Alignment explanation
Indices: 44218--44258 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
44208 AACATGCTGT
44218 AAATGCATGAAACAT-AGCTCA
1 AAATGCATGAAACATGAGCTCA
*
44239 AAATGCATGAATCATGAGCT
1 AAATGCATGAAACATGAGCT
44259 GTTAACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (22 bp):
AAATGCATGAAACATGAGCTCA
Found at i:45156 original size:52 final size:52
Alignment explanation
Indices: 45094--45193 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
45084 CGAAATATGA
**
45094 AAATTTGCCTGCATGTATCGATACATTTCAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-AACATCAGTGTATCGATACATCTGGGC
*
45146 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACATCT
1 AAATTTGCCTGCATGTATCGATACAAACATCAGTGTATCGATACATCT
45194 AATGTATCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.05
52 42 0.95
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAAACATCAGTGTATCGATACATCTGGGC
Found at i:45249 original size:13 final size:13
Alignment explanation
Indices: 45231--45346 Score: 52
Period size: 13 Copynumber: 7.5 Consensus size: 13
45221 AGCTTCGTAG
45231 CGATACATTGTAT
1 CGATACATTGTAT
45244 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
45263 CGATACATTGTAT
1 CGATACATTGTAT
45276 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
*
45295 CGATACATAGTAT
1 CGATACATTGTAT
45308 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
*
45327 CGATACATAGTAT
1 CGATACATTGTAT
45340 CGATACA
1 CGATACA
45347 ACACTTATGT
Statistics
Matches: 82, Mismatches: 3, Indels: 36
0.68 0.02 0.30
Matches are distributed among these distances:
13 33 0.40
14 2 0.02
15 2 0.02
16 14 0.17
17 2 0.02
18 2 0.02
19 27 0.33
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:45263 original size:19 final size:18
Alignment explanation
Indices: 45239--45367 Score: 117
Period size: 19 Copynumber: 7.8 Consensus size: 18
45229 AGCGATACAT
45239 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
45258 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
45271 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
45290 TGTATCGATAC--A--TA
1 TGTATCGATACAAACTTA
45304 -GTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
45322 TGTATCGATAC--A--TA
1 TGTATCGATACAAACTTA
45336 -GTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
45354 TGTATCGATACAAA
1 TGTATCGATACAAA
45368 TCATTGAAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 37
0.71 0.00 0.29
Matches are distributed among these distances:
13 31 0.34
14 5 0.05
16 6 0.07
18 6 0.07
19 44 0.48
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:45272 original size:32 final size:32
Alignment explanation
Indices: 45231--45365 Score: 243
Period size: 32 Copynumber: 4.2 Consensus size: 32
45221 AGCTTCGTAG
* *
45231 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATAGTATCGATACAACACTTATGTAT
*
45263 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATAGTATCGATACAACACTTATGTAT
45295 CGATACATAGTATCGATACAACACTTATGTAT
1 CGATACATAGTATCGATACAACACTTATGTAT
45327 CGATACATAGTATCGATACAACACTTATGTAT
1 CGATACATAGTATCGATACAACACTTATGTAT
45359 CGATACA
1 CGATACA
45366 AATCATTGAA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 101 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATAGTATCGATACAACACTTATGTAT
Found at i:46229 original size:156 final size:156
Alignment explanation
Indices: 45958--46431 Score: 729
Period size: 156 Copynumber: 3.0 Consensus size: 156
45948 GGCCTGCAAC
* * * * * *
45958 ATTGGATTTAAAGATGATGAGGATGAGAAGAGTGATTAAGGTGCCAATATGCTGATTTAGGGCCA
1 ATTGGACTTAAAGATGA--AGG-TGAGAAAAGTGATAAAGATGCCAATATGCTGATTCACGGCCA
* *
46023 ATGATATTGGACTTGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGATTTAAAGGTTAAAGA
63 ACGATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGGTTAAAGA
*
46088 TGCCAATACGCTAATTCAAGGCCAATGAT
128 TGCCAATACGCTAATTCAAGGCCAACGAT
*
46117 ATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATTTGCTGATTCACGGCCAACG
1 ATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATATGCTGATTCACGGCCAACG
46182 ATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGGTTAAAGATGC
66 ATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGGTTAAAGATGC
*
46247 CAATACTCTAATTCAAGGCCAACGAT
131 CAATACGCTAATTCAAGGCCAACGAT
*
46273 ATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATACCAATATGCTGATTCACGGCCAACG
1 ATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATATGCTGATTCACGGCCAACG
* *
46338 ATCTTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAA-G--ACAAGGTG
66 ATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGGTTA-AAGATG
** * *
46400 CCAATACGCCGATTCAAAGCCAGCGAT
130 CCAATACGCTAATTCAAGGCCAACGAT
46427 ATTGG
1 ATTGG
46432 GCCTATGCCA
Statistics
Matches: 294, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
153 1 0.00
154 32 0.11
155 1 0.00
156 241 0.82
157 3 0.01
159 16 0.05
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (156 bp):
ATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATATGCTGATTCACGGCCAACG
ATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGGTTAAAGATGC
CAATACGCTAATTCAAGGCCAACGAT
Found at i:46549 original size:43 final size:42
Alignment explanation
Indices: 46484--46627 Score: 144
Period size: 43 Copynumber: 3.2 Consensus size: 42
46474 TAAAGATGCC
* * * *
46484 AAAGGCGCCAATATACTAATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG-TTT
* *
46527 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTT
* *
46569 GAAAGATAATGTGCCAATATGTTGATTCAAGGCCAGCAATATTGGTTTT
1 -AAAG-----GTGCCAATATGCTGATTCAAGGCCAGCGATATTGG-TTT
46618 AAAGGTGCCA
1 AAAGGTGCCA
46628 CGACGTTGTG
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 44 0.52
48 35 0.42
49 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTT
Found at i:46604 original size:91 final size:87
Alignment explanation
Indices: 46313--46613 Score: 345
Period size: 87 Copynumber: 3.4 Consensus size: 87
46303 GATAAAGATA
* * *
46313 CCAATATGCTGATTCACGGCCAACGATCTTGGACTT-GTGCCAATGTGCTGATTCAAGGCCAGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCG
*
46377 ACATTGGATTTAAAGACAAGGTG
66 ACATTGG-TTTAAAGATAAGGTG
* * * * * *
46400 CCAATACGCCGATTCAAAGCCAGCGATATTGGGCCTA-TGCCAATGTGCTGATTCAAGGCCAGCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCG
* *
46464 ATATTGGTCTTAAAGATGCCAAAGGCG
66 ACATTGGT-TTAAAGAT----AAGGTG
* *
46491 CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-GTGCCAATGTGCTGATTCAAGGCCA
*
46556 GCGACATTGGTTTGAAAGATAATGTG
63 GCGACATTGGTTT-AAAGATAAGGTG
* *
46582 CCAATATGTTGATTCAAGGCCAGCAATATTGG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGG
46614 TTTTAAAGGT
Statistics
Matches: 176, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
86 1 0.01
87 67 0.38
91 66 0.38
93 1 0.01
94 2 0.01
95 39 0.22
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCG
ACATTGGTTTAAAGATAAGGTG
Found at i:46625 original size:91 final size:90
Alignment explanation
Indices: 46313--46627 Score: 340
Period size: 91 Copynumber: 3.5 Consensus size: 90
46303 GATAAAGATA
* * *
46313 CCAATATGCTGATTCACGGCCAACGATCTTGGACTT----GTGCCAATGTGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
*
46374 GCGACATTGGATTTAAAGACAAGGTG
66 GCGACATTGG-TTTAAAGATAAGGTG
* * * * *
46400 CCAATACGCCGATTCAAAGCCAGCGATATTGGGCCT--A--TGCCAATGTGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
* * *
46461 GCAATATTGGTCTTAAAGATGCCAAAGGCG
66 GCGACATTGGT-TTAAAGAT----AAGGTG
* *
46491 CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
*
46556 GCGACATTGGTTTGAAAGATAATGTG
66 GCGACATTGGTTT-AAAGATAAGGTG
* * **
46582 CCAATATGTTGATTCAAGGCCAGCAATATTGGTTTTAAAGGTGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCA
46628 CGACGTTGTG
Statistics
Matches: 188, Mismatches: 29, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
86 1 0.01
87 67 0.36
91 78 0.41
93 1 0.01
94 2 0.01
95 39 0.21
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (90 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGTTTAAAGATAAGGTG
Found at i:46755 original size:34 final size:30
Alignment explanation
Indices: 46711--46856 Score: 131
Period size: 30 Copynumber: 4.8 Consensus size: 30
46701 TGAGCTTTTG
*
46711 AAGGTTGCCACTAATTTGTGGGCTTTGTAAAAAAA
1 AAGG-TGCCACTGATTTGTGGGCTTTG----AAAA
* *
46746 AAGGTGCCACTGACTTGTGGGCTTTGGAAA
1 AAGGTGCCACTGATTTGTGGGCTTTGAAAA
*
46776 AGGGTGCCACTGATTTGTGGGCTTTG----
1 AAGGTGCCACTGATTTGTGGGCTTTGAAAA
* *
46802 AAGGTTGCCACTAACTTGTGGGCTTTG-AAA
1 AAGG-TGCCACTGATTTGTGGGCTTTGAAAA
* *
46832 AAGATGCCACTGACTTGTGGGCTTT
1 AAGGTGCCACTGATTTGTGGGCTTT
46857 TGAAGGGTGA
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
26 3 0.03
27 20 0.21
29 20 0.21
30 30 0.31
34 20 0.21
35 4 0.04
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (30 bp):
AAGGTGCCACTGATTTGTGGGCTTTGAAAA
Found at i:46793 original size:64 final size:62
Alignment explanation
Indices: 46648--46856 Score: 170
Period size: 56 Copynumber: 3.5 Consensus size: 62
46638 GACTTAAAAA
* * * * * * * *
46648 GAAAAGG-CGCCACAGAATTGTGGGC-TTAAAAATAAAAAGATACCACGGACTTGTGAGCTTTT
1 GAAAAGGATGCCACTGATTTGTGGGCTTTGAAAA-AAAAAGGTGCCACTGACTTGTGGGC-TTT
* *
46710 G--AAGGTTGCCACTAATTTGTGGGCTTTGTAAAAAAAAAGGTGCCACTGACTTGTGGGCTTT
1 GAAAAGGATGCCACTGATTTGTGGGCTTTG-AAAAAAAAAGGTGCCACTGACTTGTGGGCTTT
* *
46771 GGAAAAGGGTGCCACTGATTTGTGGGCTTTG-------AAGGTTGCCACTAACTTGTGGGCTTT
1 -GAAAAGGATGCCACTGATTTGTGGGCTTTGAAAAAAAAAGG-TGCCACTGACTTGTGGGCTTT
* *
46828 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAGGATGCCACTGATTTGTGGGCTTT
46857 TGAAGGGTGA
Statistics
Matches: 125, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
56 30 0.24
57 20 0.16
60 4 0.03
61 17 0.14
62 25 0.20
63 4 0.03
64 25 0.20
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (62 bp):
GAAAAGGATGCCACTGATTTGTGGGCTTTGAAAAAAAAAGGTGCCACTGACTTGTGGGCTTT
Found at i:46842 original size:56 final size:57
Alignment explanation
Indices: 46746--46862 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
46736 TGTAAAAAAA
* * * *
46746 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAGGTGCCACTAACTTGTGGGCTTTGGAAAAAGATGCCACTGACTTGTGGGCTTTTG
46802 AAGGTTGCCACTAACTTGTGGGCTTT-GAAAAAGATGCCACTGACTTGTGGGCTTTTG
1 AAGG-TGCCACTAACTTGTGGGCTTTGGAAAAAGATGCCACTGACTTGTGGGCTTTTG
46859 AAGG
1 AAGG
46863 GTGAGGAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
56 27 0.49
57 28 0.51
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (57 bp):
AAGGTGCCACTAACTTGTGGGCTTTGGAAAAAGATGCCACTGACTTGTGGGCTTTTG
Found at i:46849 original size:29 final size:29
Alignment explanation
Indices: 46743--46856 Score: 153
Period size: 30 Copynumber: 4.0 Consensus size: 29
46733 CTTTGTAAAA
46743 AAAAAGGTGCCACTGACTTGTGGGCTTTGG
1 AAAAAGGTGCCACTGACTTGTGGGCTTT-G
* *
46773 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAAAGGTGCCACTGACTTGTGGGCTTTG
*
46802 ---AAGGTTGCCACTAACTTGTGGGCTTTG
1 AAAAAGG-TGCCACTGACTTGTGGGCTTTG
*
46829 AAAAAGATGCCACTGACTTGTGGGCTTT
1 AAAAAGGTGCCACTGACTTGTGGGCTTT
46857 TGAAGGGTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.04
27 20 0.27
29 21 0.29
30 29 0.40
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (29 bp):
AAAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:48322 original size:17 final size:16
Alignment explanation
Indices: 48292--48407 Score: 82
Period size: 16 Copynumber: 7.2 Consensus size: 16
48282 ATCCGGACCC
48292 TTTTTGTTGTTTTGTT
1 TTTTTGTTGTTTTGTT
*
48308 TTTTTTTTGTGTTTGTT
1 TTTTTGTTGT-TTTGTT
***
48325 TTTTTGTT-TCTTTCCC
1 TTTTTGTTGT-TTTGTT
48341 TTTTT-TTGTTTT-TT
1 TTTTTGTTGTTTTGTT
*
48355 TTTGTGTTTGTTTT-TT
1 TTTTTG-TTGTTTTGTT
*
48371 TTTCTT-TTTTTTTGTT
1 TTT-TTGTTGTTTTGTT
48387 TTGTTTGCTTGTTTT-TT
1 TT-TTTG-TTGTTTTGTT
48404 TTTT
1 TTTT
48408 GGAGGACGCA
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.05
15 11 0.14
16 39 0.49
17 19 0.24
18 6 0.08
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (16 bp):
TTTTTGTTGTTTTGTT
Found at i:48359 original size:36 final size:34
Alignment explanation
Indices: 48306--48407 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 34
48296 TGTTGTTTTG
* *
48306 TTTTTTT-TTTGTGTTTGTTTTTTTGTTTCTTTCCC
1 TTTTTTTGTTTTTTTTTGTTTTTTT-TTT-TTTCCC
**
48341 TTTTTTTGTTTTTTTTTGTGTTTGTTTTTTTTTCTT
1 TTTTTTTGTTTTTTTTTGT-TTT-TTTTTTTTTCCC
48377 TTTTTTTGTTTTGTTTGCTTGTTTTTTTTTT
1 TTTTTTTGTTTT-TTT--TTGTTTTTTTTTT
48408 GGAGGACGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
35 7 0.12
36 25 0.44
37 15 0.26
38 6 0.11
39 4 0.07
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (34 bp):
TTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTCCC
Found at i:48368 original size:24 final size:25
Alignment explanation
Indices: 48341--48406 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
48331 TTTCTTTCCC
48341 TTTTTTTGTTTTTTTTTGTG-TTTG
1 TTTTTTTGTTTTTTTTTGTGTTTTG
*
48365 TTTTTTT-TTCTTTTTTTTTGTTTTG
1 TTTTTTTGTT-TTTTTTTGTGTTTTG
**
48390 TTTGCTTGTTTTTTTTT
1 TTTTTTTGTTTTTTTTT
48407 TGGAGGACGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.06
24 16 0.44
25 16 0.44
26 2 0.06
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (25 bp):
TTTTTTTGTTTTTTTTTGTGTTTTG
Found at i:48369 original size:25 final size:24
Alignment explanation
Indices: 48301--48407 Score: 60
Period size: 26 Copynumber: 4.1 Consensus size: 24
48291 CTTTTTGTTG
48301 TTTTGTTTTTTTTTTGTGTTTG-TTT
1 TTTTG-TTTTTTTTTGT-TTTGTTTT
48326 TTTTGTTTCTTTCCCTTT-TTTTGTTTTT
1 TTTTGTTT-TTT---TTTGTTTTG-TTTT
*
48354 TTTTGTGTTTGTTTTT-TTTTCTTTTT
1 TTTTGT-TTT-TTTTTGTTTT-GTTTT
48380 TTTTGTTTTGTTTGCTTGTTTT-TTTT
1 TTTTGTTTT-TTT--TTGTTTTGTTTT
48406 TT
1 TT
48408 GGAGGACGCA
Statistics
Matches: 69, Mismatches: 1, Indels: 23
0.74 0.01 0.25
Matches are distributed among these distances:
24 3 0.04
25 15 0.22
26 27 0.39
27 3 0.04
28 17 0.25
29 4 0.06
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (24 bp):
TTTTGTTTTTTTTTGTTTTGTTTT
Found at i:48407 original size:24 final size:26
Alignment explanation
Indices: 48349--48408 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
48339 CCTTTTTTTG
** *
48349 TTTTTTTTTGTGTTTGTTTTTTTTTC
1 TTTTTTTTTGTGTTTGTTTGCTTGTC
48375 TTTTTTTTTGT-TTTGTTTGCTTGT-
1 TTTTTTTTTGTGTTTGTTTGCTTGTC
48399 TTTTTTTTTG
1 TTTTTTTTTG
48409 GAGGACGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 10 0.32
25 10 0.32
26 11 0.35
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.83
Consensus pattern (26 bp):
TTTTTTTTTGTGTTTGTTTGCTTGTC
Found at i:50767 original size:19 final size:18
Alignment explanation
Indices: 50742--50806 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
50732 ATTTCAACAA
50742 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
50760 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
50776 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
50792 TTTTGTATCGATACA
1 -TTTGTATCGATACA
50807 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:50781 original size:13 final size:13
Alignment explanation
Indices: 50763--50787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50753 ACATAAGTGT
50763 TGTATCGATACAA
1 TGTATCGATACAA
50776 TGTATCGATACA
1 TGTATCGATACA
50788 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50781 original size:32 final size:32
Alignment explanation
Indices: 50744--50814 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
50734 TTCAACAATT
50744 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
50776 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
50808 TGTATCG
1 TGTATCG
50815 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:50877 original size:13 final size:13
Alignment explanation
Indices: 50859--50883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50849 ATTACTCAAA
50859 TGTATCGATACAT
1 TGTATCGATACAT
50872 TGTATCGATACA
1 TGTATCGATACA
50884 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50936 original size:52 final size:52
Alignment explanation
Indices: 50892--51020 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
50882 CACTGATCTT
*
50892 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
50944 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
50996 TGTATCGATGCATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
51021 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:53854 original size:19 final size:18
Alignment explanation
Indices: 53827--53893 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 18
53817 GAATTTCAAC
53827 AATTTGTATCGATACATA
1 AATTTGTATCGATACATA
53845 AATGTTGTATCGATAC---
1 AAT-TTGTATCGATACATA
53861 AA--TGTATCGATACATA
1 AATTTGTATCGATACATA
*
53877 AGTTTTGTATCGATACA
1 A-ATTTGTATCGATACA
53894 ATGTATCGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.27
16 3 0.07
18 3 0.07
19 24 0.59
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATTTGTATCGATACATA
Found at i:53868 original size:13 final size:13
Alignment explanation
Indices: 53850--53874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53840 ACATAAATGT
53850 TGTATCGATACAA
1 TGTATCGATACAA
53863 TGTATCGATACA
1 TGTATCGATACA
53875 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:53868 original size:32 final size:32
Alignment explanation
Indices: 53831--53901 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
53821 TTCAACAATT
53831 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
* *
53863 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
53895 TGTATCG
1 TGTATCG
53902 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:53964 original size:13 final size:13
Alignment explanation
Indices: 53946--53970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53936 ATTACTCAAA
53946 TGTATCGATACAT
1 TGTATCGATACAT
53959 TGTATCGATACA
1 TGTATCGATACA
53971 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:54023 original size:52 final size:52
Alignment explanation
Indices: 53979--54107 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
53969 CACTGATCTT
*
53979 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
54031 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
54083 TGTATCGATGCATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
54108 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:69187 original size:19 final size:19
Alignment explanation
Indices: 69163--69246 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
69153 AGCGATACAT
69163 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
69182 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
69201 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
69214 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
69233 TGTATCGATACAAA
1 TGTATCGATACAAA
69247 TCGTTGAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
16 2 0.04
18 1 0.02
19 42 0.74
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:69218 original size:32 final size:32
Alignment explanation
Indices: 69182--69244 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
69172 ACAAAACTTA
69182 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
69214 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
69245 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:69219 original size:13 final size:13
Alignment explanation
Indices: 69201--69225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69191 ACAACACTTA
69201 TGTATCGATACAT
1 TGTATCGATACAT
69214 TGTATCGATACA
1 TGTATCGATACA
69226 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70636 original size:20 final size:19
Alignment explanation
Indices: 70601--70638 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
70591 TTAATATTCC
*
70601 TTTTAATATAAAATTTTCT
1 TTTTAAAATAAAATTTTCT
70620 TTTTAAAATATAAATTTTC
1 TTTTAAAATA-AAATTTTC
70639 ATCCACAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAAAATAAAATTTTCT
Found at i:71063 original size:2 final size:2
Alignment explanation
Indices: 71056--71089 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
71046 CTTCTTTCAT
*
71056 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
71090 GCCCCCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:74712 original size:2 final size:2
Alignment explanation
Indices: 74705--74756 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
74695 TGTGATTACT
74705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74747 TA TA TA TA TA
1 TA TA TA TA TA
74757 AAACATAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75444 original size:23 final size:23
Alignment explanation
Indices: 75389--75448 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
75379 ATTAATTAAT
*
75389 TTTTTA-ATTAATTAATTATATTA
1 TTTTTATATT-ATTATTTATATTA
*
75412 -TTTTATTATTATTATTTTTATTA
1 TTTTTA-TATTATTATTTATATTA
75435 TTTTTATATT-TTAT
1 TTTTTATATTATTAT
75449 GAAAGGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 9 0.28
23 15 0.47
24 8 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTATATTATTATTTATATTA
Done.