Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005235.1 Hibiscus syriacus cultivar Beakdansim tig00011849_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 149495
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7230 original size:36 final size:37
Alignment explanation
Indices: 7190--7261 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
7180 TCAATATCAC
* *
7190 TTGAGATTATTTTTCTT-AAAACAAATTTTGTCTCAT
1 TTGAGATCATTTTTCTTAAAAACAAATTTCGTCTCAT
*
7226 TTGAGATCGTTTTTCTTAAAAACAAATTTCGTCTCA
1 TTGAGATCATTTTTCTTAAAAACAAATTTCGTCTCA
7262 CTTGCGATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (37 bp):
TTGAGATCATTTTTCTTAAAAACAAATTTCGTCTCAT
Found at i:7759 original size:21 final size:21
Alignment explanation
Indices: 7709--7786 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
7699 TTTCTAAATG
*
7709 TTTTATTTCAATTTCA-TATTAT
1 TTTTATTT-AATTT-ATTACTAT
* *
7731 ATTAATTTAATTTATTACTAT
1 TTTTATTTAATTTATTACTAT
7752 TTTTATTTACATTTTATTACTTAT
1 TTTTATTTA-A-TTTATTAC-TAT
*
7776 TATTA-TTAATT
1 TTTTATTTAATT
7787 AGAATTTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 19 0.41
22 8 0.17
23 11 0.24
24 7 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATTTAATTTATTACTAT
Found at i:9500 original size:14 final size:14
Alignment explanation
Indices: 9481--9517 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9471 CGAGTCTGGA
*
9481 GAACATAAACAAGC
1 GAACATAAACAAAC
9495 GAACATAAACAAAC
1 GAACATAAACAAAC
*
9509 AAACATAAA
1 GAACATAAA
9518 TGAACAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (14 bp):
GAACATAAACAAAC
Found at i:9523 original size:14 final size:14
Alignment explanation
Indices: 9482--9531 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9472 GAGTCTGGAG
* *
9482 AACATAAACAAGCG
1 AACATAAACAAACA
9496 AACATAAACAAACA
1 AACATAAACAAACA
**
9510 AACATAAATGAACA
1 AACATAAACAAACA
*
9524 AACCTAAA
1 AACATAAA
9532 GAAATGATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.64, C:0.20, G:0.06, T:0.10
Consensus pattern (14 bp):
AACATAAACAAACA
Found at i:11323 original size:411 final size:410
Alignment explanation
Indices: 10541--11360 Score: 1313
Period size: 411 Copynumber: 2.0 Consensus size: 410
10531 AAGCATCCGT
* * *
10541 CAAAAAAATCCTCTCAAGAGTTCGGTACTTTGGGATAAACTTTACAGCTGCAAACAGTTTGGTAG
1 CAAAAAAATCCTCTCAAGAGTTCGGTACTTTGAGATAAACTTTACAGCTGCAAACAGTTTGGCAA
*
10606 CATCTGAAGTCCTTTAGACACAAACTCACCTCTACGCTTCGGAAATGTATCCAGTTGATTAATTT
66 CATCTGAAGTCCTTTAGACACAAACTCACCTCTACGCTTCGGAAATGTATCCAGTTGAATAATTT
*
10671 AGAGAGCTTGATATTTTGAGAGGAGCTTCACATCTACATACATTTTGGCAACATTTGAGAACTTC
131 AGAGAGCTTGATATTTTAAGAGGAGCTTCACATCTACATACATTTTGGCAACATTTGAGAACTTC
* * * *
10736 TCAACAGAAGCTTACCTCAGTGCTCCAAATCATATCAAGTCGATTTATTTAGGAACATTCATGTT
196 TCAACAGAAGCTTACATCAGTACTCCAAATCATATCAAATCGATTTATTCAGGAACATTCATGTT
* * * *
10801 AATTATGCTTGAGGCATCTGACTTTATTTCTCGATTTTTTATCCTTTCCATGGCTGCCATGACTT
261 AATGATGCTTGAGGCATCTGACTTTATTTCTCGATTTTTTATCATTTCCATAGCTGCCACGACTT
*
10866 TGTAAAAAATCCAATTTTATCATTTTTAGCCCTATTTTTGTTCATTCACAAGCATCTTATAAGTA
326 TGTAAAAAATCCAATTTTATCATTTTGAGCCCTATTTTTGTTCATTCACAAGCATCTTATAAGTA
10931 GATCAACATAGTTCAAAAGG
391 GATCAACATAGTTCAAAAGG
* * *
10951 CAAATAAAATTCTCTCAAGAGTTCGGTACTTTGAGATAAGCTTTACAGCTGCAAACATTTTGGCA
1 CAAA-AAAATCCTCTCAAGAGTTCGGTACTTTGAGATAAACTTTACAGCTGCAAACAGTTTGGCA
* * *
11016 ACATCTGAAGTCCTTTCGACACAAACTCACCTCTACGCTTCGGGAATGTATCCATTTGAATAATT
65 ACATCTGAAGTCCTTTAGACACAAACTCACCTCTACGCTTCGGAAATGTATCCAGTTGAATAATT
* **
11081 TAGAGAG-TCTGATATTTTAAGAGGAGCTTCACATCTATATACATTTTGGCAACATTTGAGATTT
130 TAGAGAGCT-TGATATTTTAAGAGGAGCTTCACATCTACATACATTTTGGCAACATTTGAGAACT
*
11145 TCTCAACAGAAGCTTACATCAGTACTCCAAATCATATCAAATCGATTTATTCAGGAACGTTCATG
194 TCTCAACAGAAGCTTACATCAGTACTCCAAATCATATCAAATCGATTTATTCAGGAACATTCATG
* * *
11210 TTAATGATGCTTGAGGCATCTGACTTTATTTCTTGATTTTTTATCATTTCCATAGTTTCCACGAC
259 TTAATGATGCTTGAGGCATCTGACTTTATTTCTCGATTTTTTATCATTTCCATAGCTGCCACGAC
** *
11275 TTTGTAAAATTTCCAATTTTCTCATTTTCGAGCCTCT-TTTTT-TTCATTCACAAGCATCTTATA
324 TTTGTAAAAAATCCAATTTTATCATTTT-GAGCC-CTATTTTTGTTCATTCACAAGCATCTTATA
11338 AGTAGATCAACATAGTTCAAAAG
387 AGTAGATCAACATAGTTCAAAAG
11361 AAAACAAAAG
Statistics
Matches: 376, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
410 5 0.01
411 360 0.96
412 9 0.02
413 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (410 bp):
CAAAAAAATCCTCTCAAGAGTTCGGTACTTTGAGATAAACTTTACAGCTGCAAACAGTTTGGCAA
CATCTGAAGTCCTTTAGACACAAACTCACCTCTACGCTTCGGAAATGTATCCAGTTGAATAATTT
AGAGAGCTTGATATTTTAAGAGGAGCTTCACATCTACATACATTTTGGCAACATTTGAGAACTTC
TCAACAGAAGCTTACATCAGTACTCCAAATCATATCAAATCGATTTATTCAGGAACATTCATGTT
AATGATGCTTGAGGCATCTGACTTTATTTCTCGATTTTTTATCATTTCCATAGCTGCCACGACTT
TGTAAAAAATCCAATTTTATCATTTTGAGCCCTATTTTTGTTCATTCACAAGCATCTTATAAGTA
GATCAACATAGTTCAAAAGG
Found at i:14610 original size:44 final size:44
Alignment explanation
Indices: 14482--14951 Score: 257
Period size: 44 Copynumber: 10.7 Consensus size: 44
14472 ATTTCGTTCA
* * * *** * *
14482 ATTCTATCACAGAAGGAGGTGGATCAAAATTTTCATTTTACTCA
1 ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
* * * * * *
14526 AATCCATCGCATAA-GAAGTTGGATCAGCATCAACGTTTTGCTCG
1 ATTCCATCACAGAATG-AGGTGGATCAACATCAACATTTTGCTCG
* * *
14570 ATTCTATCACAGAATGAGGTAGATCAACATCAACTTTTTGCTCG
1 ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
** * * * * * * * *
14614 ATTATATCACAAAATGATGTAGATCAGCACCAACATTTCGTTCT
1 ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
*** *
14658 ATTCCATCACAGAA-GAAGGTGGATCAACATTTTCATTTTGCTCA
1 ATTCCATCACAGAATG-AGGTGGATCAACATCAACATTTTGCTCG
* * * * * * * *
14702 AATCCATCTC-GTAAGGAGTTGGATTAGCATAAACTTTTTGCTCG
1 ATTCCATCACAG-AATGAGGTGGATCAACATCAACATTTTGCTCG
* * * * * * *
14746 ATTCTATCACAGAATGAGGTAGATTAGCACCAACATTTCGTTCG
1 ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
* *** *
14790 ATTCCATCACAGAAGGAGAG-GGATCAACATTTTCATTTTGCTCA
1 ATTCCATCACAGAATGAG-GTGGATCAACATCAACATTTTGCTCG
* * * ** * *
14834 AATCCATCGCATAA-GAATTTGGATCAACATCAACTTTTTGCTCT
1 ATTCCATCACAGAATG-AGGTGGATCAACATCAACATTTTGCTCG
* * * * * * *
14878 ATTCTATCACAGAATAAGGTAGATCATCACCAACATTTCGTTCG
1 ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
* *
14922 ATTCCATCACAGAAGGAGGTGGACCAACAT
1 ATTCCATCACAGAATGAGGTGGATCAACAT
14952 TTTCATTTCG
Statistics
Matches: 309, Mismatches: 107, Indels: 20
0.71 0.25 0.05
Matches are distributed among these distances:
43 4 0.01
44 301 0.97
45 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (44 bp):
ATTCCATCACAGAATGAGGTGGATCAACATCAACATTTTGCTCG
Found at i:14859 original size:176 final size:176
Alignment explanation
Indices: 14472--14863 Score: 437
Period size: 176 Copynumber: 2.2 Consensus size: 176
14462 GAGAGAGAAT
* * * * *
14472 ATTTCGTTCAATTCTATCACAGAAGGAGGTGGATCAAAATTTTCATTTTACTCAAATCCATCGCA
1 ATTTCGCTCAAATCCATCACAGAAGAAGGTGGATCAACATTTTCATTTTACTCAAATCCATCGCA
* *
14537 TAAGAAGTTGGATCAGCATCAACGTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACATCA
66 TAAGAAGTTGGATCAGCATAAACGTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACACCA
* * * * *
14602 ACTTTTTGCTCGATTATATCACAAAATGATGTAGATCAGCACCAAC
131 ACATTTCGCTCGATTACATCACAAAAGGATGTAGATCAACACCAAC
* * * * * *
14648 ATTTCGTTCTATTCCATCACAGAAGAAGGTGGATCAACATTTTCATTTTGCTCAAATCCATCTCG
1 ATTTCGCTCAAATCCATCACAGAAGAAGGTGGATCAACATTTTCATTTTACTCAAATCCATCGCA
* * * * *
14713 TAAGGAGTTGGATTAGCATAAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATTAGCACCA
66 TAAGAAGTTGGATCAGCATAAACGTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACACCA
* * * ****
14778 ACATTTCGTTCGATTCCATCACAGAAGGA-G-AGGGATCAACATTTTC
131 ACATTTCGCTCGATTACATCACAAAAGGATGTA--GATCAACACCAAC
* * * **
14824 ATTTTGCTCAAATCCATCGCATAAGAATTTGGATCAACAT
1 ATTTCGCTCAAATCCATCACAGAAGAAGGTGGATCAACAT
14864 CAACTTTTTG
Statistics
Matches: 180, Mismatches: 34, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
174 1 0.01
175 1 0.01
176 178 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (176 bp):
ATTTCGCTCAAATCCATCACAGAAGAAGGTGGATCAACATTTTCATTTTACTCAAATCCATCGCA
TAAGAAGTTGGATCAGCATAAACGTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACACCA
ACATTTCGCTCGATTACATCACAAAAGGATGTAGATCAACACCAAC
Found at i:14997 original size:132 final size:132
Alignment explanation
Indices: 14591--14999 Score: 631
Period size: 132 Copynumber: 3.1 Consensus size: 132
14581 GAATGAGGTA
* * *
14591 GATCAACATCAACTTTTTGCTCGATTATATCACAAAATGATGTAGATCAGCACCAACATTTCGTT
1 GATCAACATCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATTTCGTT
* * * * *
14656 CTATTCCATCACAGAAGAAGGTGGATCAACATTTTCATTTTGCTCAAATCCATCTCGTAAGGAGT
66 CGATTCCATCACAGAAGGAGGTGGATCAACATTTTCATTTTGCTCAAATCCATCGCATAAGAAGT
14721 TG
131 TG
* * * *
14723 GATTAGCATAAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATTAGCACCAACATTTCGTT
1 GATCAACATCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATTTCGTT
*
14788 CGATTCCATCACAGAAGGAGAG-GGATCAACATTTTCATTTTGCTCAAATCCATCGCATAAGAAT
66 CGATTCCATCACAGAAGGAG-GTGGATCAACATTTTCATTTTGCTCAAATCCATCGCATAAGAAG
14852 TTG
130 TTG
* * *
14855 GATCAACATCAACTTTTTGCTCTATTCTATCACAGAATAAGGTAGATCATCACCAACATTTCGTT
1 GATCAACATCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATTTCGTT
* *
14920 CGATTCCATCACAGAAGGAGGTGGACCAACATTTTCATTTCGCTCAAATCCATCGCATAAGAAGT
66 CGATTCCATCACAGAAGGAGGTGGATCAACATTTTCATTTTGCTCAAATCCATCGCATAAGAAGT
14985 TG
131 TG
*
14987 GATCAGCATCAAC
1 GATCAACATCAAC
15000 GTTGTTTTCG
Statistics
Matches: 251, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 249 0.99
133 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (132 bp):
GATCAACATCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATTTCGTT
CGATTCCATCACAGAAGGAGGTGGATCAACATTTTCATTTTGCTCAAATCCATCGCATAAGAAGT
TG
Found at i:16454 original size:3 final size:3
Alignment explanation
Indices: 16385--16437 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
16375 TCTACAAAAA
* * * *
16385 TAT TAA TAT TAA TAT TAAT TAT TAT TAT TGT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16431 TAT TAT T
1 TAT TAT T
16438 TTTTTAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:21749 original size:15 final size:15
Alignment explanation
Indices: 21727--21761 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21717 ATATCTTTTT
21727 ATTT-AATAAAAATA
1 ATTTAAATAAAAATA
*
21741 TTTTAAATAAAAATA
1 ATTTAAATAAAAATA
21756 ATTTAA
1 ATTTAA
21762 TGTACAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAATAAAAATA
Found at i:31556 original size:18 final size:16
Alignment explanation
Indices: 31513--31557 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
31503 GGAGATGTGA
31513 GAGTTGAGAGTGAGAG
1 GAGTTGAGAGTGAGAG
31529 GAGATGTGAGAGTTGAGAG
1 GAG-T-TGAGAG-TGAGAG
31548 TGAGTTGAGA
1 -GAGTTGAGA
31558 AGCTTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 11 0.44
19 7 0.28
20 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (16 bp):
GAGTTGAGAGTGAGAG
Found at i:31557 original size:25 final size:25
Alignment explanation
Indices: 31498--31551 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
31488 CTTTGTGTGT
31498 TGAGAGGAGATGTGAGAGTTGAGAG
1 TGAGAGGAGATGTGAGAGTTGAGAG
31523 TGAGAGGAGATGTGAGAGTTGAGAG
1 TGAGAGGAGATGTGAGAGTTGAGAG
31548 TGAG
1 TGAG
31552 TTGAGAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.48, T:0.20
Consensus pattern (25 bp):
TGAGAGGAGATGTGAGAGTTGAGAG
Found at i:37328 original size:11 final size:11
Alignment explanation
Indices: 37306--37336 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
37296 CAAAAATATT
37306 ACATTCTTCATA
1 ACATT-TTCATA
37318 ACATTTTCATA
1 ACATTTTCATA
37329 ACATTTTC
1 ACATTTTC
37337 GGTTTAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (11 bp):
ACATTTTCATA
Found at i:37583 original size:20 final size:20
Alignment explanation
Indices: 37560--37601 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
37550 TTAGATAGAA
37560 TCCCTATATTTCAGATAAAT
1 TCCCTATATTTCAGATAAAT
37580 TCCCTATATTTCAGATAAAT
1 TCCCTATATTTCAGATAAAT
37600 TC
1 TC
37602 TTATAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (20 bp):
TCCCTATATTTCAGATAAAT
Found at i:38553 original size:34 final size:33
Alignment explanation
Indices: 38481--38577 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
38471 TTTTCCCTAC
* *
38481 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
38513 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
38547 TTTATTAGTGTTATTATATATATATATATAT
1 TTTATTAATTTTATTATATATGTATATATAT
38578 ATATTTATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 20 0.38
33 5 0.09
34 28 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:38725 original size:16 final size:18
Alignment explanation
Indices: 38704--38742 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
38694 TTTACTAATT
38704 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
38720 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
38738 TATTT
1 TATTT
38743 TTATATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:41953 original size:22 final size:22
Alignment explanation
Indices: 41930--41991 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
41920 CAAAAAGGGC
41930 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
41953 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
41974 AAAAAGAAAGAATAAAAA
1 AAAAAGAAA-AA-AAAAA
41992 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:42626 original size:22 final size:22
Alignment explanation
Indices: 42598--42641 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42588 AGCTACCCCA
42598 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
42620 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
42642 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:43099 original size:18 final size:18
Alignment explanation
Indices: 43076--43111 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43066 TCAACATCAA
*
43076 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
43094 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
43112 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:43592 original size:36 final size:36
Alignment explanation
Indices: 43545--43649 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
43535 GTGCTCACCA
*
43545 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
43581 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAAT
* * *
43618 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
43650 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:43639 original size:37 final size:37
Alignment explanation
Indices: 43545--43649 Score: 167
Period size: 37 Copynumber: 2.9 Consensus size: 37
43535 GTGCTCACCA
*
43545 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAAT
43581 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAAT
* * *
43618 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
43650 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 31 0.48
37 33 0.52
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAAT
Found at i:43739 original size:102 final size:102
Alignment explanation
Indices: 43563--43954 Score: 635
Period size: 102 Copynumber: 3.9 Consensus size: 102
43553 CTTGAGACAG
** * *
43563 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATTTT-TCTCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATTTTGTCTCCC
43627 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
43665 TTTCCCTTGAAATGAGTTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
43730 TGAGACAGTTTCTCTTTAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
43767 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
43832 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
43869 TTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
43933 TGAGACAGCTTATCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
43955 CAAAACCTTT
Statistics
Matches: 271, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
101 42 0.15
102 229 0.85
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:43740 original size:37 final size:37
Alignment explanation
Indices: 43681--43751 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
43671 TTGAAATGAG
* *
43681 TTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* * *
43718 TTTTTTCTCCCTTGAGACAGTTTCTCTTTAAACA
1 TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
43752 TAAACATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (37 bp):
TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:43834 original size:37 final size:37
Alignment explanation
Indices: 43767--43853 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
43757 ATTGAAAACA
** * *
43767 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
43803 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
43840 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
43854 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:43913 original size:204 final size:203
Alignment explanation
Indices: 43563--44027 Score: 653
Period size: 204 Copynumber: 2.3 Consensus size: 203
43553 CTTGAGACAG
43563 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATTTTTCTCCCT
* * * *
43628 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTATCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCATCTCTCT
* * * * *
43693 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTTAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACATAAACA
43758 TTGAAAACA
195 TTGAAAACA
** * *
43767 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATTTTGTCTCCC
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATTTT-TCTCCC
*
43831 TTGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTC
65 TTGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCATCTCTC
*
43896 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACACAAAAC
130 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACA-TAAA-
* * ***
43961 CTTTGAGATTG
193 CATTGAAAACA
* * * * *
43972 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAAT
44028 CTTTGAATTT
Statistics
Matches: 229, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
203 41 0.18
204 135 0.59
205 48 0.21
207 5 0.02
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAATTTTTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCATCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACATAAACAT
TGAAAACA
Found at i:43923 original size:36 final size:36
Alignment explanation
Indices: 43868--43937 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
43858 CATTGAAAAC
** *
43868 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
* *
43904 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGA
43938 CAGCTTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
Found at i:44004 original size:67 final size:67
Alignment explanation
Indices: 43896--44033 Score: 213
Period size: 67 Copynumber: 2.1 Consensus size: 67
43886 TTCGTCTCTC
* *
43896 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACACAAAAC
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAAC
43961 CT
66 CT
** * * *
43963 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAAC
44028 CT
66 CT
44030 TTGA
1 TTGA
44034 ATTTATCCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (67 bp):
TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAAC
CT
Found at i:44052 original size:67 final size:67
Alignment explanation
Indices: 43908--44054 Score: 199
Period size: 67 Copynumber: 2.2 Consensus size: 67
43898 GAGATAATTT
*
43908 CCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTATCTTGAAACACAAAACCTTTGAGATTGT
1 CCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAACCTTTGAGATTGT
*
43973 TT
66 TC
* * * *
43975 CCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-ATT-T
1 CCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAACCTTTGAGATTGT
44038 ATCC
66 -T-C
*
44042 CCCTTAAAACAAA
1 CCCTTGAAACAAA
44055 ATTTCATTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 4 0.06
67 65 0.93
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (67 bp):
CCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTATCTTGAAACACAAAACCTTTGAGATTGT
TC
Found at i:45263 original size:105 final size:105
Alignment explanation
Indices: 44888--45958 Score: 1539
Period size: 105 Copynumber: 10.3 Consensus size: 105
44878 GCCATCCGCG
* * * * * *
44888 ATTTCAACTCCACGAC-AGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTTACAACGA
1 ATTTCAACTTCACAACGA-AGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * * *
44952 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
44997 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
45062 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAATCTCAGAGCCA
*
45104 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45169 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
45209 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45274 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
45314 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45379 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
45414 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
45479 ACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
45519 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45584 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
45619 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
45684 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
45724 AGTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
45789 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
45824 ATTTCAACTTCACAACGAAGGATA-TGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
45888 ACGGCTGGTTGTCAACAAACAATTTCCCGTTC-CAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
* *
45928 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
45959 TGGAACAATG
Statistics
Matches: 883, Mismatches: 59, Indels: 44
0.90 0.06 0.04
Matches are distributed among these distances:
99 51 0.06
100 208 0.24
101 12 0.01
102 9 0.01
103 9 0.01
104 39 0.04
105 377 0.43
106 57 0.06
107 99 0.11
109 21 0.02
110 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:45502 original size:205 final size:205
Alignment explanation
Indices: 44888--45958 Score: 1610
Period size: 205 Copynumber: 5.2 Consensus size: 205
44878 GCCATCCGCG
* * * * * *
44888 ATTTCAACTCCACGAC-AGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTTACAACGA
1 ATTTCAACTTCACAACGA-AGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
44952 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
62 AGGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAG
* *
45017 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
121 GATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAAC
* *
45082 AATTTTCCCAATTTCAGAGCCA
185 AACTTT-CCAATCTCAGAGCCA
*
45104 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
45169 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAATGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
45234 TGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTT
45299 CCAATCTCAGAGCCA
191 CCAATCTCAGAGCCA
45314 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45379 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
45444 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAAT
45509 CTCAGAGCCA
196 CTCAGAGCCA
45519 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
45584 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
45649 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAAT
*
45714 CCCAGAGCCA
196 CTCAGAGCCA
* *
45724 AGTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
45789 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATA-TGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * **
45853 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTTCCAA
45917 T-TCCAGAGCCA
195 TCT-CAGAGCCA
* *
45928 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
45959 TGGAACAATG
Statistics
Matches: 806, Mismatches: 45, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
204 90 0.11
205 436 0.54
206 2 0.00
207 1 0.00
208 2 0.00
209 2 0.00
210 95 0.12
211 9 0.01
212 97 0.12
213 48 0.06
214 3 0.00
216 20 0.02
217 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:45545 original size:310 final size:312
Alignment explanation
Indices: 44888--45958 Score: 1560
Period size: 310 Copynumber: 3.4 Consensus size: 312
44878 GCCATCCGCG
* * * *
44888 ATTTCAACTCCACGAC-AGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTTACAACGA
1 ATTTCAACTTCACAACGA-AGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGA
* * *
44952 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
62 AGGGACCGCTGCTTGTCAACAAACAATTTC-CAA-TTCAGAGCCAATTTCAACTTCACAACGAAG
* *
45017 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
125 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAAC
*
45082 AATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
189 AACTTT--CAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
45147 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
251 AGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
* ** **
45209 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
45274 ACCGCTGCTTGTCAAC-AACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 ACCGCTGCTTGTCAACAAACAA-TTTCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
45338 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
*
45401 TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAAC
194 TCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
45465 TTCACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
259 TTCACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
* *
45519 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
*
45584 ACCGCTGCTTGTCAAC-AA-AATTT-C-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * *
45645 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-T
* * * *
45710 CAATCCCAGAGCCAAGTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAAC
195 CAAT-TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* **
45775 TTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT-C-AT-TCAGATTCA
259 TTCACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
*
45824 ATTTCAACTTCACAACGAAGGATA-TGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * ** * *
45888 ACGGCTGGTTGTCAACAAACAATTTCCCGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATAT
66 ACCGCTGCTTGTCAACAAACAATTTCCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATAT
45953 TGGACT
130 TGGACT
45959 TGGAACAATG
Statistics
Matches: 696, Mismatches: 41, Indels: 38
0.90 0.05 0.05
Matches are distributed among these distances:
304 51 0.07
305 122 0.18
306 11 0.02
307 5 0.01
308 9 0.01
309 42 0.06
310 278 0.40
311 1 0.00
312 1 0.00
314 3 0.00
315 2 0.00
316 3 0.00
317 96 0.14
318 48 0.07
319 3 0.00
321 20 0.03
322 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (312 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
AATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCA
Found at i:47004 original size:34 final size:33
Alignment explanation
Indices: 46932--47028 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
46922 TTTTCCCTAC
* *
46932 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
46964 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
46998 TTTATTAGTGTTATTATATATATATATATAT
1 TTTATTAATTTTATTATATATGTATATATAT
47029 ATATATTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 20 0.38
33 5 0.09
34 28 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:47177 original size:16 final size:18
Alignment explanation
Indices: 47156--47194 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
47146 TTTACTAATT
47156 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
47172 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
47190 TATTT
1 TATTT
47195 TTATATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:55163 original size:17 final size:17
Alignment explanation
Indices: 55138--55176 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
55128 TTAAATATTA
*
55138 TTTTA-AATAATTACAC
1 TTTTACAATAATAACAC
*
55154 TTTTACAATAATAACAT
1 TTTTACAATAATAACAC
55171 TTTTAC
1 TTTTAC
55177 GTCATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTACAATAATAACAC
Found at i:55359 original size:23 final size:20
Alignment explanation
Indices: 55319--55389 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
55309 GATTTGAATG
*
55319 CATGCAACCCTGTAGTGCATC
1 CATGC-ACCATGTAGTGCATC
55340 CATGCACC-TGCTACTAGTGCATC
1 CATGCACCATG----TAGTGCATC
*
55363 GATGCACCATGTAGTGCATC
1 CATGCACCATGTAGTGCATC
55383 CATGCAC
1 CATGCAC
55390 TCCATTTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
19 2 0.05
20 18 0.42
21 5 0.12
23 16 0.37
24 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (20 bp):
CATGCACCATGTAGTGCATC
Found at i:58004 original size:20 final size:18
Alignment explanation
Indices: 57979--58021 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
57969 AAGTTTGGTT
57979 TGAAAAATTCAATTTCTTAA
1 TGAAAAA-T-AATTTCTTAA
57999 TG-AAAATAATTTCTTAA
1 TGAAAAATAATTTCTTAA
58016 T-AAAAA
1 TGAAAAA
58022 AGGGGGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (18 bp):
TGAAAAATAATTTCTTAA
Found at i:58021 original size:17 final size:17
Alignment explanation
Indices: 57989--58021 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57979 TGAAAAATTC
*
57989 AATTTCTTAATGAAAAT
1 AATTTCTTAATAAAAAT
58006 AATTTCTTAATAAAAA
1 AATTTCTTAATAAAAA
58022 AGGGGGAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTCTTAATAAAAAT
Found at i:58086 original size:19 final size:19
Alignment explanation
Indices: 58062--58120 Score: 100
Period size: 19 Copynumber: 3.0 Consensus size: 19
58052 CAACAGTTGG
58062 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
58081 TAACAATTGATATCCTTTTGT
1 TAACAATTGATAT-CTTTT-T
58102 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
58121 CATTAAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.37
20 10 0.26
21 14 0.37
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:66589 original size:21 final size:21
Alignment explanation
Indices: 66573--66690 Score: 114
Period size: 21 Copynumber: 5.7 Consensus size: 21
66563 GCGTTGCATT
66573 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
66594 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
66614 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
66635 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
66655 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
66676 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
66691 CTACAATGTC
Statistics
Matches: 71, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 28 0.39
21 43 0.61
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:66614 original size:41 final size:41
Alignment explanation
Indices: 66569--66687 Score: 220
Period size: 41 Copynumber: 2.9 Consensus size: 41
66559 ATTCGCGTTG
66569 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
66610 CATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
66651 CATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
66688 AGTCTACAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:66619 original size:20 final size:20
Alignment explanation
Indices: 66594--66666 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
66584 TAGTTGAAAA
66594 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
66614 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
66635 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
66655 TTGCGTTGCGAT
1 TCGCGTTGCGAT
66667 AGTTGAAAAT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:66734 original size:22 final size:22
Alignment explanation
Indices: 66679--66755 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
66669 TTGAAAATCG
*
66679 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
*
66700 CATTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
66722 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
66744 CGTTGCGATAGT
1 CGTTGCGATAGT
66756 AAAAAAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 16 0.33
22 32 0.67
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:66843 original size:6 final size:6
Alignment explanation
Indices: 66832--66869 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
66822 GACACGTATT
66832 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
66870 CGAGACGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:67515 original size:22 final size:21
Alignment explanation
Indices: 67487--67580 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 21
67477 AATTTGGGAA
67487 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAGACT
* * *
67509 ATCGCAACGCGATTTTCA-ACT
1 ATCGCAACGCAACTGT-AGACT
* * **
67530 ATCGCAACG-AA-TTTGGAAA
1 ATCGCAACGCAACTGTAGACT
*
67549 AGCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAGACT
67571 ATCGCAACGC
1 ATCGCAACGC
67581 GAAATGGAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
19 12 0.22
20 1 0.02
21 19 0.35
22 22 0.41
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCAACTGTAGACT
Found at i:67596 original size:20 final size:20
Alignment explanation
Indices: 67571--67795 Score: 189
Period size: 20 Copynumber: 11.4 Consensus size: 20
67561 ACTGTAGACT
67571 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
67591 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
**
67611 ATCGCAA--CG---T-GATT
1 ATCGCAACGCGAAATGGAAA
* *
67625 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-ATGGAAA
* **
67644 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
*
67666 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
67686 ATCGCAACGCTATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
67707 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
67727 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
67747 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
67767 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
67787 ATCGCAACG
1 ATCGCAACG
67796 TGATTTTCAA
Statistics
Matches: 165, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
14 10 0.06
15 1 0.01
18 2 0.01
19 8 0.05
20 110 0.67
21 17 0.10
22 17 0.10
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:67609 original size:62 final size:62
Alignment explanation
Indices: 67469--67619 Score: 178
Period size: 62 Copynumber: 2.4 Consensus size: 62
67459 CAACGAATTT
** * * ** * *
67469 TCGCAACGAATTTGGGAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAACTA
1 TCGCAACGAAAATGGAAAAGCGCAACGACAACTGTAGACTATCGCAACGCGAAATGCAACAA
** *
67531 TCGCAACGAATTTGGAAAAGCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAA-AA
1 TCGCAACGAAAATGGAAAAGCGCAACGACAACTGTAGACTATCGCAACGCGAAATGCAACAA
*
67592 TCGCAACGCAAAATGGAAAATCGCAACG
1 TCGCAACG-AAAATGGAAAAGCGCAACG
67620 TGATTTTCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 9 0.12
62 69 0.88
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (62 bp):
TCGCAACGAAAATGGAAAAGCGCAACGACAACTGTAGACTATCGCAACGCGAAATGCAACAA
Found at i:67813 original size:21 final size:21
Alignment explanation
Indices: 67787--67840 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
67777 GAAATGGAAA
*
67787 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
67808 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
67829 ATCGCAACGCGA
1 ATCGCAACGCGA
67841 AATACAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:75857 original size:17 final size:17
Alignment explanation
Indices: 75832--75873 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
75822 TCATTTTGTC
75832 AAACAAAAT-TGAAAAAA
1 AAACAAAATAT-AAAAAA
*
75849 AAACTAAATATAAAAAA
1 AAACAAAATATAAAAAA
75866 AAATCAAA
1 AAA-CAAA
75874 TACTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (17 bp):
AAACAAAATATAAAAAA
Found at i:97331 original size:37 final size:37
Alignment explanation
Indices: 97281--97438 Score: 262
Period size: 37 Copynumber: 4.3 Consensus size: 37
97271 TAGTGAAACA
*
97281 AAGCAAATCATCTATAAGCCTTCATAGAAGAGTAGTG
1 AAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
* **
97318 AAGCAAATTATCTATAAGCCTTCATGGAAGAGTAGTG
1 AAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
*
97355 AAGCAAATCATCTATAAGCCTTCACGGAAGAGTAGTG
1 AAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
*
97392 AAGTAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
1 AAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
97429 AAGCAAATCA
1 AAGCAAATCA
97439 AGATCGAGTC
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 114 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (37 bp):
AAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGTG
Found at i:97527 original size:55 final size:55
Alignment explanation
Indices: 97442--98236 Score: 902
Period size: 55 Copynumber: 14.5 Consensus size: 55
97432 CAAATCAAGA
* * * * * *
97442 TCGAG-TCATATACTCCATAAAAGAATAGGGAACAAACACG-TTTCTTGAAGATTGT
1 TCGAGTTC-TATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTC-AGAAGATTGT
* * * * **
97497 TCAAGTTCAATGCTCCCTGAAAGAATAGGGAACGAACCC-TTTT-ATTGAAGATAAT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCA--GAAGATTGT
*** * * * * *
97552 TCGAGTTCTATACTTTTTAAAAGAATATGGAGTGAACACGTTTGCTA-AAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTC-AGAAGATTGT
* * * * * *
97607 TTGAGTCCTATACTCCCTGAAAGAATAGGGAGTGGACCCATTTTCAGAAGATCGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* **
97662 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGTGAACAAGTTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* *
97717 TCGAGTTCTATACTCCCTGAAATAATAGGGAGAGAACCCGTTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
*
97772 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* * ** ** * *
97827 TCGAGTTTTATACTCCCTGAAAGAATAGGGAGTGGTCCTATTTTCAAAAGATTAT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* *
97882 TCGAGTTCTATACTCCCTGAAATAATAGGGAGCGAACCCATTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* * * * * *
97937 TTGAGTTTTGTACTCCCTAAAAGAATAGGGAGCGAACCTGTTTTTAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* *
97992 TTGAGTTCTATACTCCTTGAAAGAATAGGGAGC-ATACCCGTTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGA-ACCCGTTTTCAGAAGATTGT
* * * *
98047 TCGACTTTTATACTCCCTGAAAGAATAGGGAGCGGACCCATTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
* *
98102 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACTCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTT-TCAGAAGATTGT
* * * * * *
98157 TAGAATTCTATACTCCCTGAAAGAATATGGAGCGAACCCATTTTCTGAATATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
**
98212 TCGAGTTCTATACTCTTTGAAAGAA
1 TCGAGTTCTATACTCCCTGAAAGAA
98237 AAGGAAGTAG
Statistics
Matches: 627, Mismatches: 101, Indels: 24
0.83 0.13 0.03
Matches are distributed among these distances:
54 3 0.00
55 617 0.98
56 6 0.01
58 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT
Found at i:106633 original size:2 final size:2
Alignment explanation
Indices: 106626--106660 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
106616 GTACTTCCTC
106626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
106661 CACAAACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:116844 original size:3 final size:3
Alignment explanation
Indices: 116838--116887 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
116828 AAATATAATA
* *
116838 ATT ATT ATT ATT AAT A-T AAT ATAT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A-TT ATT
116884 ATT A
1 ATT A
116888 AATAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:116854 original size:21 final size:21
Alignment explanation
Indices: 116829--116887 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
116819 ATTTTTCATA
116829 AATATAATAATTATTATTATT
1 AATATAATAATTATTATTATT
116850 AATATAAT-ATATATTATTATT
1 AATATAATAAT-TATTATTATT
* *
116871 -AT-TATTATTTATTATTA
1 AATATAATAATTATTATTA
116888 AATAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.32
20 5 0.15
21 18 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATAATAATTATTATTATT
Found at i:118686 original size:2 final size:2
Alignment explanation
Indices: 118679--118711 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
118669 ATAAATAATT
118679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118712 TAATATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118715 original size:146 final size:141
Alignment explanation
Indices: 118438--118720 Score: 340
Period size: 146 Copynumber: 2.0 Consensus size: 141
118428 AAAACTAATC
* * *
118438 ATATTTTCATATTTATTTATTTATTTTATTAAGAAAATGACTGTCTTAAAGCACCTAGAAGTCTT
1 ATATTTTAATATTTATTTATTTATTTTATTAAGAAAATGACTGTCTTAAAGCACCTAGAAGCCCT
* * *
118503 TTTCTGATATTTTTAAATAAATAAATATCCTACTTTTAAATTATATATATATTAATCTATTTTTA
66 TTTCTGATATTTCTAAATAAATAAATA--C-ACTTTTAAATTATATATATATTAATATATTATTA
*
118568 ATTTTTTTAGATAA
128 ATATTTTTAGATAA
*
118582 ATATTTTAATATTTATTTATTT-TTTAATATTAAATAAAAT-AGCTGTCTTAAAGCACCTAGAAG
1 ATATTTTAATATTTATTTATTTATTT--TATT-AAGAAAATGA-CTGTCTTAAAGCACCTAGAAG
* *
118645 CCCTTTTCTGATATTTCTAAGTAAATAAATA-A-TTTATATATATATATATATATATATATATAT
62 CCCTTTTCTGATATTTCTAAATAAATAAATACACTTT-TAAAT-TATATATATAT-TA-ATATAT
118708 ATATTAATATTTT
123 -TATTAATATTTT
118721 CTTAAAATTA
Statistics
Matches: 120, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
141 3 0.03
142 5 0.04
143 14 0.12
144 23 0.19
145 10 0.08
146 65 0.54
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (141 bp):
ATATTTTAATATTTATTTATTTATTTTATTAAGAAAATGACTGTCTTAAAGCACCTAGAAGCCCT
TTTCTGATATTTCTAAATAAATAAATACACTTTTAAATTATATATATATTAATATATTATTAATA
TTTTTAGATAA
Found at i:134325 original size:12 final size:13
Alignment explanation
Indices: 134302--134335 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
134292 TAGTTTACAG
134302 ACTTTTTATCTTTT
1 ACTTTTT-TCTTTT
134316 -CTTTTTTCTTTT
1 ACTTTTTTCTTTT
134328 ACTTTTTT
1 ACTTTTTT
134336 ACATTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
ACTTTTTTCTTTT
Found at i:138930 original size:65 final size:64
Alignment explanation
Indices: 138813--139007 Score: 184
Period size: 65 Copynumber: 3.0 Consensus size: 64
138803 TTTCAAGTAA
* * * * *
138813 GTGTACCGATGCATAAATCAATGCATCGATGCAC-CCTTGTTTTAATT-GAACATCGAATGGCTT
1 GTGTACCGATGCAT-AAGCCATGCATCGATGCACTCC-TGTATT-ATTAAAACATCGAATGGATT
138876 TT
63 TT
* *
138878 GTGTACCGATGCACATA-CCATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTT
1 GTGTACCGATGCATA-AGCCATGCATCGATGCACTCC-TGTATTATTAAAACATCGAATGGATTT
138942 T
64 T
* * * *
138943 ATGCACTGATGCATAAGCCATGCATCGATGCACT-CTGGCTATT-TTAAAAACATCGAATGCATT
1 GTGTACCGATGCATAAGCCATGCATCGATGCACTCCT-G-TATTATT-AAAACATCGAATGGATT
139006 TT
63 TT
139008 ATGCATCGAT
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 24 0.22
65 85 0.77
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (64 bp):
GTGTACCGATGCATAAGCCATGCATCGATGCACTCCTGTATTATTAAAACATCGAATGGATTTT
Found at i:140680 original size:12 final size:12
Alignment explanation
Indices: 140663--140689 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
140653 GAAAAGAGAT
140663 GAGCCAAAGAAG
1 GAGCCAAAGAAG
140675 GAGCCAAAGAAG
1 GAGCCAAAGAAG
140687 GAG
1 GAG
140690 ACGGAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGCCAAAGAAG
Found at i:144974 original size:29 final size:29
Alignment explanation
Indices: 144932--144989 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
144922 TGCCAATACC
144932 ACTAGAGTTAATTAATTTAGCATTTTGAG
1 ACTAGAGTTAATTAATTTAGCATTTTGAG
144961 ACTAGAGTTAATTAATTTAGCATTTTGAG
1 ACTAGAGTTAATTAATTTAGCATTTTGAG
144990 TGTTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (29 bp):
ACTAGAGTTAATTAATTTAGCATTTTGAG
Found at i:145077 original size:23 final size:22
Alignment explanation
Indices: 145047--145122 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
145037 CACTAGGTAG
145047 TGCATCGATACATCCTTTGAATA
1 TGCATCGATACATCC-TTGAATA
* *
145070 TGCATCGATACAT-CATGAAGA
1 TGCATCGATACATCCTTGAATA
* * *
145091 TGCACCGATGCATTCCTTGAATG
1 TGCATCGATACA-TCCTTGAATA
145114 TGCATCGAT
1 TGCATCGAT
145123 GCACTCTGCC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.35
22 2 0.05
23 26 0.60
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (22 bp):
TGCATCGATACATCCTTGAATA
Found at i:145615 original size:19 final size:19
Alignment explanation
Indices: 145591--145635 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
145581 TTTAATTATG
145591 TTGATTTAAAAATCACAAA
1 TTGATTTAAAAATCACAAA
* *
145610 TTGATTTGAAAATCACACA
1 TTGATTTAAAAATCACAAA
145629 TTGATTT
1 TTGATTT
145636 TTCAAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (19 bp):
TTGATTTAAAAATCACAAA
Found at i:147954 original size:64 final size:65
Alignment explanation
Indices: 147847--147985 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 65
147837 GCTTTTGTTT
147847 ACCGATGCACATACCATGCATCGATGCCTCCATGTATTATT-AAAACATCGAATTG-ATTTTATG
1 ACCGATGCACATACCATGCATCGATGCCTCCATGTATTATTAAAAACATCGAA-TGCATTTTATG
147910 C
65 C
*
147911 ACCGATGCATA-AGCCATGCATCGATGCACT-C-TGGCTATT-TTAAAAACATCGAATGCATTTT
1 ACCGATGCACATA-CCATGCATCGATGC-CTCCAT-G-TATTATTAAAAACATCGAATGCATTTT
147972 ATGC
62 ATGC
*
147976 ATCGATGCAC
1 ACCGATGCAC
147986 CCTTAGTGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
63 2 0.03
64 30 0.45
65 34 0.52
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (65 bp):
ACCGATGCACATACCATGCATCGATGCCTCCATGTATTATTAAAAACATCGAATGCATTTTATGC
Done.