Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 124 of 171
Found at i:39460873 original size:21 final size:21
Alignment explanation
Indices: 39460847--39460914 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
39460837 TTGGTTCAAA
39460847 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
39460868 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
39460889 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
39460911 TGGG
1 TGGG
39460915 CTTAATGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:39461317 original size:11 final size:11
Alignment explanation
Indices: 39461284--39461358 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
39461274 AAGTGTGATT
*
39461284 AAAAGAGGAAG
1 AAAAGAGAAAG
*
39461295 AAAATAGAAAAG
1 AAAAGAG-AAAG
39461307 AAAAGAGAAAG
1 AAAAGAGAAAG
39461318 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
39461330 AATGAGAAAAAG
1 AA-AAGAGAAAG
39461342 AAAAGAGAAAG
1 AAAAGAGAAAG
*
39461353 GAAAGA
1 AAAAGA
39461359 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39461326 original size:23 final size:23
Alignment explanation
Indices: 39461284--39461356 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
39461274 AAGTGTGATT
*
39461284 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
39461307 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
39461330 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
39461354 AAA
1 AAA
39461357 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:39463129 original size:24 final size:23
Alignment explanation
Indices: 39463092--39463138 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
39463082 AACTATTCTT
39463092 TTTATCTTAATTTG-TTGTGACAA
1 TTTATCTTAATTTGCTT-TGACAA
*
39463115 TTTATTTTATATTTGCTTTGACAA
1 TTTATCTTA-ATTTGCTTTGACAA
39463139 ATTAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 11 0.52
25 2 0.10
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTATCTTAATTTGCTTTGACAA
Found at i:39468799 original size:20 final size:20
Alignment explanation
Indices: 39468774--39468812 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39468764 ATTTTTTAAT
*
39468774 GAATATTAGAAATGTGAAAC
1 GAATATTAGAAACGTGAAAC
*
39468794 GAATATTGGAAACGTGAAA
1 GAATATTAGAAACGTGAAA
39468813 GATAGCAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (20 bp):
GAATATTAGAAACGTGAAAC
Found at i:39475206 original size:20 final size:21
Alignment explanation
Indices: 39475170--39475220 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
39475160 ATTGGCATGG
*
39475170 TTTATATTAAATGTAAATA-GA
1 TTTA-ATTAAATGTAAAAATGA
39475191 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAA-ATGTAAAAATGA
39475212 -TTAATTAAA
1 TTTAATTAAA
39475221 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (21 bp):
TTTAATTAAATGTAAAAATGA
Found at i:39488663 original size:17 final size:17
Alignment explanation
Indices: 39488638--39488680 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
39488628 ATGCATCTCA
*
39488638 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTACAT
* *
39488655 TTTAGTTGTCGTTACAT
1 TTTAATTGTCATTACAT
*
39488672 TTTACTTGT
1 TTTAATTGT
39488681 TAGTTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTACAT
Found at i:39495621 original size:21 final size:21
Alignment explanation
Indices: 39495574--39495629 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
39495564 GTTGGGAAAG
*
39495574 TTCTATCGATACAAATATGAC
1 TTCTACCGATACAAATATGAC
* * * *
39495595 TACTACCGATGCAATTATTAC
1 TTCTACCGATACAAATATGAC
*
39495616 TTCTACCAATACAA
1 TTCTACCGATACAA
39495630 CAAACCCACG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAAATATGAC
Found at i:39496939 original size:16 final size:16
Alignment explanation
Indices: 39496915--39496946 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39496905 TCCTTACAAA
*
39496915 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
39496931 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
39496947 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:39500670 original size:21 final size:21
Alignment explanation
Indices: 39500646--39500700 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
39500636 TGGGAAAGTT
39500646 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * * ** *
39500667 CTACTGATGCAATTATTCCTT
1 CTACCGATACAAGTATGACTA
39500688 CTACCGATACAAG
1 CTACCGATACAAG
39500701 AAACTCAAGA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:39502177 original size:16 final size:16
Alignment explanation
Indices: 39502153--39502184 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39502143 TCCTTACAAA
*
39502153 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
39502169 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
39502185 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:39516865 original size:13 final size:13
Alignment explanation
Indices: 39516843--39516875 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39516833 TAGACATTTT
39516843 TTTTTC-TCTTTC
1 TTTTTCTTCTTTC
39516855 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
*
39516868 CTTTTCTT
1 TTTTTCTT
39516876 TAGAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:39518929 original size:25 final size:23
Alignment explanation
Indices: 39518807--39518994 Score: 136
Period size: 23 Copynumber: 8.1 Consensus size: 23
39518797 GGAAACAATA
39518807 AGCACACACAGTGC-AATCAGTAG
1 AGCACACACAGTGCTAATCAG-AG
* * * *
39518830 -GCGCACATAGCGCAAATCAGTAG
1 AGCACACACAGTGCTAATCAG-AG
* *
39518853 -GCACACGA-AGTGCGAAACAGTAG
1 AGCACAC-ACAGTGCTAATCAG-AG
* * * *
39518876 -GCATACAAAGTGCGAAACAGAG
1 AGCACACACAGTGCTAATCAGAG
* * *
39518898 AGTACACAAAGTACTAATCAGAG
1 AGCACACACAGTGCTAATCAGAG
39518921 AGCACACACAGTGCTAATAACAGAG
1 AGCACACACAGTGCTAAT--CAGAG
* *
39518946 AGCACGAGAC-GTGCTAAACAGAG
1 AGCAC-ACACAGTGCTAATCAGAG
39518969 AGCACACACAGTGCTAATCAGAG
1 AGCACACACAGTGCTAATCAGAG
39518992 AGC
1 AGC
39518995 GCGCTAGTGT
Statistics
Matches: 137, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.12
23 100 0.73
24 1 0.01
25 17 0.12
26 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
AGCACACACAGTGCTAATCAGAG
Found at i:39522419 original size:18 final size:18
Alignment explanation
Indices: 39522396--39522432 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39522386 AGTGCGTGGA
*
39522396 ATAAAAACATGGTTAGTG
1 ATAAAAACATGGTGAGTG
*
39522414 ATAAAAGCATGGTGAGTG
1 ATAAAAACATGGTGAGTG
39522432 A
1 A
39522433 AAGAGTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.24
Consensus pattern (18 bp):
ATAAAAACATGGTGAGTG
Found at i:39522714 original size:21 final size:19
Alignment explanation
Indices: 39522681--39522721 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
39522671 TGTTATTTTC
39522681 TCACTATTTTTCTACTATT
1 TCACTATTTTTCTACTATT
*
39522700 TCACTATTATATTCTATTATT
1 TCACTATT-T-TTCTACTATT
39522721 T
1 T
39522722 TATTGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (19 bp):
TCACTATTTTTCTACTATT
Found at i:39526168 original size:27 final size:27
Alignment explanation
Indices: 39526137--39526226 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
39526127 TAAAATACTT
*
39526137 CACAAAGGTCATT-CTTTCAGAATATGC
1 CACAAAGG-CATTCCTTTCAGAATACGC
* * *
39526164 CACAAAGACATTCCTTTCCATATTACGC
1 CACAAAGGCATTCCTTT-CAGAATACGC
* * *
39526192 CACAAAGGCATTCCTTTCAGAGTTCGT
1 CACAAAGGCATTCCTTTCAGAATACGC
39526219 CACAAAGG
1 CACAAAGG
39526227 GAGTTCATAG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.08
27 25 0.48
28 23 0.44
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (27 bp):
CACAAAGGCATTCCTTTCAGAATACGC
Found at i:39528729 original size:26 final size:26
Alignment explanation
Indices: 39528689--39528752 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
39528679 ACCCTTGGCT
39528689 TTTCACCTACT-AAAAACTCTTGATC
1 TTTCACCTACTAAAAAACTCTTGATC
*
39528714 TTTCATCTACTAAAAAACTCTTGATC
1 TTTCACCTACTAAAAAACTCTTGATC
39528740 TTTCACCTACTAA
1 TTTCACCTACTAA
39528753 CTACTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 10 0.28
26 26 0.72
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.38
Consensus pattern (26 bp):
TTTCACCTACTAAAAAACTCTTGATC
Found at i:39533316 original size:16 final size:16
Alignment explanation
Indices: 39533295--39533325 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39533285 ATAATGTGAA
39533295 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
39533311 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
39533326 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:39547279 original size:27 final size:27
Alignment explanation
Indices: 39547248--39547300 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39547238 TTAGAAGATT
*
39547248 AGATTTAGTTTCTGATTATTAGGAATC
1 AGATTTAATTTCTGATTATTAGGAATC
39547275 AGATTTAATTTCTGATTATTAGGAAT
1 AGATTTAATTTCTGATTATTAGGAAT
39547301 TAGCTATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (27 bp):
AGATTTAATTTCTGATTATTAGGAATC
Found at i:39551486 original size:18 final size:18
Alignment explanation
Indices: 39551451--39551493 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39551441 AATTTTAATT
* *
39551451 TAATTAAAAATGAGTGTG
1 TAATTAAAAACGAATGTG
*
39551469 TAATTAAATACGAATGTG
1 TAATTAAAAACGAATGTG
*
39551487 CAATTAA
1 TAATTAA
39551494 TGGCGAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (18 bp):
TAATTAAAAACGAATGTG
Found at i:39551766 original size:30 final size:30
Alignment explanation
Indices: 39551727--39552043 Score: 270
Period size: 30 Copynumber: 10.6 Consensus size: 30
39551717 TAAAGAATTT
* *
39551727 GGGGCTAAAATGTAATTTTGGAAAAATTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
*
39551757 GGGGTTAAAATGTAATTTTAGG-TAAGTTTA
1 GGGGTTAAAATGTAATTTT-GGAAAAGTTTA
* * * *
39551787 AGGGTTAAAATG-AATTTTGGGAAGGTTTG
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
* * *
39551816 GGGGTCAAATTTTAATTTT-GAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGA-AAAGTTTA
* * *
39551846 -GGGTTAAAATATGATTTT-TAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGA-AAAGTTTA
* *
39551875 GGGTTTAAAATGTGATTTT-GAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGA-AAAGTTTA
* * ** *
39551905 AGGGTCAAAATGCGATTGTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
** * *
39551935 AAGGTCAAAATGTAATTTTGGAAATGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
39551965 GGGGTCAAAATGTAATTTTGG-GAAGTTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAG-TTTA
* * * *
39551995 AGGGTAAAAATGTAATTTTGGAGAAGTTCA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
39552025 GGGGTTAAAATGTAATTTT
1 GGGGTTAAAATGTAATTTT
39552044 TAAGTAAAAT
Statistics
Matches: 238, Mismatches: 41, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.01
29 46 0.19
30 182 0.76
31 8 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:39553004 original size:13 final size:13
Alignment explanation
Indices: 39552988--39553021 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39552978 AACGTTTAGT
39552988 AATAAATAACAGC
1 AATAAATAACAGC
* *
39553001 AATAAATGATAGC
1 AATAAATAACAGC
39553014 AATAAATA
1 AATAAATA
39553022 TATTAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (13 bp):
AATAAATAACAGC
Found at i:39553217 original size:28 final size:29
Alignment explanation
Indices: 39553141--39553217 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 29
39553131 TTTTGATCTA
*
39553141 TGTTTTTCTTGTGTATTAATTTTGAATCAC
1 TGTTTTT-TTGTGTATTAATTTCGAATCAC
*
39553171 TGAGTCTTTTTTGCGTATTAATTTCGAATCAC
1 T--GT-TTTTTTGTGTATTAATTTCGAATCAC
39553203 TGTTTTTTT-TGTATT
1 TGTTTTTTTGTGTATT
39553218 GCTTGGAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.12
29 6 0.15
30 3 0.07
32 23 0.56
33 4 0.10
ACGTcount: A:0.18, C:0.10, G:0.14, T:0.57
Consensus pattern (29 bp):
TGTTTTTTTGTGTATTAATTTCGAATCAC
Found at i:39553988 original size:37 final size:37
Alignment explanation
Indices: 39553946--39554091 Score: 220
Period size: 37 Copynumber: 3.9 Consensus size: 37
39553936 AACTTCATCT
39553946 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGA
* *
39553983 TTTGGTCCACTTCTCTGTATCTTATTAGGAAGATGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGA
* * *
39554020 TTAGGTCCACTTCTTTGTATCTCATCAAGAAGATGGA
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGA
* * *
39554057 TTTGGTCCACTTCTTTGTCTCTCATTAGGAAGATG
1 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATG
39554092 ACCGTTTTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (37 bp):
TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGA
Found at i:39554329 original size:85 final size:85
Alignment explanation
Indices: 39554180--39554431 Score: 297
Period size: 85 Copynumber: 3.0 Consensus size: 85
39554170 CACTTCATTA
* * * * * * * *
39554180 ATTTAGTTTACTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTAATTTAATCCACTTCTCT
1 ATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTCT
*
39554245 GTATCTCATCAGGAAGACGG
66 GTATCTCATCAGGAAGACAG
* * * *
39554265 ATTTGGTTTACTTTTCTGTATTTCATCAGGAATATGACCTCTTTATTACTTTGACCCATTTCTCT
1 ATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTCT
* * *
39554330 ATATCTCATCAAGAAAACAG
66 GTATCTCATCAGGAAGACAG
* * * * * *
39554350 ATTTGGTCTACTTCTCTGAATCTCCTCAAGAAGATGACCTATTTATTGCTTTGACCCACTTCTCT
1 ATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTCT
*
39554415 GTATCTCATTAGGAAGA
66 GTATCTCATCAGGAAGA
39554432 TGGGGTTTGA
Statistics
Matches: 137, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 137 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (85 bp):
ATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTCT
GTATCTCATCAGGAAGACAG
Found at i:39554522 original size:293 final size:294
Alignment explanation
Indices: 39554037--39554633 Score: 774
Period size: 293 Copynumber: 2.0 Consensus size: 294
39554027 CACTTCTTTG
* ** * ** * *
39554037 TATCTCATCAAGAAGATGGATTTGGTCCACTTCTTTGTCTCTCATTAGGAAGATGACCGTTTTAT
1 TATCTCATCAAGAAAACAGATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCGTTTTAT
* * *
39554102 TACTTCGACCCACTTCTTTGTATCTCATCAAGAAGATAGGGGTTTGAATTTTCACTCTCATTAAG
66 TACTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTCTCACTCTCATTAAG
* * *
39554167 CTTCACTTCATTAATTTAGTTTACTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTAATTT
131 CTTCACTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTAATTT
* * ** * *
39554232 AATCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTTACTT-TTCTGTATTTCATCAGGA
196 AATCCACTTCTCTATATCTCATCAAGAAGACGGATTTGGTCCACTTCTT-TGTATCTCATCAAGA
* *
39554296 ATATGACCTCTTTATTACTTTGACCCA-TTTCTCTA
260 AGATGACCGCTTTATTACTTTGACCCACTTT-TCTA
* *
39554331 TATCTCATCAAGAAAACAGATTTGGTCTACTTCTCTGAATCTCCTCAAGAAGATGACC-TATTTA
1 TATCTCATCAAGAAAACAGATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCGT-TTTA
* * * * *
39554395 TTGCTTTGACCCACTTCTCTGTATCTCATTAGGAAGAT-GGGGTTTGAAGTCTCATTCGT-ATTG
65 TTACTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTCTCACTC-TCATT-
* * * * *
39554458 AA-CTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCACTTCATTAA
128 AAGCTTCACTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTAA
* *
39554522 TTTAATCCACTTCTCTATATCTCATCAAGAAGGCTGATTTGGTCCACTTCTTTGTATCTCATCAA
193 TTTAATCCACTTCTCTATATCTCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAA
*
39554587 GAAGATGACCGCTTTATTACTTTGACCCACTTTTCTG
258 GAAGATGACCGCTTTATTACTTTGACCCACTTTTCTA
39554624 TATCTCATCA
1 TATCTCATCA
39554634 GGAAGATCGG
Statistics
Matches: 261, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
293 168 0.64
294 93 0.36
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (294 bp):
TATCTCATCAAGAAAACAGATTTGGTCCACTTCTCTGAATCTCATCAAGAAGATGACCGTTTTAT
TACTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTCTCACTCTCATTAAG
CTTCACTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTAATTT
AATCCACTTCTCTATATCTCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAAGAA
GATGACCGCTTTATTACTTTGACCCACTTTTCTA
Found at i:39554617 original size:85 final size:85
Alignment explanation
Indices: 39554471--39554638 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 85
39554461 TTCGCTTCAT
* * *
39554471 TGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCACTTCATTAATTTAATCCACTTCT
1 TGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTAATTTAACCCACTTCT
39554536 CTATATCTCATCAAGAAGGC
66 CTATATCTCATCAAGAAGGC
* * * * *
39554556 TGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTTATTACTTTGACCCACTTTT
1 TGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTAATTTAACCCACTTCT
* *
39554621 CTGTATCTCATCAGGAAG
66 CTATATCTCATCAAGAAG
39554639 ATCGGCTTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (85 bp):
TGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTAATTTAACCCACTTCT
CTATATCTCATCAAGAAGGC
Found at i:39554735 original size:207 final size:208
Alignment explanation
Indices: 39554324--39555008 Score: 996
Period size: 208 Copynumber: 3.3 Consensus size: 208
39554314 TTTGACCCAT
** * * *
39554324 TTCTCTATATCTCATCAAGAAAACAGATTTGGTCTACTTCTCTGAATCTCCTCAAGAAGATGACC
1 TTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACC
** * *
39554389 TATTTATTGCTTTGACCCACTTCTCTGTATCTCATTAGGAAGATGGGGTTTGAAGTCTCATTCGT
66 GCTTTATTGCTTTGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGT
* * * *
39554454 ATTGAACTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGACCACTTCAT
131 ATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCAT
*
39554519 TAATTTAATCCAC
196 TGATTTAATCCAC
* *
39554532 TTCTCTATATCTCATCAAGAAGGCTGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACC
1 TTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACC
* * * *
39554597 GCTTTATTACTTTGACCCACTTTTCTGTATCTCATCAGGAAGAT-CGGCTTGAAGTCTCATTCAT
66 GCTTTATTGCTTTGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGT
* *
39554661 TTTGAGCTTCGCTTCATTGCTTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCAT
131 ATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCAT
39554726 TGATTTAATCCAC
196 TGATTTAATCCAC
* * * * * * *
39554739 TTCTCTATATCTCATTAGGAAGGCAAATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGGCT
1 TTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACC
*
39554804 GCTTTATTGCTTTGACCCACTTCTT-TGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTTG
66 GCTTTATTGCTTTGACCCACTT-TTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCG
* * *
39554868 TATTGAGCTTCGCTTCATTGATTTGGTGTACTTCTCTGTATCTCATCAAGAAGATGATTGCTTCA
130 TATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCA
39554933 TTGATTTAATCCAC
195 TTGATTTAATCCAC
* * * * * *
39554947 TTCTCTGTATCTCATCAGGAAGGAAGATTTGGTCCACCTCTTTGTATCTCATCAGGAAGATG
1 TTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
39555009 GGGTTTGAAG
Statistics
Matches: 427, Mismatches: 48, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
207 184 0.43
208 243 0.57
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (208 bp):
TTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACC
GCTTTATTGCTTTGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGT
ATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCAT
TGATTTAATCCAC
Found at i:39554824 original size:85 final size:85
Alignment explanation
Indices: 39554681--39554845 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 85
39554671 GCTTCATTGC
* * *
39554681 TTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTA
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAACCCACTTCTCTA
*
39554746 TATCTCATTAGGAAGGCAAA
66 TATCTCATCAGGAAGGCAAA
* * * * * * *
39554766 TTTGGTCCACTTCTCTGTATCTCATTAGGAAGATG-GCTGCTTTATTGCTTTGACCCACTTCTTT
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATC-GCTTCATTGATTTAACCCACTTCTCT
*
39554830 GTATCTCATCAGGAAG
65 ATATCTCATCAGGAAG
39554846 ATGGGGTTTG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 66 0.99
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAACCCACTTCTCTA
TATCTCATCAGGAAGGCAAA
Found at i:39554991 original size:160 final size:160
Alignment explanation
Indices: 39554820--39555168 Score: 574
Period size: 160 Copynumber: 2.2 Consensus size: 160
39554810 TTGCTTTGAC
* *
39554820 CCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTTGTATTGAGCTTCGCTTCA
1 CCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCA
* *
39554885 TTGATTTGGTGTACTTCTCTGTATCTCATCAAGAAGATGATTGCTTCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTC
39554950 TCTGTATCTCATCAGGAAGGA-AGATTTGGT
131 TCTGTATCTCATCAGGAAGGAGA-ATTTGGT
*
39554980 CCACCTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCA
1 CCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCA
* * *
39555045 TTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCTCTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTC
* *
39555110 TTTGTATCTCATCAGGAAGGCGAATTTGGT
131 TCTGTATCTCATCAGGAAGGAGAATTTGGT
* *
39555140 CCACTTCTCTGTATCTTATCAGGAAGATG
1 CCACTTCTTTGTATCTCATCAGGAAGATG
39555169 ATCGCTTTAT
Statistics
Matches: 175, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
160 174 0.99
161 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (160 bp):
CCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCA
TTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTC
TCTGTATCTCATCAGGAAGGAGAATTTGGT
Found at i:39555091 original size:48 final size:48
Alignment explanation
Indices: 39555036--39555216 Score: 168
Period size: 48 Copynumber: 4.0 Consensus size: 48
39555026 CGTATTGAGC
* * *
39555036 ATCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATG
1 ATCGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
* * *
39555084 ATCGCTTCATTGATTTAATCCTCTTCTTTGTATCTCATCAGGAAG--G
1 ATCGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
* *
39555130 --CG----A---ATTTGGTCCACTTCTCTGTATCTTATCAGGAAGATG
1 ATCGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
* * * * *
39555169 ATCGCTTTATTGCTTTGACCCACTTCTCTGTATCACATTAGGAAGATG
1 ATCGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
39555217 GGGTTTGAAG
Statistics
Matches: 107, Mismatches: 15, Indels: 22
0.74 0.10 0.15
Matches are distributed among these distances:
37 28 0.26
39 1 0.01
40 1 0.01
41 2 0.02
44 2 0.02
45 1 0.01
46 1 0.01
48 71 0.66
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (48 bp):
ATCGCTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
Found at i:39555091 original size:208 final size:203
Alignment explanation
Indices: 39554877--39555374 Score: 530
Period size: 208 Copynumber: 2.4 Consensus size: 203
39554867 GTATTGAGCT
** * *
39554877 TCGCTTCATTGATTTGGTGTACTTCTCTGTATCTCATCAAGAAGATGATTGCTTCATTGATTTAA
1 TCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAAGAAGA--A-GGC--CA---ATTTAA
** * *
39554942 TCCACTTCTCTGTATCTCATCAGGAAG-GA-A-GATTTGGTCCACCTCTTTGTATCTCATCAGGA
58 TCCACTTCTCTGTATCTCATCAGGAAGAGATATGATTTGACCCACCTCTCTGTATCACATCAGGA
* *
39555004 AGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCATTGATTTGGTCTACTTCTTTGTAT
123 AGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCATTGATTTGGTCTACTTCTCTGTAT
39555069 CTCATCAGGAAGATGA
188 CTCATCAGGAAGATGA
* * **
39555085 TCGCTTCATTGATTTAATCCT-CTTCTTTGTATCTCATC-AG--GAAGGCGAATTTGGTCCACTT
1 TCGCTTCATTGATTTAAT-CTACTTCTCTGTATCTCATCAAGAAGAAGGCCAATTTAATCCACTT
* * * *
39555146 CTCTGTATCTTATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTCTGTATCACATTAGG
65 CTCTGTATCTCATCAGGAAGA-GA------TA-TGATTTGACCCACCTCTCTGTATCACATCAGG
39555211 AAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCATTGATTTGGTCTACTTCTCTGTA
122 AAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCATTGATTTGGTCTACTTCTCTGTA
*
39555276 TCTCATCATGAAGATGA
187 TCTCATCAGGAAGATGA
* * * * * * **
39555293 CCGCTTTATTGATTTAATCCACTTCTCTATATCTCATC-AG--GAAGGCGAATCTGGTCCACTTC
1 TCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAAGAAGAAGGCCAATTTAATCCACTTC
39555355 TCTGTATCTCATCAGGAAGA
66 TCTGTATCTCATCAGGAAGA
39555375 TGGTCGCTTT
Statistics
Matches: 251, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
197 30 0.12
199 2 0.01
200 1 0.00
202 2 0.01
203 1 0.00
205 2 0.01
206 1 0.00
207 3 0.01
208 208 0.83
209 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (203 bp):
TCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAAGAAGAAGGCCAATTTAATCCACTTC
TCTGTATCTCATCAGGAAGAGATATGATTTGACCCACCTCTCTGTATCACATCAGGAAGATGGGG
TTTGAAGTCTCATTCGTATTGAGCATCACTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAG
GAAGATGA
Found at i:39555103 original size:368 final size:368
Alignment explanation
Indices: 39554620--39555377 Score: 1198
Period size: 368 Copynumber: 2.1 Consensus size: 368
39554610 GACCCACTTT
* * * *
39554620 TCTGTATCTCATCAGGAAGAT-CGGCTTGAAGTCTCATTCATTTTGAGCTTCGCTTCATTGCTTT
1 TCTGTATCTCATCAGGAAGATGGGGCTTGAAGTCTCATTCATATTGAGCATCGCTTCATTGATTT
39554684 GGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTATAT
66 GGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTATAT
* * *
39554749 CTCATTAGGAAGGCAAATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATG-GCTGCTTTATTG
131 CTCATCAGGAAGGCAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATC-GCTTTATTG
* * * *
39554813 CTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTTGTATTGAGCTT
195 CTTTGACCCACTTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCAT
* * **
39554878 CGCTTCATTGATTTGGTGTACTTCTCTGTATCTCATCAAGAAGATGATTGCTTCATTGATTTAAT
260 CACTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAAT
* *
39554943 CCACTTCTCTGTATCTCATCAGGAAGGA-AGATTTGGTCCACCTC
325 CCACTTCTCTATATCTCATCAGGAAGGAGA-ATCTGGTCCACCTC
* * *
39554987 TTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCATTGATTT
1 TCTGTATCTCATCAGGAAGATGGGGCTTGAAGTCTCATTCATATTGAGCATCGCTTCATTGATTT
* * * *
39555052 GGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCTCTTCTTTGTAT
66 GGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTATAT
* *
39555117 CTCATCAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTTATCAGGAAGATGATCGCTTTATTGC
131 CTCATCAGGAAGGCAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGC
*
39555182 TTTGACCCACTTCTCTGTATCACATTAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATC
196 TTTGACCCACTTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATC
* *
39555247 ACTTCATTGATTTGGTCTACTTCTCTGTATCTCATCATGAAGATGACCGCTTTATTGATTTAATC
261 ACTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATC
* *
39555312 CACTTCTCTATATCTCATCAGGAAGGCGAATCTGGTCCACTTC
326 CACTTCTCTATATCTCATCAGGAAGGAGAATCTGGTCCACCTC
39555355 TCTGTATCTCATCAGGAAGATGG
1 TCTGTATCTCATCAGGAAGATGG
39555378 TCGCTTTATT
Statistics
Matches: 356, Mismatches: 32, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
367 20 0.06
368 334 0.94
369 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (368 bp):
TCTGTATCTCATCAGGAAGATGGGGCTTGAAGTCTCATTCATATTGAGCATCGCTTCATTGATTT
GGTCTACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTATAT
CTCATCAGGAAGGCAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGC
TTTGACCCACTTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATC
ACTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATC
CACTTCTCTATATCTCATCAGGAAGGAGAATCTGGTCCACCTC
Found at i:39555195 original size:85 final size:85
Alignment explanation
Indices: 39555048--39555213 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 85
39555038 CGCTTCATTG
* * * * *
39555048 ATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCTCTTCTTT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAACCCACTTCTCT
*
39555113 GTATCTCATCAGGAAGGCGA
66 GTATCACATCAGGAAGGCGA
* * * *
39555133 ATTTGGTCCACTTCTCTGTATCTTATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAACCCACTTCTCT
*
39555198 GTATCACATTAGGAAG
66 GTATCACATCAGGAAG
39555214 ATGGGGTTTG
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAACCCACTTCTCT
GTATCACATCAGGAAGGCGA
Found at i:39555375 original size:208 final size:208
Alignment explanation
Indices: 39554980--39555392 Score: 691
Period size: 208 Copynumber: 2.0 Consensus size: 208
39554970 AAGATTTGGT
* * *
39554980 CCACCTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCA
1 CCACCTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCA
* * *
39555045 TTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCTCTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * *
39555110 TTTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTTATCAGGAAGATGATCGCT
131 TCTATATCTCATCAGGAAGGCGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCT
39555175 TTATTGCTTTGAC
196 TTATTGCTTTGAC
* *
39555188 CCACTTCTCTGTATCACATTAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCA
1 CCACCTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCA
* *
39555253 TTGATTTGGTCTACTTCTCTGTATCTCATCATGAAGATGACCGCTTTATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
*
39555318 TCTATATCTCATCAGGAAGGCGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGTCGCT
131 TCTATATCTCATCAGGAAGGCGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCT
39555383 TTATTGCTTT
196 TTATTGCTTT
39555393 TGTAACAGCC
Statistics
Matches: 190, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
208 190 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (208 bp):
CCACCTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCATCACTTCA
TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTATATCTCATCAGGAAGGCGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCT
TTATTGCTTTGAC
Found at i:39572757 original size:19 final size:19
Alignment explanation
Indices: 39572733--39572770 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39572723 CTCTTGCAAG
*
39572733 GTATGGTTTCATTTCATCA
1 GTATGGTTTCATGTCATCA
39572752 GTATGGTTTCATGTCATCA
1 GTATGGTTTCATGTCATCA
39572771 ACAGTCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (19 bp):
GTATGGTTTCATGTCATCA
Found at i:39577194 original size:84 final size:84
Alignment explanation
Indices: 39577053--39577215 Score: 229
Period size: 84 Copynumber: 1.9 Consensus size: 84
39577043 CTTTATTGAT
* *
39577053 TTGGTCTACTTATCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGT
1 TTGGTCCACTTATCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGT
39577118 ATCTCATCAGGAAGGCGGA
66 ATCTCATCAGGAAGGCGGA
* * * * * * *
39577137 TTGGTCCACTTCTCTGTATCTTATCAAGAAGATGATCGCTTTATTGCTTTGAA-CCACTTCTTTG
1 TTGGTCCACTTATCTATATCTCATCAAGAAGATGACCGCTTCATTGATTT-AATCCACTTCTCTG
39577201 TATCTCATCAGGAAG
65 TATCTCATCAGGAAG
39577216 ATGAGGTTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 67 0.97
85 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (84 bp):
TTGGTCCACTTATCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGT
ATCTCATCAGGAAGGCGGA
Found at i:39577787 original size:49 final size:49
Alignment explanation
Indices: 39577730--39577978 Score: 184
Period size: 49 Copynumber: 5.1 Consensus size: 49
39577720 CGAGATTTAC
* *
39577730 CATTGCGGCTTCAATCTGCTTCTC-T-ACATCTTTAGGGTATAAGAGTT-GT
1 CATTGCGGCTTCAATCT--TTCCCTTCACATCTCTAGGGTATAAG-GTTCGT
* *
39577779 CATTGCGGCTTCGATCTTTCCCTTCATATCTCTAGGGTATAAGGTTCGT
1 CATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGT
* * ** * * **
39577828 CATTGTGGCTTCCA-CATTTCCC-TCTTTATCTTTAGGGTATAAGATTCAC
1 CATTGCGGCTTCAATC-TTTCCCTTC-ACATCTCTAGGGTATAAGGTTCGT
* ** * * **
39577877 CGTTGTAGCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTTTT
1 CATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGT
* * * * * * *
39577926 CGTTGCGGCTTCAACCTTTCTCATCACATCTCTAAGGTATAAGATTCGC
1 CATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGT
39577975 CATT
1 CATT
39577979 ATGACTTTAA
Statistics
Matches: 159, Mismatches: 34, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
47 4 0.03
48 7 0.04
49 145 0.91
50 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (49 bp):
CATTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGT
Found at i:39577965 original size:98 final size:98
Alignment explanation
Indices: 39577786--39577972 Score: 223
Period size: 98 Copynumber: 1.9 Consensus size: 98
39577776 TGTCATTGCG
* * * * * * *
39577786 GCTTCGATCTTTCCCTTCATATCTCTAGGGTATAAGGTTCGTCATTGTGGCTTCCACATTTCCCT
1 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTCCAT
** * *
39577851 CTTTATCTTTAGGGTATAAGATTCACCGTTGTA
66 CTACATCTCTAAGGTATAAGATTCACCGTTGTA
** * *
39577884 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTTTTCGTTGCGGCTTCAACCTTTCTCA
1 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTC-CA
39577949 TC-ACATCTCTAAGGTATAAGATTC
65 TCTACATCTCTAAGGTATAAGATTC
39577973 GCCATTATGA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
98 70 0.96
99 3 0.04
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (98 bp):
GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTCCAT
CTACATCTCTAAGGTATAAGATTCACCGTTGTA
Found at i:39577991 original size:98 final size:98
Alignment explanation
Indices: 39577786--39578003 Score: 217
Period size: 98 Copynumber: 2.2 Consensus size: 98
39577776 TGTCATTGCG
* * * * * * *
39577786 GCTTCGATCTTTCCCTTCATATCTCTAGGGTATAAGGTTCGTCATTGTGGCTTCCACATTTCCCT
1 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTCCAT
** * * * *
39577851 CTTTATCTTTAGGGTATAAGATTCACCGTTGTA
66 CTACATCTCTAAGGTATAAGATTCACCATTATA
** * *
39577884 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTTTTCGTTGCGGCTTCAACCTTTCTCA
1 GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTC-CA
*
39577949 TC-ACATCTCTAAGGTATAAGATTCGCCATTAT-
65 TCTACATCTCTAAGGTATAAGATTCACCATTATA
*
39577981 GACTTTAATCTCTT-CCTTCACAT
1 G-CTTCAATCT-TTCCCTTCACAT
39578004 TCTTATGGTA
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
97 1 0.01
98 92 0.94
99 5 0.05
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (98 bp):
GCTTCAATCTTTCCCTTCACATCGCTAAGGTATAAGGTTCGTCATTGCGGCTTCAACATTTCCAT
CTACATCTCTAAGGTATAAGATTCACCATTATA
Found at i:39582258 original size:15 final size:15
Alignment explanation
Indices: 39582238--39582267 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39582228 TCAGGAGATA
39582238 AATTACAATCTTGAT
1 AATTACAATCTTGAT
39582253 AATTACAATCTTGAT
1 AATTACAATCTTGAT
39582268 CATCTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AATTACAATCTTGAT
Found at i:39586374 original size:18 final size:18
Alignment explanation
Indices: 39586331--39586374 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
39586321 TATTTTAATT
* *
39586331 TAATTAAAAATGAGTGTG
1 TAATTAAAAACGAATGTG
*
39586349 TAAATTAAATACGAATGTG
1 T-AATTAAAAACGAATGTG
39586368 TAATTAA
1 TAATTAA
39586375 TGGCGAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (18 bp):
TAATTAAAAACGAATGTG
Found at i:39586645 original size:30 final size:30
Alignment explanation
Indices: 39586602--39586740 Score: 102
Period size: 30 Copynumber: 4.6 Consensus size: 30
39586592 CGAAGAATTT
* *
39586602 GGGGCTAATATGTAATTTTGGAAAAATTCA
1 GGGGTTAAAATGTAATTTTGGAAAAATTCA
* ** *
39586632 GGGGTTAAAATGTAATTTTAGGTAAGTTTGA
1 GGGGTTAAAATGTAATTTT-GGAAAAATTCA
* * * * * *
39586663 -GGGTCAAAATATGATTTTTGTAAAGTTCTA
1 GGGGTTAAAATGTAATTTTGGAAAAATTC-A
* * *
39586693 GGGG-TAAAATGTAATTTTAGAGAACTTCA
1 GGGGTTAAAATGTAATTTTGGAAAAATTCA
*
39586722 GGGGTCAAAATGTAATTTT
1 GGGGTTAAAATGTAATTTT
39586741 TAAGTAAAAT
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
29 11 0.13
30 63 0.75
31 10 0.12
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAAATTCA
Found at i:39588034 original size:30 final size:30
Alignment explanation
Indices: 39587965--39588035 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 30
39587955 TTTTGATCTG
* *
39587965 TGTTTTTCTTGTGTATTAATTTCGAATCAC
1 TGTTTTTTTTGCGTATTAATTTCGAATCAC
39587995 TGAGTTTTTTTTGCGTATTAATTTCGAATCAC
1 T--GTTTTTTTTGCGTATTAATTTCGAATCAC
39588027 TGTTTTTTT
1 TGTTTTTTT
39588036 GTATTGCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 9 0.24
32 28 0.76
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.56
Consensus pattern (30 bp):
TGTTTTTTTTGCGTATTAATTTCGAATCAC
Found at i:39588466 original size:27 final size:27
Alignment explanation
Indices: 39588435--39588493 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
39588425 TATTTAAAAG
*
39588435 ATTAGATTTAGTTTCTGATTATTAGGA
1 ATTAGATTTAATTTCTGATTATTAGGA
*
39588462 ATTAGATTTAATTTCTTATTATTAGGA
1 ATTAGATTTAATTTCTGATTATTAGGA
39588489 ATTAG
1 ATTAG
39588494 CTATTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (27 bp):
ATTAGATTTAATTTCTGATTATTAGGA
Found at i:39591881 original size:3 final size:3
Alignment explanation
Indices: 39591873--39591915 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39591863 CATGAAACCC
39591873 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39591916 TTGGGCCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39592431 original size:42 final size:42
Alignment explanation
Indices: 39592385--39592473 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
39592375 TCTACGCTTA
** * * *
39592385 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTTCACACTTG
1 GGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACCTG
39592427 GGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACCTG
1 GGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACCTG
39592469 GGCCT
1 GGCCT
39592474 GACCTCCACA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACCTG
Found at i:39592471 original size:56 final size:58
Alignment explanation
Indices: 39592411--39592528 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 58
39592401 GAAAAGTAAA
*
39592411 TGGGCCT-T-CACACTTGGGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTCCACACATGGGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACC
**
39592467 TGGGCCTGACCTCCACACATGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCT---CTCCACACATGGGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACC
39592528 T
1 T
39592529 AAGCCTCTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
56 7 0.13
60 1 0.02
61 46 0.85
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (58 bp):
TGGGCCTCTCCACACATGGGCCTCTAAATAAAATGAAAAGTAAATGGACCTCCACACC
Found at i:39592479 original size:19 final size:19
Alignment explanation
Indices: 39592455--39592492 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39592445 AAAGTAAATG
*
39592455 GACCTCCACACCTGGGCCT
1 GACCTCCACACATGGGCCT
39592474 GACCTCCACACATGGGCCT
1 GACCTCCACACATGGGCCT
39592493 CTAAATGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (19 bp):
GACCTCCACACATGGGCCT
Found at i:39592521 original size:42 final size:42
Alignment explanation
Indices: 39592474--39592632 Score: 212
Period size: 42 Copynumber: 3.8 Consensus size: 42
39592464 ACCTGGGCCT
* *
39592474 GACCTCCACACATGGGCCTCTAAATGCAATGAAAAGTAAATG
1 GACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATG
*
39592516 GACCTCCACACCTAAGCCTCTAAATGCAATGAAAAGTAAATG
1 GACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATG
* * * * * *
39592558 GGCACT-CACACCTGGGCCTCTGAATACGATGAAACGTAAATG
1 GAC-CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATG
*
39592600 GGCCTCCACACCTAGGCCTCTAAATGCAATGAA
1 GACCTCCACACCTAGGCCTCTAAATGCAATGAA
39592633 TGCTTTCCTT
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.02
42 97 0.96
43 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (42 bp):
GACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATG
Found at i:39592550 original size:103 final size:103
Alignment explanation
Indices: 39592385--39592576 Score: 296
Period size: 103 Copynumber: 1.9 Consensus size: 103
39592375 TCTACGCTTA
* * * **
39592385 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTTCACACTTGGGCCTCTAAATAAAATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTAAATAAAATGAAAAGT
39592450 AAATGGAC-CTCCACACCTGGGCCTGACCTCCACACATG
66 AAATGGACACT-CACACCTGGGCCTGACCTCCACACATG
**
39592488 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTAAATGCAATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTAAATAAAATGAAAAGT
*
39592553 AAATGGGCACTCACACCTGGGCCT
66 AAATGGACACTCACACCTGGGCCT
39592577 CTGAATACGA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 78 0.98
104 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (103 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTAAATAAAATGAAAAGT
AAATGGACACTCACACCTGGGCCTGACCTCCACACATG
Found at i:39593065 original size:16 final size:16
Alignment explanation
Indices: 39593040--39593070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39593030 TCTCTTTCTA
*
39593040 TTTTTTTTCTTTTTTC
1 TTTTTCTTCTTTTTTC
39593056 TTTTTCTTCTTTTTT
1 TTTTTCTTCTTTTTT
39593071 TATATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTCTTCTTTTTTC
Found at i:39604561 original size:24 final size:24
Alignment explanation
Indices: 39604529--39604651 Score: 201
Period size: 24 Copynumber: 5.1 Consensus size: 24
39604519 CAATGTTTCT
*
39604529 TATATTAGCTGACGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACG
39604553 TATATTAGCTGGCGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACG
* *
39604577 CATATTAGCTGACGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACG
*
39604601 TATATTAGCTGGCGAGCGTAAACA
1 TATATTAGCTGGCGAGCGTAAACG
*
39604625 TATATTAGCTGGCGAGCATAAACG
1 TATATTAGCTGGCGAGCGTAAACG
39604649 TAT
1 TAT
39604652 TGTTGAATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
TATATTAGCTGGCGAGCGTAAACG
Found at i:39604730 original size:24 final size:24
Alignment explanation
Indices: 39604713--39604759 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39604703 TTAAATTTTG
39604713 TTTAATTGTTTCAATTAAACTCTA
1 TTTAATTGTTTCAATTAAACTCTA
*
39604737 TTTATTTGTTTCAATTAAACTCT
1 TTTAATTGTTTCAATTAAACTCT
39604760 GTTTCAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTAATTGTTTCAATTAAACTCTA
Found at i:39606710 original size:59 final size:59
Alignment explanation
Indices: 39606613--39606930 Score: 512
Period size: 59 Copynumber: 5.4 Consensus size: 59
39606603 TTTGGATATC
39606613 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* * *
39606671 CAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
** *
39606730 CGGGGGTAAAATGGTAATTTTTGGTGAAAGAGGGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* * *
39606789 CGGGGGTAATATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTCGAAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* * *
39606848 CGGGGGTAATATGGTAATTTTTGGTGAAATCGTGGTTAAAAATGGAATTTTAGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
*
39606907 TGGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
39606931 AAGTTTCGGG
Statistics
Matches: 241, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
58 16 0.07
59 225 0.93
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:39607190 original size:162 final size:162
Alignment explanation
Indices: 39607000--39607341 Score: 497
Period size: 162 Copynumber: 2.1 Consensus size: 162
39606990 AGGCATCCAG
* * * * *
39607000 CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGGGCCAATTTTATGATTAAATAAGAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAAAGT
* * **
39607065 TGATTTGGGGACTAAATTAAAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAATG-CAAA
66 GGATCTAAGGACTAAATTAAAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAA-GCCAAA
*
39607129 AAATGACACGTGGCAGCCCCTGGTGCAGTCAAA
130 AAATGACACGTGGCAGCCCCTGGTGCAATCAAA
* *
39607162 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAAAGT
* * * *
39607227 GGATCTAAGGATTAAATTAAAATAAATTAAAAATGTCAGGGACTAAATGCATCAATAAGCCAAAA
66 GGATCTAAGGACTAAATTAAAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAAGCCAAAA
* *
39607292 AGTGACACGTGGCAGCCTCTGGTGCAATCAAA
131 AATGACACGTGGCAGCCCCTGGTGCAATCAAA
*
39607324 CAGTCAAAGGATTAAATT
1 CAGTCAAAGGACTAAATT
39607342 GAAAACCAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
161 1 0.01
162 158 0.99
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAAAGT
GGATCTAAGGACTAAATTAAAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAAGCCAAAA
AATGACACGTGGCAGCCCCTGGTGCAATCAAA
Found at i:39608199 original size:3 final size:3
Alignment explanation
Indices: 39608191--39608237 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
39608181 TTTCCCTTTT
* *
39608191 TTA TTA TTA TTA TTTA TTTA TTA TTA TTA TTA TTA ATA TCA TTA TTA
1 TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39608238 ATAGCATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 32 0.82
4 7 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39608213 original size:14 final size:13
Alignment explanation
Indices: 39608190--39608225 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
39608180 GTTTCCCTTT
39608190 TTTATTATTATTA
1 TTTATTATTATTA
39608203 TTTATTTATTATTA
1 TTTA-TTATTATTA
39608217 -TTATTATTA
1 TTTATTATTA
39608226 ATATCATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:39610793 original size:20 final size:20
Alignment explanation
Indices: 39610756--39610795 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39610746 GGGTTTATGA
* *
39610756 TTTATCTTACTTTAAAATTT
1 TTTATCTAAATTTAAAATTT
*
39610776 TTTATCTAAATTTTAAATTT
1 TTTATCTAAATTTAAAATTT
39610796 GTCAAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATCTAAATTTAAAATTT
Found at i:39611958 original size:51 final size:51
Alignment explanation
Indices: 39611863--39612109 Score: 166
Period size: 51 Copynumber: 4.9 Consensus size: 51
39611853 TTTTTTAATG
** * **
39611863 AAAATCACTACTTTACTTAAAAATTTAAACTTTTAT-TTCGAAATAGTTAAA
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTT-TCTTTAAAATAGTTAAA
* * **
39611914 AAAATCAAAAATGTATTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AA
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAGTTAAA
* ** ** ** ** *
39611964 AAAA-CAGATTTTTATTTTTAAAAACATAAAC--TTTCTTT-ATTTTTTTAATG
1 AAAATCAAAACTTTA--TTTAAAAATTTAAACTTTTTCTTTAAAATAGTTAA-A
** ** **
39612014 AAAATCACTACTTTATTTAAAAATCCAAACTTTTAT-TTCGAAATAGTTAAA
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTT-TCTTTAAAATAGTTAAA
*
39612065 AAAATCAAAACTTTATTTAGAAATTTAAACTTTTTCTTTAAAATA
1 AAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATA
39612110 ACTAAAAGAC
Statistics
Matches: 144, Mismatches: 41, Indels: 22
0.70 0.20 0.11
Matches are distributed among these distances:
48 3 0.02
49 26 0.18
50 12 0.08
51 96 0.67
52 7 0.05
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (51 bp):
AAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAGTTAAA
Found at i:39612026 original size:151 final size:148
Alignment explanation
Indices: 39611711--39612367 Score: 795
Period size: 151 Copynumber: 4.4 Consensus size: 148
39611701 TGATTAAAAC
* *
39611711 AAAATCACTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTT
* * * * * *
39611776 TGTTTAAAAATTTAAAGTTTTTTCTTTAAAATCACTAAAAAATAGATTTTTATTTTTTTTAAAAT
65 TATTTAAAAATTTAAA-CTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA--TTTTTAAAAAC
* *
39611841 GTAAACTTTATTTTTTTTAATG
127 ATAAACTTTTTTTTTTTTAATG
** * *
39611863 AAAATCACTACTTTACTTAAAAATTTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAATGT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
39611928 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAACATAA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAACATAA
39611993 ACTTTCTTTATTTTTTTAATG
131 AC-TT-TTT-TTTTTTTAATG
*
39612014 AAAATCACTACTTTATTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * *
39612079 ATTTAGAAATTTAAACTTTTTCTTTAAAATAACTAAAAGACAGATTTTTATTTTTAAAAATATAA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAACATAA
**
39612144 ACTTTCTCATTTTTTAATG
131 ACTTT-TTTTTTTTTAATG
* *
39612163 AAAATCACTACTTT-CTTAAAAATCTATACTTTTATTTCGAAATAGTTAAAAAAAAAATCAAAAC
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT---AAAAAAATCAAAAC
** * *
39612227 TTTGCTTAAAAATTT-AA---TTT-TTT---CT-A--AAAAAACATATTTTTATTTTTAAAAATC
63 TTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAA-C
* *
39612281 -TAAAC-TTTTTTTTTTAAAAG
127 ATAAACTTTTTTTTTTTTAATG
* * *
39612301 AAAATCACTATTTTACTTAAAAAT-CAAAGCTTTTATTTCGAAATTGTTTAAAAAAAACCAAAAC
1 AAAATCACTACTTTACTTAAAAATCCAAA-CTTTTATTTCGAAATAG-TT-AAAAAAATCAAAAC
39612365 TTT
63 TTT
39612368 TCCCAAAATC
Statistics
Matches: 452, Mismatches: 42, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
138 41 0.09
139 27 0.06
140 31 0.07
142 1 0.00
143 1 0.00
146 3 0.01
147 3 0.01
148 44 0.10
149 27 0.06
150 39 0.09
151 192 0.42
152 43 0.10
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (148 bp):
AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAACATAA
ACTTTTTTTTTTTTAATG
Found at i:39612788 original size:3 final size:3
Alignment explanation
Indices: 39612780--39612825 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
39612770 ATGAAACCCA
* * * *
39612780 ACT ACT ACT ACT ACA ACA ACA ACA ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
39612826 ATAATAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (3 bp):
ACT
Found at i:39612830 original size:3 final size:3
Alignment explanation
Indices: 39612824--39612860 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39612814 CTACTACTAC
39612824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39612861 TTGGGCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39615043 original size:22 final size:23
Alignment explanation
Indices: 39615014--39615071 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
39615004 AAAAGCTATC
39615014 TACAAATCA-AGTC-TCT-AAGAT
1 TACAAATCATA-TCTTCTAAAGAT
39615035 TACAGAATCATATCTTCTAAAGAT
1 TACA-AATCATATCTTCTAAAGAT
*
39615059 TACATATCA-ATCT
1 TACAAATCATATCT
39615072 AAGATATTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.12
22 11 0.34
23 8 0.25
24 9 0.28
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (23 bp):
TACAAATCATATCTTCTAAAGAT
Found at i:39615066 original size:18 final size:20
Alignment explanation
Indices: 39615050--39615094 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
39615040 AATCATATCT
39615050 TCTAA-AGATTACATATCAA
1 TCTAAGAGATTACATATCAA
*
39615069 TCTAAGATATTACATATCAAA
1 TCTAAGAGATTACATATC-AA
39615090 TCTAA
1 TCTAA
39615095 TATTGCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 11 0.48
21 7 0.30
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (20 bp):
TCTAAGAGATTACATATCAA
Found at i:39617665 original size:23 final size:22
Alignment explanation
Indices: 39617639--39617759 Score: 134
Period size: 23 Copynumber: 5.2 Consensus size: 22
39617629 ACACTAGCGC
*
39617639 GCTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACT-TGTGT
*
39617662 GCTCTCTGTTTATCACTGTGTGT
1 GCTCTCTGTTTAGCACT-TGTGT
*
39617685 GCTCTTTGTTATTAGCACTTCGTGT
1 GCTCTCTG-T-TTAGCACTT-GTGT
*
39617710 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTT-GTGT
*
39617733 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-TTGTGT
39617756 GCTC
1 GCTC
39617760 AGCACCTTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
23 66 0.75
24 4 0.05
25 18 0.20
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACTTGTGT
Found at i:39617710 original size:48 final size:46
Alignment explanation
Indices: 39617639--39617759 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 46
39617629 ACACTAGCGC
* *
39617639 GCTCTTTGT-TTAGCACTGTGTGTGCTCTCTGTTTATCACTGT-GTGT
1 GCTCTTTGTATTAGCACT-TGTGTGCTCTCTGATTAGCACT-TCGTGT
39617685 GCTCTTTGTTATTAGCACTTCGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTTTG-TATTAGCACTT-GTGTGCTCTCTGATTAGCACTTCGTGT
*
39617733 GCTCTCTG-ATTAGCACTTTGTGTGCTC
1 GCTCTTTGTATTAGCAC-TTGTGTGCTC
39617760 AGCACCTTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
46 24 0.36
47 5 0.07
48 38 0.57
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (46 bp):
GCTCTTTGTATTAGCACTTGTGTGCTCTCTGATTAGCACTTCGTGT
Found at i:39617790 original size:19 final size:17
Alignment explanation
Indices: 39617744--39617809 Score: 100
Period size: 17 Copynumber: 4.0 Consensus size: 17
39617734 CTCTCTGATT
39617744 AGCA-CTTTGTGTGCTC
1 AGCACCTTTGTGTGCTC
39617760 AGCACCTTTGTGTGCTC
1 AGCACCTTTGTGTGCTC
39617777 AGCACCTTTGTGTGCTC
1 AGCACCTTTGTGTGCTC
**
39617794 ATTA-CTTTGTGTGCTC
1 AGCACCTTTGTGTGCTC
39617810 TCTGTTTAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.34
17 31 0.66
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (17 bp):
AGCACCTTTGTGTGCTC
Found at i:39617802 original size:33 final size:33
Alignment explanation
Indices: 39617744--39617809 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
39617734 CTCTCTGATT
39617744 AGCACTTTGTGTGCTCAGCACCTTTGTGTGCTC
1 AGCACTTTGTGTGCTCAGCACCTTTGTGTGCTC
**
39617777 AGCACCTTTGTGTGCTCATTA-CTTTGTGTGCTC
1 AGCA-CTTTGTGTGCTCAGCACCTTTGTGTGCTC
39617810 TCTGTTTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (33 bp):
AGCACTTTGTGTGCTCAGCACCTTTGTGTGCTC
Found at i:39617844 original size:23 final size:22
Alignment explanation
Indices: 39617800--39617909 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 22
39617790 GCTCATTACT
39617800 TTGTGTGCTCTCTGTTTAGCAC
1 TTGTGTGCTCTCTGTTTAGCAC
*
39617822 -TGTGTGCTCTCTGTTATTTGCAC
1 TTGTGTGCTCTCTG-T-TTAGCAC
* *
39617845 TTTGTGTGCTCTCTATTACCCAGCAC
1 -TTGTGTGCTCTCTGTT---TAGCAC
* *
39617871 TTATGTGCTCTCTGTTTAGTAC
1 TTGTGTGCTCTCTGTTTAGCAC
*
39617893 TT-TGATACTCTCTGTTT
1 TTGTG-TGCTCTCTGTTT
39617910 GTTCCATTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
21 15 0.21
22 18 0.25
23 7 0.10
24 1 0.01
25 26 0.37
26 4 0.06
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (22 bp):
TTGTGTGCTCTCTGTTTAGCAC
Found at i:39624122 original size:19 final size:19
Alignment explanation
Indices: 39624095--39624131 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39624085 CAATATTACC
39624095 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
*
39624114 CACCGTAATCAAATTTGT
1 CACCATAATCAAATTTGT
39624132 CATTAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (19 bp):
CACCATAATCAAATTTGTT
Found at i:39624758 original size:50 final size:50
Alignment explanation
Indices: 39624701--39624800 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
39624691 AGAGGAGAGT
39624701 AAAAATTTT-A-AAAGGAAA-GTGGAAGGTAGTAAAAGTTTT-GAGGAAAAATA
1 AAAAATTTTGAGAAAGGAAATG-GGAA-G-AGTAAAA-TTTTGGAGGAAAAATA
* *
39624751 AAAAATTTTGAGAAAGTAAATGGGAAGAGTAAAATTTTGGAGGGAAAATA
1 AAAAATTTTGAGAAAGGAAATGGGAAGAGTAAAATTTTGGAGGAAAAATA
39624801 TTAAAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
49 4 0.09
50 26 0.59
51 2 0.05
52 11 0.25
53 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (50 bp):
AAAAATTTTGAGAAAGGAAATGGGAAGAGTAAAATTTTGGAGGAAAAATA
Found at i:39624845 original size:160 final size:162
Alignment explanation
Indices: 39624590--39624914 Score: 396
Period size: 160 Copynumber: 2.0 Consensus size: 162
39624580 TTTGGGGAGT
39624590 AAAATTTTGAGGAAGAGAAGATAGGAGAGTAAAATTTTGAAGGGAAAATATTTAAAAAAAATTAA
1 AAAATTTTGAGGAAGAGAAGATAGGAGAGTAAAATTTTGAAGGGAAAATATTTAAAAAAAATTAA
*
39624655 GGGGGAATGTGTTTGGGGTAAATAGGGGGTGAAATAAGAGGAGAGTAAAAATTTTAAAAGGAAAG
66 GGGGGAATGAGTTTGGGGTAAATAGGGGGTGAAATAAGAGGAGAGTAAAAATTTT-AAAGGAAAG
*
39624720 TG-GAAGGTAGTAAAAGTTTT-GAGGAAAAATAA
130 TGAGAAGG-AATAAAAGTTTTGGAGGAAAAATAA
* *
39624752 AAAATTTTGA-GAA-AGTAA-ATGGGAAGAGTAAAATTTTGGAGGGAAAATA-TT-AAAAAAATT
1 AAAATTTTGAGGAAGAG-AAGATAGG-AGAGTAAAATTTTGAAGGGAAAATATTTAAAAAAAATT
* * * ** * * * ***
39624812 -TGGAGGGAAATGAGTTTGGGGTAGATTGGGGGTGGGATGAGAGGGGAGTAAAAGTTTTTGGGGA
64 AAGG-GGG-AATGAGTTTGGGGTAAATAGGGGGTGAAATAAGAGGAGAGTAAAAATTTTAAAGGA
*
39624876 AAGTGAGAAGGAATAAAAGTTTTGGAGGAAAAGTAA
127 AAGTGAGAAGGAATAAAAGTTTTGGAGGAAAAATAA
39624912 AAA
1 AAA
39624915 TGTTTGGGGT
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
158 2 0.01
159 31 0.22
160 69 0.49
161 29 0.21
162 10 0.07
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (162 bp):
AAAATTTTGAGGAAGAGAAGATAGGAGAGTAAAATTTTGAAGGGAAAATATTTAAAAAAAATTAA
GGGGGAATGAGTTTGGGGTAAATAGGGGGTGAAATAAGAGGAGAGTAAAAATTTTAAAGGAAAGT
GAGAAGGAATAAAAGTTTTGGAGGAAAAATAA
Found at i:39624971 original size:9 final size:9
Alignment explanation
Indices: 39624957--39624981 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39624947 TATAATTAGA
39624957 TATTCGAGT
1 TATTCGAGT
39624966 TATTCGAGT
1 TATTCGAGT
39624975 TATTCGA
1 TATTCGA
39624982 ATTCAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (9 bp):
TATTCGAGT
Found at i:39626481 original size:19 final size:19
Alignment explanation
Indices: 39626423--39626482 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 19
39626413 ATTCCTTCTC
*
39626423 TTTAATTTTTTATATCCAGTT
1 TTTAATTTTTT-T-TCTAGTT
* *
39626444 CTT-ATTTTTTTTATA--T
1 TTTAATTTTTTTTCTAGTT
39626460 TTTAATTTTTTTTCTAGTT
1 TTTAATTTTTTTTCTAGTT
39626479 TTTA
1 TTTA
39626483 TCTGTCTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
16 3 0.10
17 11 0.35
18 2 0.06
19 6 0.19
20 7 0.23
21 2 0.06
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTTCTAGTT
Found at i:39626544 original size:17 final size:18
Alignment explanation
Indices: 39626507--39626544 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39626497 ACGCTTTTTC
*
39626507 TTTGCCTTATGGTACGCT
1 TTTGCCTTATGGCACGCT
39626525 TTTGCCTTATGGCACG-T
1 TTTGCCTTATGGCACGCT
39626542 TTT
1 TTT
39626545 CGTCTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (18 bp):
TTTGCCTTATGGCACGCT
Found at i:39627721 original size:26 final size:27
Alignment explanation
Indices: 39627665--39627722 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
39627655 TTTAGGAGAG
* ** *
39627665 TTAAAATGTAAATTTATTTTTATTAAT
1 TTAAAATGTAAATTTATTTTAAAAAAA
*
39627692 TTAAAATTTAAATTT-TTTTAAAAAAA
1 TTAAAATGTAAATTTATTTTAAAAAAA
39627718 TTAAA
1 TTAAA
39627723 TAATAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAAAATGTAAATTTATTTTAAAAAAA
Found at i:39631351 original size:21 final size:21
Alignment explanation
Indices: 39631307--39631353 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39631297 ATGAAACAAT
* *
39631307 AAAATTTAAAAAAAAATCTTG
1 AAAATTCAAAAAAAAATCTAG
39631328 AAAATTCAAAAAAAAAT-TAAG
1 AAAATTCAAAAAAAAATCT-AG
39631349 AAAAT
1 AAAAT
39631354 CATGAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAATTCAAAAAAAAATCTAG
Found at i:39631797 original size:23 final size:22
Alignment explanation
Indices: 39631770--39631821 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
39631760 AAAAATTTCA
39631770 ATAAATAAAAAAATAAAAAAAT
1 ATAAATAAAAAAATAAAAAAAT
** * *
39631792 ATTAAATATTAAAATAATATAAT
1 A-TAAATAAAAAAATAAAAAAAT
39631815 ATAAATA
1 ATAAATA
39631822 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAATAAAAAAATAAAAAAAT
Found at i:39639268 original size:18 final size:18
Alignment explanation
Indices: 39639245--39639279 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39639235 TTTCAACTAT
39639245 TACATAATATAATTATTA
1 TACATAATATAATTATTA
39639263 TACATAATATAATTATT
1 TACATAATATAATTATT
39639280 CTAGAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TACATAATATAATTATTA
Found at i:39639418 original size:23 final size:22
Alignment explanation
Indices: 39639375--39639420 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39639365 CCCTAATTAC
* * *
39639375 TTTTAAAACTTTATTTGTAAAA
1 TTTTAAAAATTTATGTATAAAA
39639397 TTTTAAAAATTTAATGTATAAAA
1 TTTTAAAAATTT-ATGTATAAAA
39639420 T
1 T
39639421 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTTAAAAATTTATGTATAAAA
Found at i:39641231 original size:2 final size:2
Alignment explanation
Indices: 39641226--39641278 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
39641216 AAAAAAATTA
39641226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39641268 AT AT AT AT AT A
1 AT AT AT AT AT A
39641279 CAAAAATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39641636 original size:414 final size:414
Alignment explanation
Indices: 39640864--39641662 Score: 1539
Period size: 414 Copynumber: 1.9 Consensus size: 414
39640854 AAGTCATTTG
39640864 ACAAAAATTGAAATTGTAATAGGCTTATATTTAACAAAGATTTTAATAATGTTAATAATTCTTAA
1 ACAAAAATTGAAATTGTAATAGGCTTATATTTAACAAAGATTTTAATAATGTTAATAATTCTTAA
39640929 AATTCATGTAAGAATTTTAATTAAAATAAAGTATTTATATTAACTAATAACATTGTAAAGGTTGA
66 AATTCATGTAAGAATTTTAATTAAAATAAAGTATTTATATTAACTAATAACATTGTAAAGGTTGA
*
39640994 GATATCAAATTATATTAAAAGTTAAAGTATAAAGGTTAAGTCTCAAATTTTAGTATAGTATAGAG
131 GATATCAAATTATATTAAAAGTTAAAGTATAAAAGTTAAGTCTCAAATTTTAGTATAGTATAGAG
39641059 ATCAAAATTAAAATTTAACCATTAATATATAATATTAAAAATAAAGAGATCAGAATTTAAATTTA
196 ATCAAAATTAAAATTTAACCATTAATATATAATATTAAAAATAAAGAGATCAGAATTTAAATTTA
* *
39641124 ATTACTATCTTATATTGTAAAAAAAAAATGACTTAAACTTTTATCATGTAAGGAAAGCCTAACAT
261 ACTACTATCTTATATTGTAAAAAAAAAATGACTTAAACTTTTATCATGTAAGGAAAACCTAACAT
39641189 TATAAAGTTGAGGTATCAAATTATATAAAAAAAATTAATATATATATATATATATATATATATAT
326 TATAAAGTTGAGGTATCAAATTATATAAAAAAAATTAATATATATATATATATATATATATATAT
39641254 ATATATATATATATATATATATAT
391 ATATATATATATATATATATATAT
39641278 ACAAAAATTGAAATTGTAATAGGCTTATATTTAACAAAGATTTTAATAATGTTAATAATTCTTAA
1 ACAAAAATTGAAATTGTAATAGGCTTATATTTAACAAAGATTTTAATAATGTTAATAATTCTTAA
39641343 AATTCATGTAAGAATTTTAATTAAAATAAAGTATTTATATTAACTAATAACATTGTAAAGGTTGA
66 AATTCATGTAAGAATTTTAATTAAAATAAAGTATTTATATTAACTAATAACATTGTAAAGGTTGA
39641408 GATATCAAATTATATTAAAAGTTAAAGTATAAAAGTTAAGTCTCAAATTTTAAG-ATAGTATAGA
131 GATATCAAATTATATTAAAAGTTAAAGTATAAAAGTTAAGTCTCAAATTTT-AGTATAGTATAGA
39641472 GATCAAAATTAAAATTTAACCATTAATATATAATATTAAAAATAAAGAGATCAGAATTTAAATTT
195 GATCAAAATTAAAATTTAACCATTAATATATAATATTAAAAATAAAGAGATCAGAATTTAAATTT
39641537 AACTACTATCTTATATTGTAAAAAAAAAATGACTTAAACTTTTATCATGTAAGGAAAACCTAACA
260 AACTACTATCTTATATTGTAAAAAAAAAATGACTTAAACTTTTATCATGTAAGGAAAACCTAACA
39641602 TTATAAAAGTTGAGGTATCAAATTATAT-AAAAAAATTAATATATATATATATATATATATA
325 TTAT-AAAGTTGAGGTATCAAATTATATAAAAAAAATTAATATATATATATATATATATATA
39641663 ATTACGAATA
Statistics
Matches: 380, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
414 355 0.93
415 25 0.07
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (414 bp):
ACAAAAATTGAAATTGTAATAGGCTTATATTTAACAAAGATTTTAATAATGTTAATAATTCTTAA
AATTCATGTAAGAATTTTAATTAAAATAAAGTATTTATATTAACTAATAACATTGTAAAGGTTGA
GATATCAAATTATATTAAAAGTTAAAGTATAAAAGTTAAGTCTCAAATTTTAGTATAGTATAGAG
ATCAAAATTAAAATTTAACCATTAATATATAATATTAAAAATAAAGAGATCAGAATTTAAATTTA
ACTACTATCTTATATTGTAAAAAAAAAATGACTTAAACTTTTATCATGTAAGGAAAACCTAACAT
TATAAAGTTGAGGTATCAAATTATATAAAAAAAATTAATATATATATATATATATATATATATAT
ATATATATATATATATATATATAT
Found at i:39647739 original size:493 final size:493
Alignment explanation
Indices: 39646813--39647800 Score: 1958
Period size: 493 Copynumber: 2.0 Consensus size: 493
39646803 CATGACAATC
39646813 GTAAAATATGATTGGTAGAGGAATAGGAGAATCAACGGCAACATTCTTGTACCGAATCTAGAAAT
1 GTAAAATATGATTGGTAGAGGAATAGGAGAATCAACGGCAACATTCTTGTACCGAATCTAGAAAT
39646878 GATACGCCCAATCGAAGAACACTTGCAAGTCATCCCAACAAAATTAGAGATCATTGATAGCATTA
66 GATACGCCCAATCGAAGAACACTTGCAAGTCATCCCAACAAAATTAGAGATCATTGATAGCATTA
39646943 GAAATGAAACTTAGTTTCTCCTTAATTTAGTGTATAATTTGTTCCTTTTGTACCATTTCTAGCAT
131 GAAATGAAACTTAGTTTCTCCTTAATTTAGTGTATAATTTGTTCCTTTTGTACCATTTCTAGCAT
39647008 GCATTTTTAGCATTTCATATTTAGGATATACATTTTCTAACTCAGTGCTGTTTGATCTTACTTTC
196 GCATTTTTAGCATTTCATATTTAGGATATACATTTTCTAACTCAGTGCTGTTTGATCTTACTTTC
39647073 TTTCATTTTATCTCTTTTGTGCCATTAATGTCACTGTATTTAGCACTGGTTTTGCGTCTAGAGTT
261 TTTCATTTTATCTCTTTTGTGCCATTAATGTCACTGTATTTAGCACTGGTTTTGCGTCTAGAGTT
39647138 GTCAACACAGAAATCCACTTGGAAAGATTAGAATTGGAAAGCATTTAGAGTGCGGTCACAAGATG
326 GTCAACACAGAAATCCACTTGGAAAGATTAGAATTGGAAAGCATTTAGAGTGCGGTCACAAGATG
39647203 ATCTAGAATTGCGGCCAAAGATGTTGTCACATGAATGCTTCCACAATTTATCAAAAATTTCACAC
391 ATCTAGAATTGCGGCCAAAGATGTTGTCACATGAATGCTTCCACAATTTATCAAAAATTTCACAC
*
39647268 TGCTAACATATCCAGAAGCACCAGCGCAGGAGAAAATT
456 TGCTAACATATCCAGAAGCACCAGCACAGGAGAAAATT
39647306 GTAAAATATGATTGGTAGAGGAATAGGAGAATCAACGGCAACATTCTTGTACCGAATCTAGAAAT
1 GTAAAATATGATTGGTAGAGGAATAGGAGAATCAACGGCAACATTCTTGTACCGAATCTAGAAAT
39647371 GATACGCCCAATCGAAGAACACTTGCAAGTCATCCCAACAAAATTAGAGATCATTGATAGCATTA
66 GATACGCCCAATCGAAGAACACTTGCAAGTCATCCCAACAAAATTAGAGATCATTGATAGCATTA
39647436 GAAATGAAACTTAGTTTCTCCTTAATTTAGTGTATAATTTGTTCCTTTTGTACCATTTCTAGCAT
131 GAAATGAAACTTAGTTTCTCCTTAATTTAGTGTATAATTTGTTCCTTTTGTACCATTTCTAGCAT
39647501 GCATTTTTAGCATTTCATATTTAGGATATACATTTTCTAACTCAGTGCTGTTTGATCTTACTTTC
196 GCATTTTTAGCATTTCATATTTAGGATATACATTTTCTAACTCAGTGCTGTTTGATCTTACTTTC
39647566 TTTCATTTTATCTCTTTTGTGCCATTAATGTCACTGTATTTAGCACTGGTTTTGCGTCTAGAGTT
261 TTTCATTTTATCTCTTTTGTGCCATTAATGTCACTGTATTTAGCACTGGTTTTGCGTCTAGAGTT
39647631 GTCAACACAGAAATCCACTTGGAAAGATTAGAATTGGAAAGCATTTAGAGTGCGGTCACAAGATG
326 GTCAACACAGAAATCCACTTGGAAAGATTAGAATTGGAAAGCATTTAGAGTGCGGTCACAAGATG
39647696 ATCTAGAATTGCGGCCAAAGATGTTGTCACATGAATGCTTCCACAATTTATCAAAAATTTCACAC
391 ATCTAGAATTGCGGCCAAAGATGTTGTCACATGAATGCTTCCACAATTTATCAAAAATTTCACAC
*
39647761 TGCTAACATATCTAGAAGCACCAGCACAGGAGAAAATT
456 TGCTAACATATCCAGAAGCACCAGCACAGGAGAAAATT
39647799 GT
1 GT
39647801 TGTAGCAAAT
Statistics
Matches: 493, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
493 493 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (493 bp):
GTAAAATATGATTGGTAGAGGAATAGGAGAATCAACGGCAACATTCTTGTACCGAATCTAGAAAT
GATACGCCCAATCGAAGAACACTTGCAAGTCATCCCAACAAAATTAGAGATCATTGATAGCATTA
GAAATGAAACTTAGTTTCTCCTTAATTTAGTGTATAATTTGTTCCTTTTGTACCATTTCTAGCAT
GCATTTTTAGCATTTCATATTTAGGATATACATTTTCTAACTCAGTGCTGTTTGATCTTACTTTC
TTTCATTTTATCTCTTTTGTGCCATTAATGTCACTGTATTTAGCACTGGTTTTGCGTCTAGAGTT
GTCAACACAGAAATCCACTTGGAAAGATTAGAATTGGAAAGCATTTAGAGTGCGGTCACAAGATG
ATCTAGAATTGCGGCCAAAGATGTTGTCACATGAATGCTTCCACAATTTATCAAAAATTTCACAC
TGCTAACATATCCAGAAGCACCAGCACAGGAGAAAATT
Found at i:39656427 original size:17 final size:16
Alignment explanation
Indices: 39656386--39656439 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
39656376 CACGAGATGA
39656386 AGGAGCAAGAAAAGAAG
1 AGGAG-AAGAAAAGAAG
*
39656403 AGAAAGAAGAAAAGGAAG
1 AG-GAGAAGAAAA-GAAG
39656421 AGGAGAAGGAAGAAGAAG
1 AGGAGAA-GAA-AAGAAG
39656439 A
1 A
39656440 AAGTATTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 13 0.42
18 16 0.52
19 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (16 bp):
AGGAGAAGAAAAGAAG
Found at i:39661012 original size:70 final size:70
Alignment explanation
Indices: 39660899--39661038 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
39660889 AAGATAGAAG
39660899 CATTAACTCGGTCAAAGAAACTTAAACCAACAACAAAGTCATAGTCATCAAGTGGTATTACCTTA
1 CATTAACTCGGTCAAAGAAACTTAAACCAACAACAAAGTCATAGTCATCAAGTGGTATTACCTTA
39660964 ATGTT
66 ATGTT
*
39660969 CATTAACTCGGTTAAAGAAACTTAAACCAACAACAAAGTCATAGTCATCAAGTGGTATTACCTTA
1 CATTAACTCGGTCAAAGAAACTTAAACCAACAACAAAGTCATAGTCATCAAGTGGTATTACCTTA
39661034 ATGTT
66 ATGTT
39661039 TGCTTTACCG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (70 bp):
CATTAACTCGGTCAAAGAAACTTAAACCAACAACAAAGTCATAGTCATCAAGTGGTATTACCTTA
ATGTT
Found at i:39665169 original size:30 final size:30
Alignment explanation
Indices: 39665133--39665199 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
39665123 GACGTGGAAG
*
39665133 TCAACCTATGGTGGAGCTTGACCCAGAGGA
1 TCAACCTATGGTGGAGCCTGACCCAGAGGA
* *
39665163 TCAACCTATGGTGGAGCCTGACTCGGAGGA
1 TCAACCTATGGTGGAGCCTGACCCAGAGGA
39665193 TCAACCT
1 TCAACCT
39665200 CCGAACACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.21
Consensus pattern (30 bp):
TCAACCTATGGTGGAGCCTGACCCAGAGGA
Found at i:39668521 original size:16 final size:15
Alignment explanation
Indices: 39668500--39668529 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39668490 AATTTTTAAA
39668500 TTAAAAAAAATCATAT
1 TTAAAAAAAA-CATAT
39668516 TTAAAAAAAACATA
1 TTAAAAAAAACATA
39668530 CACATTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
TTAAAAAAAACATAT
Found at i:39678935 original size:34 final size:34
Alignment explanation
Indices: 39678892--39678959 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
39678882 GAGTAAAATC
39678892 AATCATTCTGTACCAAGTTGATAGACGGTTATGG
1 AATCATTCTGTACCAAGTTGATAGACGGTTATGG
39678926 AATCATTCTGTACCAAGTTGATAGACGGTTATGG
1 AATCATTCTGTACCAAGTTGATAGACGGTTATGG
39678960 TAATGAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (34 bp):
AATCATTCTGTACCAAGTTGATAGACGGTTATGG
Found at i:39679930 original size:6 final size:6
Alignment explanation
Indices: 39679919--39679948 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
39679909 AGAGTTGAGT
39679919 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
39679949 ACCTTTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TTTGGG
Found at i:39683871 original size:27 final size:26
Alignment explanation
Indices: 39683817--39683876 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39683807 TGTTTTAATT
* *
39683817 TATATATTTTTTTAATAATTTATGTA
1 TATATATTTTTTTAATAATATATATA
* *
39683843 TATATTTTGTTTTTAATTATATATATA
1 TATATATT-TTTTTAATAATATATATA
39683870 TATATAT
1 TATATAT
39683877 ATATATACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TATATATTTTTTTAATAATATATATA
Found at i:39684030 original size:24 final size:24
Alignment explanation
Indices: 39684003--39684048 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
39683993 AAAAAAAAAT
39684003 GTAAGGATCAAGTTGAGGAAAACC
1 GTAAGGATCAAGTTGAGGAAAACC
39684027 GTAAGGATCAAGTTGAGGAAAA
1 GTAAGGATCAAGTTGAGGAAAA
39684049 TTGTCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.17
Consensus pattern (24 bp):
GTAAGGATCAAGTTGAGGAAAACC
Found at i:39694287 original size:23 final size:24
Alignment explanation
Indices: 39694258--39694304 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39694248 GATAAAAACT
39694258 AAACCCT-AAAACCTAAAAACAAA
1 AAACCCTCAAAACCTAAAAACAAA
* *
39694281 AAACCCTCAAAACGTAAACACAAA
1 AAACCCTCAAAACCTAAAAACAAA
39694305 TTTCTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.62, C:0.28, G:0.02, T:0.09
Consensus pattern (24 bp):
AAACCCTCAAAACCTAAAAACAAA
Found at i:39694447 original size:24 final size:24
Alignment explanation
Indices: 39694402--39694447 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
39694392 AGTCAAATAA
* * *
39694402 ATTATGCTATTAAATGCAAAATGT
1 ATTATACTAATAAATACAAAATGT
*
39694426 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACAAAAT
39694448 CTTCTAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (24 bp):
ATTATACTAATAAATACAAAATGT
Found at i:39699533 original size:20 final size:20
Alignment explanation
Indices: 39699520--39699558 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39699510 TTAAATAGGT
*
39699520 TTAATTAAAGTTAAAAATGG
1 TTAATTAAACTTAAAAATGG
*
39699540 TTAATTAAACTTAATAATG
1 TTAATTAAACTTAAAAATG
39699559 AAAGTCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
TTAATTAAACTTAAAAATGG
Found at i:39706756 original size:20 final size:20
Alignment explanation
Indices: 39706743--39706781 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39706733 TTAAATAGGT
*
39706743 TTAATTAAAGTTAAAAATGG
1 TTAATTAAACTTAAAAATGG
*
39706763 TTAATTAAACTTAATAATG
1 TTAATTAAACTTAAAAATG
39706782 AAAGTCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
TTAATTAAACTTAAAAATGG
Found at i:39710916 original size:24 final size:24
Alignment explanation
Indices: 39710888--39710947 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
39710878 ATTTAGCTCA
39710888 CACGAGCCTAGAATGGTTAACTCT
1 CACGAGCCTAGAATGGTTAACTCT
* *
39710912 CACGAGCCCAGAATGGTTAGCTCT
1 CACGAGCCTAGAATGGTTAACTCT
*
39710936 TACGAGCCTAGA
1 CACGAGCCTAGA
39710948 TAGAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (24 bp):
CACGAGCCTAGAATGGTTAACTCT
Found at i:39713385 original size:29 final size:29
Alignment explanation
Indices: 39713340--39713614 Score: 157
Period size: 30 Copynumber: 9.3 Consensus size: 29
39713330 GAAAATGAAG
* * *
39713340 TTTTAGGGAA-TTCAGGGTTAAAATACAC
1 TTTTAGGAAAGTTTAGGGTTAAAATACAA
**
39713368 TTTT-GGAAAAGTTTAGGGTTAAAATGTAA
1 TTTTAGG-AAAGTTTAGGGTTAAAATACAA
**
39713397 TTTTAGGAAAGTTTAGGGTTAAAATGTAA
1 TTTTAGGAAAGTTTAGGGTTAAAATACAA
* **
39713426 TTTTAGAGAAA-TTTAGAGATTAAAATGTAA
1 TTTTAG-GAAAGTTTAG-GGTTAAAATACAA
* * *
39713456 TTTTA-GAGAAGTTTGAGAGTCAAAATGCAA
1 TTTTAGGA-AAGTTT-AGGGTTAAAATACAA
* * * ***
39713486 TTTT-GGAGAAATTTGGGGGTCAAAATGTGA
1 TTTTAGGA-AAGTTT-AGGGTTAAAATACAA
* * * ***
39713516 TTTTGGGAAAGTTTTGGGGTGAAAATGTGA
1 TTTTAGGAAAG-TTTAGGGTTAAAATACAA
*
39713546 TTTTAGGAAAGTTTAGGGGTTAAAATATAA
1 TTTTAGGAAAGTTTA-GGGTTAAAATACAA
* * *
39713576 TTTTAGAAAAGTTTAAGGGTCAAAATATAA
1 TTTTAGGAAAGTTT-AGGGTTAAAATACAA
39713606 TTTT-GGAAA
1 TTTTAGGAAA
39713615 CATTTGGGCT
Statistics
Matches: 209, Mismatches: 25, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
27 2 0.01
28 8 0.04
29 60 0.29
30 130 0.62
31 9 0.04
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTTAGGAAAGTTTAGGGTTAAAATACAA
Found at i:39713451 original size:30 final size:31
Alignment explanation
Indices: 39713375--39713609 Score: 238
Period size: 30 Copynumber: 7.9 Consensus size: 31
39713365 CACTTTTGGA
39713375 AAAGTTTA-GGGTTAAAATGTAATTTTAG-G
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
39713404 AAAGTTTA-GGGTTAAAATGTAATTTTAGAG
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
* *
39713434 AAA-TTTAGAGATTAAAATGTAATTTTAGAG
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
* * * *
39713464 -AAGTTT-GAGAGTCAAAATGCAATTTTGGAG
1 AAAGTTTAG-GGGTTAAAATGTAATTTTAGAG
* * * *
39713494 AAA-TTTGGGGGTCAAAATGTGATTTT-GGG
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
* * *
39713523 AAAGTTTTGGGGTGAAAATGTGATTTTAG-G
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
*
39713553 AAAGTTTAGGGGTTAAAATATAATTTTAGA-
1 AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
* * *
39713583 AAAGTTTAAGGGTCAAAATATAATTTT
1 AAAGTTTAGGGGTTAAAATGTAATTTT
39713610 GGAAACATTT
Statistics
Matches: 177, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
29 40 0.23
30 133 0.75
31 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (31 bp):
AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
Found at i:39718097 original size:24 final size:24
Alignment explanation
Indices: 39718046--39718097 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39718036 TTCATAAGTC
* *
39718046 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
39718070 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
39718094 AAAT
1 AAAT
39718098 TTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:39722581 original size:16 final size:16
Alignment explanation
Indices: 39722560--39722590 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39722550 TGGTGTATCC
39722560 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
39722576 CATTTTATCTTTATT
1 CATTTTACCTTTATT
39722591 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:39726185 original size:38 final size:38
Alignment explanation
Indices: 39726142--39726237 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
39726132 AGGCTGTCCT
*
39726142 TGCATAAATATTCTTCAATTTGCATCCAGAACTATCAC
1 TGCATAAGTATTCTTCAATTTGCATCCAGAACTATCAC
* * *
39726180 TGCATAAGTATTCTTCAAATTGCATCTAGAACTATCGC
1 TGCATAAGTATTCTTCAATTTGCATCCAGAACTATCAC
39726218 TGCATAAGTATTCTTCAATT
1 TGCATAAGTATTCTTCAATT
39726238 GCACCTAGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (38 bp):
TGCATAAGTATTCTTCAATTTGCATCCAGAACTATCAC
Found at i:39732420 original size:12 final size:12
Alignment explanation
Indices: 39732399--39732441 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
39732389 CACATCCGAG
39732399 AAAG-AAAGGAA
1 AAAGAAAAGGAA
*
39732410 ACAGAAAAGGAA
1 AAAGAAAAGGAA
* *
39732422 AAAAAAAAGAAA
1 AAAGAAAAGGAA
39732434 AAAGAAAA
1 AAAGAAAA
39732442 AAAACTGACG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGGAA
Found at i:39734974 original size:27 final size:29
Alignment explanation
Indices: 39734944--39734998 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
39734934 TTTCTTAAAT
39734944 AATTATAAAAA-TATAAAAG-TTATTAAG
1 AATTATAAAAATTATAAAAGATTATTAAG
*
39734971 AATTATAAAAATTATAAATGATTATTAA
1 AATTATAAAAATTATAAAAGATTATTAA
39734999 TTATTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.44
28 7 0.28
29 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTATAAAAATTATAAAAGATTATTAAG
Found at i:39734995 original size:10 final size:9
Alignment explanation
Indices: 39734939--39734988 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
39734929 AGTGATTTCT
39734939 TAAATAATTA
1 TAAA-AATTA
39734949 TAAAAA-TA
1 TAAAAATTA
*
39734957 TAAAAGTTA
1 TAAAAATTA
*
39734966 TTAAGAATTA
1 -TAAAAATTA
39734976 TAAAAATTA
1 TAAAAATTA
39734985 TAAA
1 TAAA
39734989 TGATTATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.21
9 16 0.47
10 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:39735097 original size:30 final size:31
Alignment explanation
Indices: 39735063--39735121 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39735053 ATGTGTGCTT
* *
39735063 GAATTATAA-GAAATTATAAAAAAAAATTAA
1 GAATTATAATAAAATAATAAAAAAAAATTAA
*
39735093 GAATTATAATAAAATAATAAAATAAAATT
1 GAATTATAATAAAATAATAAAAAAAAATT
39735122 TATTAACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (31 bp):
GAATTATAATAAAATAATAAAAAAAAATTAA
Found at i:39737807 original size:4 final size:4
Alignment explanation
Indices: 39737798--39737826 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39737788 AAATAATATT
39737798 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
39737827 TTATTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:39738362 original size:30 final size:31
Alignment explanation
Indices: 39738295--39738362 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
39738285 TCTAATATGA
* *
39738295 AAAGTTTCATATTTAAATTTGAACCACAATT
1 AAAGTTTCATATGTAAATTTGAACCACAATC
* *
39738326 AAAGTTTCATATGTATAA-TTGCACTAC-ATC
1 AAAGTTTCATATGTA-AATTTGAACCACAATC
39738356 AAAGTTT
1 AAAGTTT
39738363 ATGTATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 9 0.28
31 21 0.66
32 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (31 bp):
AAAGTTTCATATGTAAATTTGAACCACAATC
Found at i:39740152 original size:16 final size:16
Alignment explanation
Indices: 39740131--39740166 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39740121 TTTTCATCTC
39740131 ATTTGCACTTAGGTTA
1 ATTTGCACTTAGGTTA
* *
39740147 ATTTGCATTTAGTTTA
1 ATTTGCACTTAGGTTA
39740163 ATTT
1 ATTT
39740167 AACATCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (16 bp):
ATTTGCACTTAGGTTA
Found at i:39744642 original size:111 final size:111
Alignment explanation
Indices: 39744438--39744665 Score: 393
Period size: 111 Copynumber: 2.1 Consensus size: 111
39744428 TGATGAATAT
*
39744438 GACTTGTACCGTCTCAGTATCGAAACATGAAAAACATTATGAATCTTTTCAAGTTTTGGGGGTAA
1 GACTCGTACCGTCTCAGTATCGAAACATGAAAAACATTATGAATCTTTTCAAGTTTTGGGGGTAA
* *
39744503 AGCTAGCCTGTAAGCTATAGAACTAAATCTTCCTGTAATCTTAAAC
66 AGCTAGCCTGTAAGCTATAGAACCAAATCTTCCTGTAATCTCAAAC
* *
39744549 GACTCGTACTGTCTCAGTATCGAAACATGAAAAACGTTATGAATCTTTTCAAGTTTTGGGGGTAA
1 GACTCGTACCGTCTCAGTATCGAAACATGAAAAACATTATGAATCTTTTCAAGTTTTGGGGGTAA
* *
39744614 AGCTAGCCTGTAAGCTATAGAACCAAATCTTCTTGTAATCTCATAC
66 AGCTAGCCTGTAAGCTATAGAACCAAATCTTCCTGTAATCTCAAAC
39744660 GACTCG
1 GACTCG
39744666 ATAAACCTTG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (111 bp):
GACTCGTACCGTCTCAGTATCGAAACATGAAAAACATTATGAATCTTTTCAAGTTTTGGGGGTAA
AGCTAGCCTGTAAGCTATAGAACCAAATCTTCCTGTAATCTCAAAC
Found at i:39754404 original size:33 final size:35
Alignment explanation
Indices: 39754374--39754456 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 35
39754364 GAGCCCAACT
*
39754374 CTAGTTGGATTAACCAACGATT-T-GCACCCAATG
1 CTAGTTGGATAAACCAACGATTATGGCACCCAATG
**
39754407 CTAGTTGGATAAACTGACGATTATGGCACCCAATG
1 CTAGTTGGATAAACCAACGATTATGGCACCCAATG
39754442 CCTAG-TGGATAAACC
1 -CTAGTTGGATAAACC
39754457 GCAAATGTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 19 0.44
34 1 0.02
35 19 0.44
36 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (35 bp):
CTAGTTGGATAAACCAACGATTATGGCACCCAATG
Found at i:39766678 original size:11 final size:11
Alignment explanation
Indices: 39766609--39766679 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
39766599 AAGCCTCTCA
39766609 CTTTTCTTTCT
1 CTTTTCTTTCT
*
39766620 CATTTT-TCTCT
1 C-TTTTCTTTCT
* *
39766631 CATTCCTTTCT
1 CTTTTCTTTCT
39766642 -TATTTCTTTCT
1 CT-TTTCTTTCT
39766653 CTTTTCTTT-T
1 CTTTTCTTTCT
39766663 CCTTTTCTTTCT
1 -CTTTTCTTTCT
39766675 CTTTT
1 CTTTT
39766680 AATCACTCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.06
11 39 0.81
12 6 0.12
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (11 bp):
CTTTTCTTTCT
Found at i:39767252 original size:20 final size:20
Alignment explanation
Indices: 39767224--39767268 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39767214 TGACCAACTG
*
39767224 TTGATCATTGACTTTGACCA
1 TTGACCATTGACTTTGACCA
*
39767244 TTGACCATTGACTTTGACTA
1 TTGACCATTGACTTTGACCA
39767264 TTGAC
1 TTGAC
39767269 TTTTTCGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGACCATTGACTTTGACCA
Found at i:39773806 original size:22 final size:23
Alignment explanation
Indices: 39773781--39773856 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 23
39773771 TCCTAAAGCC
*
39773781 TCTCACTTTTCTTTCTCATTT-T
1 TCTCTCTTTTCTTTCTCATTTCT
* * *
39773803 TCTCTCATTCCTTTCTTATTTCT
1 TCTCTCTTTTCTTTCTCATTTCT
39773826 T-TCTCTTTTCATTTC-CATTTCT
1 TCTCTCTTTTC-TTTCTCATTTCT
39773848 T-TCTCTTTT
1 TCTCTCTTTT
39773857 AATCACTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
22 39 0.87
23 6 0.13
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (23 bp):
TCTCTCTTTTCTTTCTCATTTCT
Found at i:39773827 original size:11 final size:11
Alignment explanation
Indices: 39773788--39773852 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
39773778 GCCTCTCACT
39773788 TTTCTTTCTCA
1 TTTCTTTCTCA
39773799 TTT-TTCTCTCA
1 TTTCTT-TCTCA
* *
39773810 TTCCTTTCTTA
1 TTTCTTTCTCA
*
39773821 TTTCTTTCTCT
1 TTTCTTTCTCA
39773832 TTTCATTTC-CA
1 TTTC-TTTCTCA
39773843 TTTCTTTCTC
1 TTTCTTTCTC
39773853 TTTTAATCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 6 0.14
11 32 0.73
12 6 0.14
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTCTTTCTCA
Found at i:39774392 original size:7 final size:7
Alignment explanation
Indices: 39774377--39774465 Score: 62
Period size: 7 Copynumber: 13.4 Consensus size: 7
39774367 ACTATTGACC
*
39774377 GACCATT
1 GACCGTT
39774384 GACCGTT
1 GACCGTT
*
39774391 GATCGTT
1 GACCGTT
39774398 GACC---
1 GACCGTT
39774402 GACCGTT
1 GACCGTT
*
39774409 GACCGTA
1 GACCGTT
*
39774416 GACCTTT
1 GACCGTT
39774423 GACCGTT
1 GACCGTT
*
39774430 GACCATT
1 GACCGTT
*
39774437 GA-CTTT
1 GACCGTT
*
39774443 GATCGTT
1 GACCGTT
*
39774450 GA-CTTT
1 GACCGTT
*
39774456 GACTGTT
1 GACCGTT
39774463 GAC
1 GAC
39774466 TTTTTCGAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
4 4 0.06
6 10 0.16
7 50 0.78
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:39774405 original size:25 final size:25
Alignment explanation
Indices: 39774371--39774452 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
39774361 AGTCAAACTA
39774371 TTGACCGACCATTGACCGTTGATCG
1 TTGACCGACCATTGACCGTTGATCG
* * * *
39774396 TTGACCGACCGTTGACCGTAGACCT
1 TTGACCGACCATTGACCGTTGATCG
*
39774421 TTGACCGTTGACCATTGA-CTTTGATCG
1 TTGACC---GACCATTGACCGTTGATCG
39774448 TTGAC
1 TTGAC
39774453 TTTGACTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
25 27 0.60
27 10 0.22
28 8 0.18
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
TTGACCGACCATTGACCGTTGATCG
Found at i:39774451 original size:13 final size:13
Alignment explanation
Indices: 39774435--39774468 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
39774425 CCGTTGACCA
39774435 TTGACTTTGA-TCG
1 TTGACTTTGACT-G
39774448 TTGACTTTGACTG
1 TTGACTTTGACTG
39774461 TTGACTTT
1 TTGACTTT
39774469 TTCGAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.50
Consensus pattern (13 bp):
TTGACTTTGACTG
Found at i:39780519 original size:41 final size:40
Alignment explanation
Indices: 39780450--39780574 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
39780440 AGATTGGGTT
* * *
39780450 ATGG-TTTCAATCCGCCCCATGATTGGGGTAAGAGATTGG
1 ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATTGG
* *
39780489 ATGGTTTTCAAATTTGCCCCATGATCGGGGTAAGAGATTAG
1 ATGGTTTT-AAATCTGCCCCATGATCGGGGTAAGAGATTGG
*
39780530 ATGGTTTTTAATCTGCCCCATGATCGGGGTAAGAGATTGG
1 ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATTGG
*
39780570 CTGGT
1 ATGGT
39780575 GATGTAACTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
39 4 0.05
40 36 0.48
41 35 0.47
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (40 bp):
ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATTGG
Found at i:39780558 original size:40 final size:40
Alignment explanation
Indices: 39780450--39780567 Score: 166
Period size: 41 Copynumber: 3.0 Consensus size: 40
39780440 AGATTGGGTT
* * * *
39780450 ATGG-TTTCAATCCGCCCCATGATTGGGGTAAGAGATTGG
1 ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATTAG
*
39780489 ATGGTTTTCAAATTTGCCCCATGATCGGGGTAAGAGATTAG
1 ATGGTTTT-AAATCTGCCCCATGATCGGGGTAAGAGATTAG
*
39780530 ATGGTTTTTAATCTGCCCCATGATCGGGGTAAGAGATT
1 ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATT
39780568 GGCTGGTGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
39 4 0.06
40 31 0.44
41 35 0.50
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (40 bp):
ATGGTTTTAAATCTGCCCCATGATCGGGGTAAGAGATTAG
Done.