Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1172281 original size:31 final size:31
Alignment explanation
Indices: 1172246--1172369 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 31
1172236 ATCCTCGGCA
* *
1172246 ACTGTCCATAGGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* **
1172277 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
*
1172308 ACTATCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-A-T
* * *
1172341 A-TGTCCATATGTTCCGTAGAACCTAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
1172370 AACCCTCGAC
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 22 0.29
33 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:1172362 original size:63 final size:62
Alignment explanation
Indices: 1172250--1172369 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 62
1172240 TCGGCAACTG
* *
1172250 TCCATAGGTCCCGAAGAACCTAGGTATACTGTCCATATGTTCCTTAGAACATAGGTATACTA
1 TCCATAGGTCCCGAAGAACATAGGTATACTGTCCATATGTTCCGTAGAACATAGGTATACTA
* *
1172312 TCCATATGTCCCGAA-AGACATAGGTAATTA-TGTCCATATGTTCCGTAGAACCTAGGTA
1 TCCATAGGTCCCGAAGA-ACATAGGT-A-TACTGTCCATATGTTCCGTAGAACATAGGTA
1172370 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 1 0.02
62 21 0.41
63 27 0.53
64 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (62 bp):
TCCATAGGTCCCGAAGAACATAGGTATACTGTCCATATGTTCCGTAGAACATAGGTATACTA
Found at i:1173248 original size:21 final size:21
Alignment explanation
Indices: 1173224--1173268 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1173214 CCATGTTCGT
* *
1173224 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1173245 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1173266 TTG
1 TTG
1173269 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1175371 original size:51 final size:51
Alignment explanation
Indices: 1175315--1175502 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 51
1175305 ACTTGATGTG
* * * * *
1175315 ATACTTTCAATTTATGCATTTTGGTCACTATTTATTTTTGATTTGGCTACT
1 ATACTTTCATTTTATGCATTTTAGTCACTATTTATTTCTGATTTAGCTATT
* * * *
1175366 GTACTTTTATTTTATGCATTTTAGTCAATGTTTATTTCTGATTTAGCTATT
1 ATACTTTCATTTTATGCATTTTAGTCACTATTTATTTCTGATTTAGCTATT
* * * *
1175417 TTTCTTTTATTTTATGCATTTTAGACACTATTTATTTCTGATTTAGCTATT
1 ATACTTTCATTTTATGCATTTTAGTCACTATTTATTTCTGATTTAGCTATT
** * *
1175468 ATTTTTTCATTTTATGCATTTTGGTCACTTTTTAT
1 ATACTTTCATTTTATGCATTTTAGTCACTATTTAT
1175503 GCTTCTTTAT
Statistics
Matches: 117, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (51 bp):
ATACTTTCATTTTATGCATTTTAGTCACTATTTATTTCTGATTTAGCTATT
Found at i:1176590 original size:19 final size:18
Alignment explanation
Indices: 1176558--1176614 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
1176548 ACTATGAATG
* *
1176558 AATAGAATGTAATGCGAAA
1 AATAAAATGCAATGC-AAA
*
1176577 TATAAAATGCAATGCAAA
1 AATAAAATGCAATGCAAA
*
1176595 AATAAAATGTATATGCAAA
1 AATAAAATGCA-ATGCAAA
1176614 A
1 A
1176615 TGCAAGTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (18 bp):
AATAAAATGCAATGCAAA
Found at i:1180770 original size:2 final size:2
Alignment explanation
Indices: 1180763--1180800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1180753 GGCAAATGCA
1180763 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
1180801 TTAGGGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1181115 original size:2 final size:2
Alignment explanation
Indices: 1181110--1181135 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1181100 ACATGCGCAA
1181110 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
1181136 TAATGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1184266 original size:23 final size:25
Alignment explanation
Indices: 1184240--1184292 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1184230 TTTTCAGGGT
*
1184240 TTACAAACCCAA-ACA-GGGTCCAA
1 TTACAAACCCAAGACATGGGCCCAA
*
1184263 TTAC-AACTCAAGACATGGGCCCAA
1 TTACAAACCCAAGACATGGGCCCAA
1184287 TTACAA
1 TTACAA
1184293 GCAAACCTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 7 0.28
24 11 0.44
25 1 0.04
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (25 bp):
TTACAAACCCAAGACATGGGCCCAA
Found at i:1191692 original size:14 final size:14
Alignment explanation
Indices: 1191675--1191710 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1191665 AAAAGACAGA
*
1191675 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
1191689 AAATTAAAGGACTG
1 AAATTAAAGGAATG
1191703 AAATTAAA
1 AAATTAAA
1191711 TAAAGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:1191973 original size:23 final size:22
Alignment explanation
Indices: 1191900--1191973 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
1191890 AAGGTTAGCG
*
1191900 GTTAGTGGTTAGCAGATAGAAAT
1 GTTAGTGGTTAGAAG-TAGAAAT
* * *
1191923 GTTAATTGTTAGAAG-AGACAGT
1 GTTAGTGGTTAGAAGTAGA-AAT
*
1191945 GTTTAGTGGTTAGTAGTTAGAAAT
1 G-TTAGTGGTTAGAAG-TAGAAAT
1191969 GTTAG
1 GTTAG
1191974 CTGTTAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 27 0.69
24 3 0.08
25 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (22 bp):
GTTAGTGGTTAGAAGTAGAAAT
Found at i:1192986 original size:15 final size:15
Alignment explanation
Indices: 1192947--1192975 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1192937 CTCAAAAGAA
1192947 AGAAAGAAAAATTGG
1 AGAAAGAAAAATTGG
1192962 AGAAAGAAAAATTG
1 AGAAAGAAAAATTG
1192976 AGAGCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (15 bp):
AGAAAGAAAAATTGG
Found at i:1194125 original size:139 final size:139
Alignment explanation
Indices: 1193892--1194273 Score: 435
Period size: 139 Copynumber: 2.8 Consensus size: 139
1193882 TTAAATAAGT
* * *
1193892 CATTGTTCCTTCATGTTGAGGACTTTTAGCCGTATTT-G-GATAATTTGGAGACAATGTGGTTCC
1 CATTGTTCATTCATGTTGAGGACATTTAGCCGTATTTGGAGATAATTTGGAGACAATATGGTTCC
** * * * * *
1193955 TTCGTGTTGAAGAAGTTTGATTGTCTAAGGATGACACTACTTCTTCACGTTGAAGAGATCTGGTT
66 TTCGCATTGAGGAAGTATGATTGTCTGAGGATGACACTACTTCTTCACGTTGAAGAGATCTGATC
*
1194020 GGTGGATGA
131 GGTGGACGA
* * * * * * * *
1194029 CCTTGTTCTTTCATGTTGAGGACGTTTAGCCATATTTGGAGATAATTTAGAGACAACACGGTTCT
1 CATTGTTCATTCATGTTGAGGACATTTAGCCGTATTTGGAGATAATTTGGAGACAATATGGTTCC
* * *** * *
1194094 TTCGCATTGAGGAAGTATGATTGTCTGAGGATGACATTGCTTCTTTGTGTTGAGGAGATTTGATC
66 TTCGCATTGAGGAAGTATGATTGTCTGAGGATGACACTACTTCTTCACGTTGAAGAGATCTGATC
1194159 GGTGGACGA
131 GGTGGACGA
* * * *
1194168 CATTGTTCAGTCGTGTTGAGGACATCTAGCTGTATTTGGAGATAATTTGGAGACAATATGGTTCC
1 CATTGTTCATTCATGTTGAGGACATTTAGCCGTATTTGGAGATAATTTGGAGACAATATGGTTCC
* * * * *
1194233 TTCTCTTTGAGGAAGTCTGATTGCCTGATGATGACACTACT
66 TTCGCATTGAGGAAGTATGATTGTCTGAGGATGACACTACT
1194274 CCTCCATGTT
Statistics
Matches: 200, Mismatches: 43, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
137 33 0.17
138 1 0.00
139 166 0.83
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (139 bp):
CATTGTTCATTCATGTTGAGGACATTTAGCCGTATTTGGAGATAATTTGGAGACAATATGGTTCC
TTCGCATTGAGGAAGTATGATTGTCTGAGGATGACACTACTTCTTCACGTTGAAGAGATCTGATC
GGTGGACGA
Found at i:1194733 original size:102 final size:100
Alignment explanation
Indices: 1194616--1194928 Score: 420
Period size: 97 Copynumber: 3.1 Consensus size: 100
1194606 TTTCAAAAGA
* *
1194616 AACTATCTCAAGTGAGGTAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTTCGTTTCAAGGG
1 AACTATCTCAAGTGAGAT-AAATTTTGTTTCAAGTGAAACAATTTCAAAATTTT-GTTTCAAGGG
* *
1194681 AAAATTATCTCAAGCGAGACGAAATTTGTTTTGAGAG
64 AAAATTGTCTCAAGCGAGATGAAATTTGTTTTGAGAG
*
1194718 AACTATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAA--T--AAATTTGTGTTT-AGAGGG
1 AACTATCTCAAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTT-TGTTTCA-AGGG
1194778 AAAATTGTCTCAAGCGAGATGAAATTTGTTTTGAGAG
64 AAAATTGTCTCAAGCGAGATGAAATTTGTTTTGAGAG
* * *
1194815 AACTATATCAAGTGAGATCAATTTTTGTTTCAAGTGAAACAATTTCAAAATTTTTGTTTCGAGGG
1 AACTATCTCAAGTGAGAT-AAATTTTGTTTCAAGTGAAACAATTTCAAAA-TTTTGTTTCAAGGG
* **
1194880 AAAACTGTCTCAAGCGAGATGAAATTTGTTTCAAGAG
64 AAAATTGTCTCAAGCGAGATGAAATTTGTTTTGAGAG
*
1194917 AAACAATCTCAA
1 -AACTATCTCAA
1194929 AGGTGACAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
96 1 0.01
97 66 0.35
98 22 0.12
99 1 0.01
100 1 0.01
101 21 0.11
102 63 0.34
103 12 0.06
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (100 bp):
AACTATCTCAAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTTGTTTCAAGGGAA
AATTGTCTCAAGCGAGATGAAATTTGTTTTGAGAG
Found at i:1196940 original size:25 final size:24
Alignment explanation
Indices: 1196885--1196949 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
1196875 TTTTATTTTT
* *
1196885 AAAATTTTGAAAAATATCAATTAA
1 AAAATTTTAAAAAATATCAATCAA
* *
1196909 AAGAATTTTAAAAAATGTTTAATCAA
1 AA-AATTTTAAAAAAT-ATCAATCAA
*
1196935 AAAATTTGAAAAAAT
1 AAAATTTTAAAAAAT
1196950 TACCCTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 2 0.06
25 24 0.71
26 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (24 bp):
AAAATTTTAAAAAATATCAATCAA
Found at i:1197796 original size:19 final size:20
Alignment explanation
Indices: 1197772--1197851 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 20
1197762 ACTTGATCTG
1197772 TTTTCTTTCTTTTTT-TTCT
1 TTTTCTTTCTTTTTTCTTCT
1197791 TTTTCTTTTCTTTGTTTCTTCT
1 TTTTC-TTTCTTT-TTTCTTCT
*
1197813 TTTTCCTCTTCTTTTCTCTT-T
1 TTTT-CT-TTCTTTTTTCTTCT
*
1197834 TCTTTGTTTCTTATTTTC
1 T-TTTCTTTCTT-TTTTC
1197852 CTGTCCTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 10 0.20
22 17 0.33
23 7 0.14
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCTTTCTTTTTTCTTCT
Found at i:1197797 original size:15 final size:15
Alignment explanation
Indices: 1197777--1197816 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1197767 ATCTGTTTTC
1197777 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTTCTT
* *
1197792 TTTCTTTTCTTTGTT
1 TTTCTTTTTTTTCTT
1197807 TCTTCTTTTT
1 T-TTCTTTTT
1197817 CCTCTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:1197799 original size:12 final size:12
Alignment explanation
Indices: 1197772--1197838 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 12
1197762 ACTTGATCTG
*
1197772 TTTTCTTTCTTTT
1 TTTTCTTT-TTCT
1197785 TTTTCTTTTTC-
1 TTTTCTTTTTCT
*
1197796 TTTTCTTTGT-T
1 TTTTCTTTTTCT
* *
1197807 TCTTCTTTTTCC
1 TTTTCTTTTTCT
*
1197819 TCTTC-TTTTCT
1 TTTTCTTTTTCT
1197830 CTTTTCTTT
1 -TTTTCTTT
1197839 GTTTCTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 22 0.51
12 11 0.26
13 10 0.23
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:1197817 original size:28 final size:26
Alignment explanation
Indices: 1197777--1197845 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
1197767 ATCTGTTTTC
* *
1197777 TTTCTTTTTTTTCTTTTTCTTTTCTTT
1 TTTC-TTTTTTTCTTCTTCTTTTCTCT
*
1197804 GTTTCTTCTTTTTCCTCTTCTTTTCTCT
1 -TTTCTT-TTTTTCTTCTTCTTTTCTCT
*
1197832 TTTCTTTGTTTCTT
1 TTTCTTTTTTTCTT
1197846 ATTTTCCTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.17
27 8 0.23
28 21 0.60
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTCTTTTTTTCTTCTTCTTTTCTCT
Found at i:1197851 original size:34 final size:34
Alignment explanation
Indices: 1197787--1197853 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 34
1197777 TTTCTTTTTT
*
1197787 TTCTTTTTCTTTTCTTTGTTTCTTCTTTTTCCTC
1 TTCTTTTTCTTTTCTTTGTTTCTTCATTTTCCTC
1197821 TTCTTTTCTCTTTTCTTTGTTTCTT-ATTTTCCT
1 TTCTTTT-TCTTTTCTTTGTTTCTTCATTTTCCT
1197854 GTCCTCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.73
Consensus pattern (34 bp):
TTCTTTTTCTTTTCTTTGTTTCTTCATTTTCCTC
Found at i:1202450 original size:15 final size:16
Alignment explanation
Indices: 1202430--1202464 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1202420 ATAAAGAGAA
*
1202430 TAAAAG-GCATAAATT
1 TAAAAGTGCATAAAAT
1202445 TAAAAGTGCATAAAAT
1 TAAAAGTGCATAAAAT
1202461 TAAA
1 TAAA
1202465 TAACTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (16 bp):
TAAAAGTGCATAAAAT
Found at i:1202681 original size:39 final size:39
Alignment explanation
Indices: 1202633--1202707 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1202623 CGGTTAGTGT
*
1202633 TTAGCAGTTAGAAAGGTTA-ATTGTTAGAAAAGTTAGCAC
1 TTAGCAGTTAGAAAGGTTAGA-TGTTAAAAAAGTTAGCAC
* *
1202672 TTAGTAGTTAGAAATGTTAGATGTTAAAAAAGTTAG
1 TTAGCAGTTAGAAAGGTTAGATGTTAAAAAAGTTAG
1202708 TGGTTAGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (39 bp):
TTAGCAGTTAGAAAGGTTAGATGTTAAAAAAGTTAGCAC
Found at i:1203745 original size:14 final size:15
Alignment explanation
Indices: 1203715--1203746 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1203705 CTCAAAAGAA
1203715 AGAAAGAAAATATGG
1 AGAAAGAAAATATGG
1203730 AGAAAGAAAA-ATGG
1 AGAAAGAAAATATGG
1203744 AGA
1 AGA
1203747 GCAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.09
Consensus pattern (15 bp):
AGAAAGAAAATATGG
Found at i:1204100 original size:19 final size:21
Alignment explanation
Indices: 1204076--1204117 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204066 TTCGGACAAA
1204076 ATTAAGG-TAT-TATATAGAT
1 ATTAAGGATATATATATAGAT
*
1204095 ATTAAGGATATATATATATAT
1 ATTAAGGATATATATATAGAT
1204116 AT
1 AT
1204118 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (21 bp):
ATTAAGGATATATATATAGAT
Found at i:1205641 original size:81 final size:81
Alignment explanation
Indices: 1205506--1205670 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
1205496 AAAAAATAAC
1205506 TTTATCATATAATACATTTAGTATATTATTTTCTGAAGTACTAATTATTATTGGTCTAAAGACGT
1 TTTATCATATAATACATTTAGTATATTATTTTCTGAAGTACTAATTATTATTGGTCTAAAGACGT
1205571 CGTGTACTCCTGGAGT
66 CGTGTACTCCTGGAGT
*
1205587 TTTATCATATAATGCATTTAGTATATTATTTTCTGAAGTACTAATTATTATTGGTCTAAAGACGT
1 TTTATCATATAATACATTTAGTATATTATTTTCTGAAGTACTAATTATTATTGGTCTAAAGACGT
1205652 CGTGTACTCCTGGAGT
66 CGTGTACTCCTGGAGT
1205668 TTT
1 TTT
1205671 CTCCATTTGC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (81 bp):
TTTATCATATAATACATTTAGTATATTATTTTCTGAAGTACTAATTATTATTGGTCTAAAGACGT
CGTGTACTCCTGGAGT
Found at i:1206115 original size:39 final size:38
Alignment explanation
Indices: 1206072--1206155 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
1206062 AGCCAAATAT
*
1206072 GAAGACTACACGACTGCATGACGTCTTTAGGCAAAT-GAA
1 GAAGACTACA--ACTGCATGACGTCTTTAGACAAATGGAA
*
1206111 GAAGACCCTACAACTGCATGGCGTCTTTAGACAAATGGAA
1 GAAGA--CTACAACTGCATGACGTCTTTAGACAAATGGAA
1206151 -AAGAC
1 GAAGAC
1206156 CCTTTAAGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
37 1 0.03
39 31 0.77
40 3 0.08
41 5 0.12
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (38 bp):
GAAGACTACAACTGCATGACGTCTTTAGACAAATGGAA
Found at i:1206156 original size:39 final size:39
Alignment explanation
Indices: 1206084--1206199 Score: 121
Period size: 39 Copynumber: 3.0 Consensus size: 39
1206074 AGACTACACG
*
1206084 ACTGCATGACGTCTTTAGGCAAATGAAGAAGACCCTACA
1 ACTGCATGACGTCTTTAGACAAATGAAGAAGACCCTACA
* **
1206123 ACTGCATGGCGTCTTTAGACAAATGGAA-AAGACCCTTTA
1 ACTGCATGACGTCTTTAGACAAAT-GAAGAAGACCCTACA
* * * * *
1206162 AGTGTACGACGTCTTCAGACCAAT-AAGAAG-CCCTACA
1 ACTGCATGACGTCTTTAGACAAATGAAGAAGACCCTACA
1206199 A
1 A
1206200 AAAATAATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
37 8 0.13
38 3 0.05
39 49 0.78
40 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (39 bp):
ACTGCATGACGTCTTTAGACAAATGAAGAAGACCCTACA
Found at i:1210148 original size:34 final size:35
Alignment explanation
Indices: 1210109--1210218 Score: 107
Period size: 36 Copynumber: 3.1 Consensus size: 35
1210099 TAAGAAATTT
* *
1210109 TTTTTTATTTTAGTAT-TTT-TTTAAATAGTTATTA
1 TTTTTTATTTTAATATATTTATGTAAATA-TTATTA
* *
1210143 TTTTTTATATTAATATATTTATGTAAATATTATTT
1 TTTTTTATTTTAATATATTTATGTAAATATTATTA
** * *
1210178 TTTTTTATTAAAATAATATTTATATAATTATTATTTA
1 TTTTTTATTTTAAT-ATATTTATGTAAATATTA-TTA
1210215 TTTT
1 TTTT
1210219 GAATTATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 14 0.23
35 19 0.31
36 23 0.37
37 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (35 bp):
TTTTTTATTTTAATATATTTATGTAAATATTATTA
Found at i:1211970 original size:21 final size:21
Alignment explanation
Indices: 1211940--1211987 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1211930 GCAGGGGTAC
* *
1211940 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1211961 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1211982 ATGCCA
1 ATGCCA
1211988 TCTCCGCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1212015 original size:21 final size:21
Alignment explanation
Indices: 1211991--1212084 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
1211981 TATGCCATCT
*
1211991 CCGCAGTGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1212012 CCGCAGGGTTACATTCTGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1212033 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1212054 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
*
1212075 CCACAGGGTT
1 CCGCAGGGTT
1212085 TTATACCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1212657 original size:34 final size:34
Alignment explanation
Indices: 1212607--1212704 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
1212597 AAATGTTTTT
*
1212607 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1212641 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1212675 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1212705 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1213264 original size:128 final size:128
Alignment explanation
Indices: 1213105--1213602 Score: 921
Period size: 128 Copynumber: 3.9 Consensus size: 128
1213095 TTACCTGATT
1213105 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1213170 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1213233 TACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1213298 TGACAAAATAATGGAAGGCGCGCCTCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1213361 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1213426 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1213489 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATTTTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1213554 TG---AAATAATAGAAGGCGCGCCCTCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1213603 ACTCCAATTA
Statistics
Matches: 362, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
125 45 0.12
128 317 0.88
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1213686 original size:8 final size:8
Alignment explanation
Indices: 1213673--1213713 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1213663 TCACAAGCTT
1213673 TCAAATTC
1 TCAAATTC
1213681 TCAAATTC
1 TCAAATTC
* *
1213689 CCAAACTC
1 TCAAATTC
1213697 T-AAATTC
1 TCAAATTC
1213704 TCAAATTC
1 TCAAATTC
1213712 TC
1 TC
1213714 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1219330 original size:29 final size:29
Alignment explanation
Indices: 1219297--1219360 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1219287 AAAAATTCGG
1219297 TTAATTCAGTTCGGTTAATAATTTTCAAA
1 TTAATTCAGTTCGGTTAATAATTTTCAAA
** *
1219326 TTAATTTGGTTCGGTTAATAATTTTTAAA
1 TTAATTCAGTTCGGTTAATAATTTTCAAA
*
1219355 TAAATT
1 TTAATT
1219361 TTGGTTCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.48
Consensus pattern (29 bp):
TTAATTCAGTTCGGTTAATAATTTTCAAA
Found at i:1219361 original size:29 final size:30
Alignment explanation
Indices: 1219305--1219373 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
1219295 GGTTAATTCA
*
1219305 GTTCGGTTAATAATTTTCAAATTAA-TTTG
1 GTTCGGTTAATAATTTTCAAATAAATTTTG
*
1219334 GTTCGGTTAATAATTTTTAAATAAATTTTG
1 GTTCGGTTAATAATTTTCAAATAAATTTTG
*
1219364 GTTCGATTAA
1 GTTCGGTTAA
1219374 CCGAACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (30 bp):
GTTCGGTTAATAATTTTCAAATAAATTTTG
Found at i:1219467 original size:29 final size:29
Alignment explanation
Indices: 1219434--1219614 Score: 102
Period size: 29 Copynumber: 6.2 Consensus size: 29
1219424 AAAAAATCGG
*
1219434 TTAATTCAGTTAGGTTAATAATTTTCAAA
1 TTAATTCAGTCAGGTTAATAATTTTCAAA
* *
1219463 TTAATTCGGTCCGGTTAATAATTTTCAAA
1 TTAATTCAGTCAGGTTAATAATTTTCAAA
* * * * ***
1219492 TTAA-CCGAATC-GAATTAACCGAATTTT-TGC
1 TTAATTC-AGTCAG-GTTAA--TAATTTTCAAA
** * *
1219522 TTCGGTTAATTC-GGTTAATAATTTTCAAA
1 TT-AATTCAGTCAGGTTAATAATTTTCAAA
* **
1219551 TTAATTCGGTTGGGTTAATAATTTTCAAA
1 TTAATTCAGTCAGGTTAATAATTTTCAAA
*
1219580 TTAATTCGGTTC-GGTTAATAATTTTCAAA
1 TTAATTCAG-TCAGGTTAATAATTTTCAAA
*
1219609 TAAATT
1 TTAATT
1219615 TTGGTTTGAT
Statistics
Matches: 114, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
28 11 0.10
29 86 0.75
30 7 0.06
31 10 0.09
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (29 bp):
TTAATTCAGTCAGGTTAATAATTTTCAAA
Found at i:1219743 original size:20 final size:20
Alignment explanation
Indices: 1219701--1219743 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1219691 ATTAGTCGTG
* ***
1219701 AATAATTTATTTAATTTTTT
1 AATAATTTATTTAAATAAAT
1219721 AATAATTTATTTAAATAAAT
1 AATAATTTATTTAAATAAAT
1219741 AAT
1 AAT
1219744 TTATTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATTTATTTAAATAAAT
Found at i:1220844 original size:23 final size:23
Alignment explanation
Indices: 1220809--1220905 Score: 122
Period size: 23 Copynumber: 4.2 Consensus size: 23
1220799 CCAGTAATTA
** *
1220809 ACCTATTTTATTATATAAGCACT
1 ACCTATTACATTATATAAGCGCT
* * *
1220832 ATCTATTACATTATATAACCGTT
1 ACCTATTACATTATATAAGCGCT
*
1220855 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAGCGCT
*
1220878 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
1220901 ACCTA
1 ACCTA
1220906 ATATGTTGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1221473 original size:274 final size:275
Alignment explanation
Indices: 1220984--1221535 Score: 1016
Period size: 274 Copynumber: 2.0 Consensus size: 275
1220974 GTTTTAAAAT
*
1220984 TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
1 TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
*
1221049 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
66 ATATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
1221114 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCATAA
131 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCATAA
* *
1221179 CATAAAAATAAATCATTAGACGTGTATGATTACTAAATTAATATCTTAAAACTCACTAAAAAA-A
196 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAATA
1221243 TAACATAACCGATTA
261 TAACATAACCGATTA
*
1221258 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1 TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
*
1221323 ATATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAATAATTTTAACCAA
66 ATATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
*
1221388 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
131 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCATAA
1221453 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAATA
196 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAATA
* *
1221518 TAACATAATCGGTTA
261 TAACATAACCGATTA
1221533 TTT
1 TTT
1221536 ACTGGAAACA
Statistics
Matches: 268, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
274 251 0.94
275 17 0.06
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (275 bp):
TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
ATATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCATAA
CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAATA
TAACATAACCGATTA
Found at i:1221801 original size:155 final size:156
Alignment explanation
Indices: 1221517--1221821 Score: 585
Period size: 155 Copynumber: 2.0 Consensus size: 156
1221507 ACTAAAAAAT
1221517 ATAACATAATCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGTAAAAAAAAAT
1 ATAACATAATCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT-AAAAAAAAT
*
1221582 AGGCGCTACTTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCCATTTAAATAA
65 AGGCGCTACCTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCCATTTAAATAA
1221647 GTATCGACACTTTTGGAATTACCAAGG
130 GTATCGACACTTTTGGAATTACCAAGG
1221674 ATAACATAATCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT-AAAAAAATA
1 ATAACATAATCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGTAAAAAAAATA
1221738 GGCGCTACCTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCCATTTAAATAAG
66 GGCGCTACCTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCCATTTAAATAAG
1221803 TATCGACACTTTTGGAATT
131 TATCGACACTTTTGGAATT
1221822 TAAAAGAAAA
Statistics
Matches: 147, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
155 92 0.63
157 55 0.37
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (156 bp):
ATAACATAATCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGTAAAAAAAATA
GGCGCTACCTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCCATTTAAATAAG
TATCGACACTTTTGGAATTACCAAGG
Found at i:1221992 original size:23 final size:23
Alignment explanation
Indices: 1221965--1222015 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1221955 CCAGTAATTA
**
1221965 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1221988 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
1222011 ACCTA
1 ACCTA
1222016 ATATGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1222075 original size:87 final size:87
Alignment explanation
Indices: 1221939--1222102 Score: 310
Period size: 87 Copynumber: 1.9 Consensus size: 87
1221929 ATATGTTGAA
*
1221939 GTGCTTGATAATTTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
1 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
*
1222004 AAGCGCTACCTAATATGTTATT
66 AAACGCTACCTAATATGTTATT
1222026 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
1 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
1222091 AAACGCTACCTA
66 AAACGCTACCTA
1222103 TTACATCATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (87 bp):
GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
AAACGCTACCTAATATGTTATT
Found at i:1222087 original size:23 final size:23
Alignment explanation
Indices: 1222052--1222108 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1222042 CCAGTAATTA
** *
1222052 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAACGCT
1222075 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
1222098 ACCTATTACAT
1 ACCTATTACAT
1222109 CATAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:1222901 original size:31 final size:31
Alignment explanation
Indices: 1222863--1222961 Score: 134
Period size: 31 Copynumber: 3.3 Consensus size: 31
1222853 ATCCATTAAA
1222863 TTTAGGGTTAGGAATTTACAAATTTATGTAT
1 TTTAGGGTTAGGAATTTACAAATTTATGTAT
* **
1222894 TTTAGGGTTTGGAA-TTACAACAAAT-TG-A-
1 TTTAGGGTTAGGAATTTACAA-ATTTATGTAT
1222922 TTTAGGGTTAGGAATTTACAAATTTATGTAT
1 TTTAGGGTTAGGAATTTACAAATTTATGTAT
1222953 TTTAGGGTT
1 TTTAGGGTT
1222962 TGTAATTACA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
28 15 0.26
29 9 0.16
30 9 0.16
31 24 0.42
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.43
Consensus pattern (31 bp):
TTTAGGGTTAGGAATTTACAAATTTATGTAT
Found at i:1222929 original size:59 final size:59
Alignment explanation
Indices: 1222862--1222976 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
1222852 CATCCATTAA
1222862 ATTTAGGGTTAGGAATTTACAAATTTATGTATTTTAGGGTTTGGAATTACAACAAATTG
1 ATTTAGGGTTAGGAATTTACAAATTTATGTATTTTAGGGTTTGGAATTACAACAAATTG
*
1222921 ATTTAGGGTTAGGAATTTACAAATTTATGTATTTTAGGGTTTGTAATTACAACAAA
1 ATTTAGGGTTAGGAATTTACAAATTTATGTATTTTAGGGTTTGGAATTACAACAAA
1222977 GTGAGGATAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (59 bp):
ATTTAGGGTTAGGAATTTACAAATTTATGTATTTTAGGGTTTGGAATTACAACAAATTG
Found at i:1223164 original size:20 final size:20
Alignment explanation
Indices: 1223139--1223177 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1223129 CAATGAATCA
*
1223139 GCTGAAAACCGGTAGAACCG
1 GCTGAAAACCGGTAAAACCG
1223159 GCTGAAAACCGGTAAAACC
1 GCTGAAAACCGGTAAAACC
1223178 AGGGTGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.26, T:0.10
Consensus pattern (20 bp):
GCTGAAAACCGGTAAAACCG
Found at i:1223214 original size:29 final size:29
Alignment explanation
Indices: 1223143--1223217 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1223133 GAATCAGCTG
* *
1223143 AAAACCGGTAGAACCGGCTGAAAACCGGT
1 AAAACCGGTTGAACCGGCTGAAAACCGAT
*
1223172 AAAACCAGGGTGAACCGGCTG-AAACCGAT
1 AAAACC-GGTTGAACCGGCTGAAAACCGAT
1223201 AAAACCGGTTTGAACCG
1 AAAACCGG-TTGAACCG
1223218 CCAGTTCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.05
29 26 0.65
30 12 0.30
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (29 bp):
AAAACCGGTTGAACCGGCTGAAAACCGAT
Found at i:1225785 original size:2 final size:2
Alignment explanation
Indices: 1225778--1225807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1225768 TATTAAACAA
1225778 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
1225808 TAGTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1235872 original size:9 final size:9
Alignment explanation
Indices: 1235852--1235918 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
1235842 CCATTTTGTC
1235852 TTTTATTTTA
1 TTTTA-TTTA
1235862 TTTTATTTA
1 TTTTATTTA
* *
1235871 TTTGACTTTC
1 TTTTA-TTTA
1235881 TTTTA-TTA
1 TTTTATTTA
1235889 TTTTAATTT-
1 TTTT-ATTTA
1235898 TTTTATTGT-
1 TTTTATT-TA
1235907 TTTT-TTTA
1 TTTTATTTA
1235915 TTTT
1 TTTT
1235919 CTTTTTTACT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
7 1 0.02
8 15 0.31
9 18 0.38
10 14 0.29
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1235872 original size:14 final size:13
Alignment explanation
Indices: 1235857--1235925 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
1235847 TTGTCTTTTA
1235857 TTTTATTTTATTT
1 TTTTATTTTATTT
* * *
1235870 ATTTGACTTTCTTT
1 -TTTTATTTTATTT
*
1235884 TATTATTTTAATTT
1 TTTTATTTT-ATTT
*
1235898 TTTTATTGT-TTT
1 TTTTATTTTATTT
*
1235910 TTTTATTTTCTTT
1 TTTTATTTTATTT
1235923 TTT
1 TTT
1235926 ACTAACTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
12 11 0.26
13 12 0.28
14 20 0.47
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:1241379 original size:84 final size:82
Alignment explanation
Indices: 1241238--1242129 Score: 868
Period size: 84 Copynumber: 10.8 Consensus size: 82
1241228 TAAATGAACT
* * * * * *
1241238 ATTTGTAGCATAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-AC-AAAGACCTTCGAGTTCGACTACA
* *
1241303 CTCAGCTCAAAGGCACAAC
64 CTCAGCTCGAAGGCACATC
* * * **
1241322 ATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCATACAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC--ACAAAGACCTTCGAGTTCGACTACA
* *
1241387 CTCAGCTCTAAGGCATATC
64 CTCAGCTCGAAGGCACATC
* * *
1241406 ATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTGCG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A-CAAAGACCTTCGAGTTCGACTACA
*
1241471 CTCAGCTCCAAGGCACATC
64 CTCAGCTCGAAGGCACATC
* * * * *
1241490 ATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACACT
* *
1241553 CAGCTTCGAGGGCATATC
66 CAGC-TCGAAGGCACATC
* * * * * *
1241571 ATTTACAGCATAACTCAAGGCTACAAGGGTTATCTGTCCACAAGAGACCTTCAAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CCACAA-AGACCTTCGAGTTCGACTACA
*
1241636 CTCAGCTCCG-AGGCATATC
64 CTCAGCT-CGAAGGCACATC
* * *
1241655 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A-CAAAGACCTTCGAGTTCGACTACA
*
1241720 CTCAGCTCTAAGGCACATC
64 CTCAGCTCGAAGGCACATC
* * * * * * *
1241739 ATTTGCAGTATAGCTTAAATCGAGAAGGGCTATCTG-C-CAAAGACCCTAGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACACT
* *
1241802 CAACTCGAGGGCACATC
66 CAGCTCGAAGGCACATC
* * * * * * *
1241819 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATATGTCTC-CAAAAGACCTTCGAGTTCGTCTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-CAC-AAAGACCTTCGAGTTCGACTAC
* *
1241883 GCTCAGCTCTAAGGCACATC
63 ACTCAGCTCGAAGGCACATC
* * * * *
1241903 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTTGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACACT
* * *
1241966 CAACTTCGAGGGCGCATC
66 CAGC-TCGAAGGCACATC
* * * * * * * *
1241984 ATTTACATCATAACTCAAGGCTAGAAGAGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA-C-AAAGACCTTCGAGTTCGACTACA
*
1242049 CTCAGCTCAAAGGCACCATC
64 CTCAGCTCGAAGGCA-CATC
* * *
1242069 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTA-AAA-ACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACA
1242130 TTCAACTTAG
Statistics
Matches: 667, Mismatches: 120, Indels: 45
0.80 0.14 0.05
Matches are distributed among these distances:
80 113 0.17
81 97 0.15
82 4 0.01
83 9 0.01
84 353 0.53
85 91 0.14
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACACT
CAGCTCGAAGGCACATC
Found at i:1241642 original size:165 final size:163
Alignment explanation
Indices: 1241244--1242124 Score: 677
Period size: 164 Copynumber: 5.3 Consensus size: 163
1241234 AACTATTTGT
*
1241244 AGCATAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGC
* * * *
1241309 TCAAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCATACAAAGACCTTC
65 TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C---CAAAGACCCTC
** * *
1241374 GAGTTCGACTATGCTCAGCTCTAAGGCATATCATTTGC
126 GAGTTCGACTACACTCAGCTCGAAGGCATATCATTTAC
* * *
1241412 AGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTGCGCTCAG
1 AGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAG
*
1241476 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAG
64 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAG
* *
1241541 TTCGATTACACTCAGCTTCGAGGGCATATCATTTAC
129 TTCGACTACACTCAGC-TCGAAGGCATATCATTTAC
* * *
1241577 AGCATAACTCAAGGCTACAAGGGTTATCTGTCC-ACAAGAGACCTTCAAGTTCGACTACACTCAG
1 AGCATAACTCAAGGCTAGAAGGGTTATCTG-CCAACAA-AGACCTTCGAGTTCGACTACGCTCAG
* * * * * *
1241641 CTCCGAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
64 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCT
* * * * *
1241706 TGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGC
125 CGAGTTCGACTACACTCAGCTCGAAGGCATATCATTTAC
* * * ** * * * * * * *
1241745 AGTATAGCTTAAATCGAGAAGGGCTATCTG-C--CAAAGACCCTAGAGTTCGATTACACTCAACT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCT
* * * * * * * * * * *
1241807 CGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATATGTCTCCAAAAGACCTTCG
66 CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCG
* * * * *
1241872 AGTTCGTCTACGCTCAGCTCTAAGGCACATCATTTGC
127 AGTTCGACTACACTCAGCTCGAAGGCATATCATTTAC
* * * * * * * * * *
1241909 AGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTTGATTACACTCAACT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-
* * * * * * * * * * * *
1241971 TCGAGGGCGCATCATTTACATCATAACTCAAGGCTAGAAGAGTTATCTGTCACCAAAAGACCTTC
65 TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTC
* * * *
1242036 GAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGC
126 GAGTTCGACTACACTCAGCTCGAAGGCA-TATCATTTAC
* * * * *
1242075 AGCATAGCTTAAGTCGAGAAGGGTTATCTG-CTA-AAA-ACCTTCGAGTTCGA
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
1242125 TTACATTCAA
Statistics
Matches: 619, Mismatches: 79, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
163 2 0.00
164 194 0.31
165 194 0.31
166 57 0.09
167 6 0.01
168 138 0.22
169 28 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTT
CGACTACACTCAGCTCGAAGGCATATCATTTAC
Found at i:1242018 original size:413 final size:416
Alignment explanation
Indices: 1241244--1242124 Score: 1242
Period size: 413 Copynumber: 2.1 Consensus size: 416
1241234 AACTATTTGT
* * * *
1241244 AGCATAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
1241309 TCAAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCATACAAAGACCTTC
66 TCAAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCC--ACAAAGACCCTA
** * * * * * *
1241374 GAGTTCGACTATGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTAT
129 GAGTTCGACTACACTCAACTCGAAGGCACATCATTTACAGCATAACTCAAGCTGAGAAGGGTTAT
* *
1241439 CTGCCAACCAAAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
194 ATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
* * *
1241504 TTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATA
259 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACA
* *
1241569 TCATTTACAGCATAACTCAAGGCTACAAGGGTTATCTGTC-CACAAGAGACCTTCAAGTTCGACT
324 TCATTTACAGCATAACTCAAGGCTACAAGAGTTATCTGTCAC-CAAAAGACCTTCAAGTTCGACT
** *
1241633 ACACTCAGCTCCGAGGCA-TATCATTTAC
388 ACACTCAGCTCAAAGGCACCATCATTTAC
* *
1241661 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
1 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
* * *
1241726 TCTAAGGCACATCATTTGCAGTATAGCTTAAATCGAGAAGGGCTATCTG-C-CAAAGACCCTAGA
66 TCAAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCACAAAGACCCTAGA
* * *
1241789 GTTCGATTACACTCAACTCGAGGGCACATCATTTACAGTATAACTCAAGGCT-AGAAGGGTTATA
131 GTTCGACTACACTCAACTCGAAGGCACATCATTTACAGCATAACTCAA-GCTGAGAAGGGTTATA
* * * *
1241853 TGTC-TCCAAAAGACCTTCGAGTTCGTCTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGC
195 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
* *
1241917 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAACTTCGAGGGCGCA
259 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACA
* * * *
1241982 TCATTTACATCATAACTCAAGGCTAGAAGAGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTA
324 TCATTTACAGCATAACTCAAGGCTACAAGAGTTATCTGTCACCAAAAGACCTTCAAGTTCGACTA
*
1242047 CACTCAGCTCAAAGGCACCATCATTTGC
389 CACTCAGCTCAAAGGCACCATCATTTAC
* *
1242075 AGCATAGCTTAAGTCGAGAAGGGTTATCTG-C--TAAAA-ACCTTCGAGTTCGA
1 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
1242125 TTACATTCAA
Statistics
Matches: 413, Mismatches: 47, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
410 13 0.03
411 3 0.01
412 2 0.00
413 249 0.60
414 40 0.10
416 1 0.00
417 105 0.25
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (416 bp):
AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
TCAAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCACAAAGACCCTAGA
GTTCGACTACACTCAACTCGAAGGCACATCATTTACAGCATAACTCAAGCTGAGAAGGGTTATAT
GCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTT
AAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATC
ATTTACAGCATAACTCAAGGCTACAAGAGTTATCTGTCACCAAAAGACCTTCAAGTTCGACTACA
CTCAGCTCAAAGGCACCATCATTTAC
Found at i:1242235 original size:249 final size:246
Alignment explanation
Indices: 1241246--1242183 Score: 924
Period size: 249 Copynumber: 3.8 Consensus size: 246
1241236 CTATTTGTAG
* * * * *
1241246 CATAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTC
* * * * ** * *
1241311 AAAGGCACAACATTTGCAGCATAGCTTAAATCGAGAAGGGCTATCTGCCATACAAAGACCTTCGA
62 AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-TACAAAGACCTTCGA
** * * *
1241376 GTTCGACTATGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCT
126 GTTCGACTACACTCAGCTCTAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCT
* * *
1241441 GCCAACCAAAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCACATCATTTGCAG
191 GCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT-CAAGGCACATCATTTGCAT
* * * *
1241498 CATAGCTTAA-GTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGA
1 CATAACTCAAGGCT-AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGC-TCAA
* * * * * *
1241562 GGGCATATCATTTACAGCATAACTCAAGGCTACAAGGGTTATCTGTCCACAAGAGACCTTCAAGT
64 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCTACAA-AGACCTTCGAGT
** *
1241627 TCGACTACACTCAGCTCCGAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGC
128 TCGACTACACTCAGCTCTAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGC
* *
1241692 CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGT
193 CAACCAAAGACCTTCGAGTTCGACTACACTCAGCTC-AAGGCACATCATTTGCA-T
* * ** * * * * *
1241748 -ATAGCTTAAATCGAGAAGGGCTATCTGCCAAAGACCCTAGAGTTCGATTACACTCAACTCGAGG
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCAAAG
* * * *
1241812 GCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATATGTCTCCAAAAGACCTTCGAGTTC
66 GCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCTAC-AAAGACCTTCGAGTTC
* * * * *
1241877 GTCTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---
130 GACTACACTCAGCTCTAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCA
* * * * * * *
1241939 -CCAAAGACCCTCGAGTTTGATTACACTCAACTTCGAGGGCGCATCATTTACAT
195 ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TC-AAGGCACATCATTTGCAT
* * *
1241992 CATAACTCAAGGCTAGAAGAGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTG---CC-AAAGACCCTCGAGTTCGATTACACTCAGCTC
* * * *
1242057 AAAGGCACCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-CTA-AAA-ACCTTCGA
62 AAAGGCA-CATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCTACAAAGACCTTCGA
* * * * * * * *
1242119 GTTCGATTACATTCAACT-TAGAGGCAGATCAAGTTTACAGCATAGCTCAAGGCAAGAAGGGCTA
126 GTTCGACTACACTCAGCTCTA-AGGCATATC-A-TTTACAGCATAACTTAAGTCGAGAAGGGCTA
1242183 T
188 T
1242184 ATGTCAATAA
Statistics
Matches: 577, Mismatches: 92, Indels: 38
0.82 0.13 0.05
Matches are distributed among these distances:
244 26 0.05
245 38 0.07
246 29 0.05
247 4 0.01
248 176 0.31
249 248 0.43
250 33 0.06
251 3 0.01
252 20 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (246 bp):
CATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCAAAG
GCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCTACAAAGACCTTCGAGTTCG
ACTACACTCAGCTCTAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAGGCACATCATTTGCAT
Found at i:1243810 original size:18 final size:18
Alignment explanation
Indices: 1243781--1243819 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1243771 TTTTATTTTA
1243781 TTTTATTTATTTGAATTTC
1 TTTTATTTATTTGAA-TTC
*
1243800 TTTTA-TTATTTTAATTC
1 TTTTATTTATTTGAATTC
1243817 TTT
1 TTT
1243820 ATTGTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATTTATTTGAATTC
Found at i:1245492 original size:20 final size:20
Alignment explanation
Indices: 1245467--1245618 Score: 164
Period size: 20 Copynumber: 7.5 Consensus size: 20
1245457 GATTTTCCAG
* *
1245467 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
1245487 AATCGCAACGAGTATCCGTAAA
1 AATCGCAACGCGTATCCGT--A
1245509 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1245529 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1245549 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1245570 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * **
1245590 AATCGCAACGAGAATCTATA
1 AATCGCAACGCGTATCCGTA
1245610 AATCGCAAC
1 AATCGCAAC
1245619 ACTGAAATTT
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
20 76 0.67
21 19 0.17
22 19 0.17
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1245585 original size:41 final size:40
Alignment explanation
Indices: 1245486--1245618 Score: 164
Period size: 41 Copynumber: 3.2 Consensus size: 40
1245476 GCGAACACAT
* *
1245486 AAATCGCAACGAGTATCCGTAAAAATCGCAACG-CGTATCCGT-
1 AAATCGCAACGCGTATCCGT--AAATCGCAACGAC-AAT-CGTA
1245528 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAAT-CGTA
*
1245569 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATC-TA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATCGTA
1245608 TAAATCGCAAC
1 -AAATCGCAAC
1245619 ACTGAAATTT
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
39 2 0.02
40 27 0.32
41 36 0.43
42 19 0.23
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGACAATCGTA
Found at i:1245599 original size:61 final size:61
Alignment explanation
Indices: 1245467--1245618 Score: 207
Period size: 61 Copynumber: 2.5 Consensus size: 61
1245457 GATTTTCCAG
* ** *
1245467 AATCGCAACGCGAACACATAAATCGCAACGAGTATCCGTAAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGATC-CATAAATCGCAACGACAATACGTAAAAATCGCAACGCGTATCCGTA
*
1245529 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-AAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCG-ATCCATAAATCGCAACGACAATACGTAAAAATCGCAACGCGTATCCGTA
* *
1245590 AATCGCAACGAGAATCTATAAATCGCAAC
1 AATCGCAACGCG-ATCCATAAATCGCAAC
1245619 ACTGAAATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
61 47 0.59
62 31 0.39
63 2 0.03
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (61 bp):
AATCGCAACGCGATCCATAAATCGCAACGACAATACGTAAAAATCGCAACGCGTATCCGTA
Found at i:1246350 original size:24 final size:24
Alignment explanation
Indices: 1246311--1246357 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1246301 AAATTTGGTC
1246311 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1246335 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1246358 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1246539 original size:12 final size:12
Alignment explanation
Indices: 1246522--1246546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1246512 ATATAATCCT
1246522 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1246534 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1246546 G
1 G
1246547 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1248908 original size:33 final size:34
Alignment explanation
Indices: 1248838--1248992 Score: 172
Period size: 33 Copynumber: 4.4 Consensus size: 34
1248828 CTTAATGATT
* * * *
1248838 ATCGCAACGCGGAAATTACAATCGCAACGA-GAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGATGAAA
*
1248872 ATCGCAATGCGAAATGAAAATCCCAAC-ATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
1248905 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAAATCGCAA--C-G--ATGAAA
*
1248945 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
1248978 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
1248993 TTCAGTTCGC
Statistics
Matches: 106, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 45 0.42
34 25 0.24
36 2 0.02
37 1 0.01
39 16 0.15
40 16 0.15
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
Found at i:1248922 original size:20 final size:20
Alignment explanation
Indices: 1248899--1248970 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
1248889 AAATCCCAAC
1248899 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGCGGAA
1248919 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGCGGAA
1248939 ATGAAAATCGCAATGC-GAA
1 ATGAAAATCGCAATGCGGAA
1248958 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1248971 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 16 0.31
20 36 0.69
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.15
Consensus pattern (20 bp):
ATGAAAATCGCAATGCGGAA
Found at i:1249109 original size:14 final size:14
Alignment explanation
Indices: 1249086--1249119 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1249076 AAATCTATTG
1249086 AATCAACTTTTACA
1 AATCAACTTTTACA
*
1249100 AATCATCTTTTACA
1 AATCAACTTTTACA
1249114 AATCAA
1 AATCAA
1249120 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:1249359 original size:18 final size:18
Alignment explanation
Indices: 1249338--1249374 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1249328 GTAATTGGAG
1249338 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1249356 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1249374 T
1 T
1249375 ATAAATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1249381 original size:24 final size:24
Alignment explanation
Indices: 1249330--1249382 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1249320 CTTCATATGT
* * *
1249330 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1249354 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1249378 AATTT
1 AATTT
1249383 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1249787 original size:19 final size:19
Alignment explanation
Indices: 1249759--1249898 Score: 264
Period size: 19 Copynumber: 7.4 Consensus size: 19
1249749 GCGAAAGTCA
1249759 AATG-GAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249777 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249796 AATGCGGAAATGAAAATCGC
1 AATGC-GAAATGAAAATCGC
1249816 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249835 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249854 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249873 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
1249892 AATGCGA
1 AATGCGA
1249899 TAGTCATTTT
Statistics
Matches: 120, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
18 4 0.03
19 97 0.81
20 19 0.16
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.16
Consensus pattern (19 bp):
AATGCGAAATGAAAATCGC
Found at i:1250102 original size:14 final size:14
Alignment explanation
Indices: 1250079--1250112 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1250069 TCTACTATTG
1250079 AATCAACTTTTACA
1 AATCAACTTTTACA
*
1250093 AATCATCTTTTACA
1 AATCAACTTTTACA
1250107 AATCAA
1 AATCAA
1250113 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:1250103 original size:84 final size:84
Alignment explanation
Indices: 1250006--1250170 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
1249996 CATCAATTAA
***
1250006 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTATTTCCTCATC
1 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTATTTCCTCATC
1250071 TACTATTGAATCAACTTTT
66 TACTATTGAATCAACTTTT
1250090 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTATTTCCTCATC
1 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTATTTCCTCATC
1250155 TACTATTGAATCAACT
66 TACTATTGAATCAACT
1250171 ATTGCAGACA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (84 bp):
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTATTTCCTCATC
TACTATTGAATCAACTTTT
Found at i:1252019 original size:19 final size:19
Alignment explanation
Indices: 1251977--1252130 Score: 112
Period size: 19 Copynumber: 8.6 Consensus size: 19
1251967 TAGTTTACTT
* *
1251977 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1251997 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1252016 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1252035 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1252054 TCGCAA--CGACAT---AA
1 TCGCAACGCGAAATGAAAA
*
1252068 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
1252087 TCACAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
**
1252101 TCGCAATTCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1252120 TCGCAATGCGA
1 TCGCAACGCGA
1252131 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 62 0.58
20 12 0.11
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1252079 original size:33 final size:33
Alignment explanation
Indices: 1251993--1252125 Score: 149
Period size: 33 Copynumber: 3.9 Consensus size: 33
1251983 CACGAAACTT
*
1251993 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G--A-C
1252031 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
* * * *
1252064 ATAATCGCAATGCGAAATGAAAATCACAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
* **
1252097 AGAATCGCAATTCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
1252126 TGCGATTTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
33 56 0.64
34 1 0.01
36 1 0.01
38 29 0.33
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:1252161 original size:14 final size:14
Alignment explanation
Indices: 1252142--1252200 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1252132 TTTGGTTTCG
1252142 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1252156 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
1252173 CACGTTGCGATTCTAT
1 --CGTTGCGATTTTGT
1252189 CGTTGCGATTTT
1 CGTTGCGATTTT
1252201 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1252168 original size:33 final size:33
Alignment explanation
Indices: 1252126--1252220 Score: 145
Period size: 33 Copynumber: 2.9 Consensus size: 33
1252116 AAAATCGCAA
*
1252126 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTATCGT
* *
1252159 TGCGATTTTGGTTTCACGTTGCGATTCTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTATCGT
**
1252192 TGCGATTTTCATTTCGCGTTGCGATTTTA
1 TGCGATTTTGGTTTCGCGTTGCGATTTTA
1252221 AGTTTCGTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTATCGT
Found at i:1252180 original size:19 final size:18
Alignment explanation
Indices: 1252126--1252184 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
1252116 AAAATCGCAA
1252126 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTC-CGT
1252145 TGCGATTTT-G--T-CGT
1 TGCGATTTTGGTTTCCGT
1252159 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGGTTTC-CGT
1252178 TGCGATT
1 TGCGATT
1252185 CTATCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.08, C:0.15, G:0.29, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGGTTTCCGT
Found at i:1252213 original size:19 final size:20
Alignment explanation
Indices: 1252189--1252235 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1252179 GCGATTCTAT
*
1252189 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTAAGTTTCG
1252208 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAAGTTTCG
*
1252228 TGTTGCGA
1 CGTTGCGA
1252236 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTAAGTTTCG
Found at i:1252399 original size:83 final size:86
Alignment explanation
Indices: 1252283--1252556 Score: 297
Period size: 94 Copynumber: 3.1 Consensus size: 86
1252273 ATGGATTGCA
* **
1252283 TTACTTCAACCAATAGACAAAACAAAGACAAATACTAACTTCAG-G-G-TA-TTAGTTTAGCAGA
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAGCAGA
1252344 ATTGGCAGCAACCGAACAAAT
66 ATTGGCAGCAACCGAACAAAT
*
1252365 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTT--CAGTG----AG-ATACACAGT
*
1252429 TTAGCAGAATTGGCAGCAACCGAATAAAT
58 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1252458 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTC--AGTG----AG-ATACACAGT
* *
1252523 TTAGCAGTATTGGCAGCAACCGAATAAAT
58 TTAGCAGAATTGGCAGCAACCGAACAAAT
1252552 TTACT
1 TTACT
1252557 AAGCAATCTA
Statistics
Matches: 168, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 22 0.13
93 48 0.29
94 55 0.33
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (86 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAGCAGA
ATTGGCAGCAACCGAACAAAT
Found at i:1252492 original size:93 final size:93
Alignment explanation
Indices: 1252333--1252556 Score: 378
Period size: 94 Copynumber: 2.4 Consensus size: 93
1252323 TCAGGGTATT
*
1252333 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAA
* *
1252398 TACT-ATTTCACAGTGTTAAAGAATACAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
1252426 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAAC-AAAGACAAA
*
1252491 TACTAACTTCATAGTGTTAAAGAATAAAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
*
1252520 AGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1252557 AAGCAATCTA
Statistics
Matches: 124, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
92 19 0.15
93 48 0.39
94 57 0.46
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAAT
ACTAACTTCACAGTGTTAAAGAATAAAC
Found at i:1254317 original size:19 final size:19
Alignment explanation
Indices: 1254253--1254367 Score: 167
Period size: 19 Copynumber: 5.9 Consensus size: 19
1254243 TCTTTTGGTT
* *
1254253 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
** *
1254272 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
1254292 GGAAATGAAAATCGCAACGC
1 -GAAATGAAAATCGCAACGC
1254312 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1254331 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1254350 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1254368 AGAGAATTGC
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 58 0.67
20 26 0.30
21 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1254385 original size:33 final size:36
Alignment explanation
Indices: 1254295--1254389 Score: 133
Period size: 38 Copynumber: 2.7 Consensus size: 36
1254285 GCAATGCGGA
1254295 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGCG
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG
1254332 AAATGAAAATCGCAACGCGAAATGAAAATCGCAA-CG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
* *
1254368 -A-GAGAATTGCAACGCGAAATGA
1 AATGAAAATCGCAACGCGAAATGA
1254390 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
33 19 0.35
34 1 0.02
36 2 0.04
38 33 0.60
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (36 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
Found at i:1254426 original size:14 final size:14
Alignment explanation
Indices: 1254407--1254463 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1254397 TTTGGTTTCG
1254407 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1254421 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
1254440 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
1254454 CGTTGCGATT
1 CGTTGCGATT
1254464 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1254432 original size:33 final size:33
Alignment explanation
Indices: 1254390--1254471 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
1254380 CGCGAAATGA
** *
1254390 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1254423 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1254456 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1254472 TCTCGTTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
Found at i:1254474 original size:21 final size:21
Alignment explanation
Indices: 1254448--1254526 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1254438 CGCGTTGCAA
1254448 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1254469 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
1254491 TT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1254511 TTCTCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
1254527 CTTCTGCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.18
21 32 0.64
22 9 0.18
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1255066 original size:20 final size:20
Alignment explanation
Indices: 1255041--1255177 Score: 143
Period size: 20 Copynumber: 6.7 Consensus size: 20
1255031 CTTTAAAAAT
*
1255041 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1255061 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1255081 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1255102 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1255122 CGCGTTGCGATTTTTGCGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * *
1255144 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
1255164 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
1255178 TGTGTTCGCG
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.02
20 57 0.58
21 21 0.21
22 18 0.18
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1255100 original size:41 final size:41
Alignment explanation
Indices: 1255041--1255177 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 41
1255031 CTTTAAAAAT
* *
1255041 CGCGTTGTGATTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
*
1255081 TGTCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATA
1 CG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
* * ** * *
1255122 CGCGTTGCGATTTTTGCGGATACTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGA--TTTACGGATACGCGTTGCGATTTTACGGATA
1255164 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
1255178 TGTGTTCGCG
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
40 20 0.25
41 28 0.35
42 28 0.35
43 5 0.06
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (41 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
Found at i:1255168 original size:42 final size:42
Alignment explanation
Indices: 1255051--1255176 Score: 116
Period size: 42 Copynumber: 3.0 Consensus size: 42
1255041 CGCGTTGTGA
* * * *
1255051 TTTACGGATACGCGTTGCGATTTTACGTAT-TGTCGTTGCGA--
1 TTTACGGATACGCGTTGCGA-TGTAAGAATACG-CGTTGCGATT
* * *
1255092 TTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATT
1 TTTACGGATACGCGTTGCGATGTAAGAATACGCGTTGCGATT
* *
1255134 TTTGCGGATACTCGTTGCGATAGTAAGAAT-CGCGTTGCGATT
1 TTTACGGATACGCGTTGCGAT-GTAAGAATACGCGTTGCGATT
1255176 T
1 T
1255177 ATGTGTTCGC
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
40 16 0.22
41 21 0.28
42 32 0.43
43 5 0.07
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (42 bp):
TTTACGGATACGCGTTGCGATGTAAGAATACGCGTTGCGATT
Found at i:1255186 original size:20 final size:19
Alignment explanation
Indices: 1255163--1255215 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1255153 ATAGTAAGAA
*
1255163 TCGCGTTGCGATTT-ATGTGT
1 TCGCGTTGCGATTTCA--TAT
1255183 TCGCGTTGCGACTTTCATAT
1 TCGCGTTGCGA-TTTCATAT
1255203 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1255216 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 24 0.80
21 3 0.10
22 1 0.03
ACGTcount: A:0.11, C:0.21, G:0.26, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTCATAT
Found at i:1261329 original size:16 final size:16
Alignment explanation
Indices: 1261308--1261339 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1261298 TTTAAGCAGC
1261308 AATGATTTACAATTAT
1 AATGATTTACAATTAT
1261324 AATGATTTACAATTAT
1 AATGATTTACAATTAT
1261340 TGAAAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
AATGATTTACAATTAT
Found at i:1263058 original size:19 final size:19
Alignment explanation
Indices: 1263034--1263087 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1263024 TTGTTATGAG
1263034 TGTATGAGTAATATGTTAT
1 TGTATGAGTAATATGTTAT
* * *
1263053 TGTATGTGTAACATGAT-T
1 TGTATGAGTAATATGTTAT
*
1263071 TGTATGAAT-ATATGTTA
1 TGTATGAGTAATATGTTA
1263088 GTACTATAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
17 5 0.19
18 8 0.30
19 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (19 bp):
TGTATGAGTAATATGTTAT
Found at i:1263266 original size:33 final size:33
Alignment explanation
Indices: 1263224--1263307 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
1263214 TATGAAAGTG
1263224 AAAATATATGTCTATGAAGAGCCATAATAGGAC
1 AAAATATATGTCTATGAAGAGCCATAATAGGAC
*
1263257 AATATATATGTCTATGAAGAGCCATAATAGGAC
1 AAAATATATGTCTATGAAGAGCCATAATAGGAC
*
1263290 AAAATATAAGTCATATGA
1 AAAATATATGTC-TATGA
1263308 TAATGAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 42 0.89
34 5 0.11
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (33 bp):
AAAATATATGTCTATGAAGAGCCATAATAGGAC
Found at i:1275892 original size:8 final size:8
Alignment explanation
Indices: 1275879--1275903 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1275869 CTATAGTATT
1275879 ATGCATGA
1 ATGCATGA
1275887 ATGCATGA
1 ATGCATGA
1275895 ATGCATGA
1 ATGCATGA
1275903 A
1 A
1275904 CATGAGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
ATGCATGA
Found at i:1297450 original size:282 final size:281
Alignment explanation
Indices: 1296946--1297509 Score: 1028
Period size: 282 Copynumber: 2.0 Consensus size: 281
1296936 AAAAAAGACG
1296946 AGAGTAATTTCATATTAAACATGAATTATCAGATCTAATGAGAAGTGAAAAAAAAGAGAGTTAGA
1 AGAGTAATTTCATATTAAACATGAATTATCAGATCTAATGAGAAGTGAAAAAAAAGAGAGTTA-A
*
1297011 GGATACCGGCGACAATAGAATACCCATCTCTCTATAACGATCAACAAAGATCGACGGTATCTTTG
65 GGATACCGGCGACAATAGAATACCCATATCTCTATAACGATCAACAAAGATCGACGGTATCTTTG
*
1297076 AAGGTCACGTGATCAAGTAGAAGTGTCGTTATGTCTTGGAACATAAAAACATCAAACACCAAAAA
130 AAGGTCACGTGATCAAGTAGAAGTGTCGTTATGTCTTGGAACATAAAAACATCAAACAACAAAAA
1297141 AATTTAACATTTATTACCAAACAACAAGACATCTTTTACACTTTTTATTTTATGCTTTCAGAACA
195 AATTTAACATTTATTACCAAACAACAAGACATCTTTTACACTTTTTATTTTATGCTTTCAGAACA
1297206 CCGACAAAG-AAAAGAGGAAAAA
260 CCGACAAAGAAAAAGA-GAAAAA
1297228 AGAGTAATTTCATATTAAACATGAATTATCAGATCTAATGAGAAGTGAAAAAAAAGAGAGTT-AG
1 AGAGTAATTTCATATTAAACATGAATTATCAGATCTAATGAGAAGTGAAAAAAAAGAGAGTTAAG
1297292 GATACCGGCGACAATAGAATACCCATATCTCTATAACGATCAACAAAGATGTCGACGGTATCTTT
66 GATACCGGCGACAATAGAATACCCATATCTCTATAACGATCAACAAAGA--TCGACGGTATCTTT
1297357 GAAGGTCACGTGATCAAGTAGAAGTGTCGTTATGTCTTGGAACAT-AAAACATCAAACCAACAAA
129 GAAGGTCACGTGATCAAGTAGAAGTGTCGTTATGTCTTGGAACATAAAAACATCAAA-CAACAAA
1297421 AAAA-TTAACATTTTATTACCAAACAACAAGACATCTTTTACACTTTTTATTTTATGCTTTCAGA
193 AAAATTTAACA-TTTATTACCAAACAACAAGACATCTTTTACACTTTTTATTTTATGCTTTCAGA
1297485 ACACCGACAAAGAAAAAGAGAAAAA
257 ACACCGACAAAGAAAAAGAGAAAAA
1297510 GTTTTTCTGA
Statistics
Matches: 275, Mismatches: 2, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
280 50 0.18
281 17 0.06
282 202 0.73
283 6 0.02
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (281 bp):
AGAGTAATTTCATATTAAACATGAATTATCAGATCTAATGAGAAGTGAAAAAAAAGAGAGTTAAG
GATACCGGCGACAATAGAATACCCATATCTCTATAACGATCAACAAAGATCGACGGTATCTTTGA
AGGTCACGTGATCAAGTAGAAGTGTCGTTATGTCTTGGAACATAAAAACATCAAACAACAAAAAA
ATTTAACATTTATTACCAAACAACAAGACATCTTTTACACTTTTTATTTTATGCTTTCAGAACAC
CGACAAAGAAAAAGAGAAAAA
Found at i:1298865 original size:18 final size:20
Alignment explanation
Indices: 1298844--1298880 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1298834 ATTGATATTT
1298844 TTAAA-TAA-ATTTTATGTG
1 TTAAATTAATATTTTATGTG
1298862 TTAAATTAATATTTTATGT
1 TTAAATTAATATTTTATGT
1298881 AAAATTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTAAATTAATATTTTATGTG
Found at i:1300260 original size:35 final size:35
Alignment explanation
Indices: 1300214--1300291 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
1300204 ACATAGTCAT
* *
1300214 AATTACATTCTAAACCCCAAAATCCAAAATGCTTC
1 AATTACATTCTAAACCCCAAAATCCAAAATACATC
* *
1300249 AATTACATTCTAAACCTCAAATTCCAAAATACATC
1 AATTACATTCTAAACCCCAAAATCCAAAATACATC
1300284 AATTACAT
1 AATTACAT
1300292 GCCCAACCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAAATCCAAAATACATC
Found at i:1300305 original size:35 final size:35
Alignment explanation
Indices: 1300214--1300307 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
1300204 ACATAGTCAT
* * * * * *
1300214 AATTACATTCTAAACCCCAAAATCCAAAATGCTTC
1 AATTACATGCCAAACCACAAATTCCAAAATACATC
* * *
1300249 AATTACATTCTAAACCTCAAATTCCAAAATACATC
1 AATTACATGCCAAACCACAAATTCCAAAATACATC
*
1300284 AATTACATGCCCAACCACAAATTC
1 AATTACATGCCAAACCACAAATTC
1300308 ATAATTCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.26
Consensus pattern (35 bp):
AATTACATGCCAAACCACAAATTCCAAAATACATC
Found at i:1300736 original size:146 final size:145
Alignment explanation
Indices: 1300456--1300723 Score: 423
Period size: 151 Copynumber: 1.8 Consensus size: 145
1300446 AAATACTCAA
1300456 TTCAGTTTATAAAATAGTTGACTCGAATTTTTTTCTATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAATTTTTTTCTATTTGAGTTTATAAAATTTAAATCAAGTC
*
1300521 GATTTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATGTTATAATAT
66 GATTTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCA---TATAATAT
1300586 TATTTTATTCTAATTCAG
128 TATTTTATTCTAATTCAG
*
1300604 TTCAGTTTATAAAATAGTTGACTC-AATTTTTTT-TATTTGAGTTTATAAATTTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAATTTTTTTCTATTTGAGTTTATAAAATTTAAATCAAGTC
*
1300667 GAATTGAATTGAATTGAATTTTCGAGTTTTTGTTTAAATTTAATTATAAATATTTAT
66 G-A-T---TTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTAT
1300724 AATACATATA
Statistics
Matches: 112, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
146 30 0.27
147 10 0.09
148 25 0.22
151 47 0.42
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (145 bp):
TTCAGTTTATAAAATAGTTGACTCGAATTTTTTTCTATTTGAGTTTATAAAATTTAAATCAAGTC
GATTTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATAATATTAT
TTTATTCTAATTCAG
Found at i:1301241 original size:35 final size:35
Alignment explanation
Indices: 1301202--1301281 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
1301192 GAGGTCGGGC
*
1301202 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGTTTAGA
* *
1301237 ATGTAATTAAAGTATTTTGAAATTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGTTTAGA
*
1301272 ATATAATTGA
1 ATGTAATTGA
1301282 TAATTGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTGAGGTTTAGA
Found at i:1303511 original size:60 final size:60
Alignment explanation
Indices: 1303403--1303516 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
1303393 GTATATATGT
* * * *
1303403 ATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGGGAATCAATTTAGAATGAAGGTA
1 ATAGTTTGGGATGAAACTAAAATATTCAAAAAGTTTGGGAATCAATTTAAAATGAAGGTA
* * *
1303463 ATAGTTTAGGGATGAAGCTAAAATATTC-AAAAGTTTGAGGACT-GATTTAAAATG
1 ATAGTTT-GGGATGAAACTAAAATATTCAAAAAGTTTG-GGAATCAATTTAAAATG
1303517 GTAATCATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
60 25 0.56
61 20 0.44
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAACTAAAATATTCAAAAAGTTTGGGAATCAATTTAAAATGAAGGTA
Found at i:1307355 original size:29 final size:29
Alignment explanation
Indices: 1307311--1307380 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
1307301 AAAAATCTGT
*
1307311 CAAACTTTGAATCATGCACCATTCGGTGC
1 CAAACTTTGAACCATGCACCATTCGGTGC
*
1307340 CAAAATTTGAACCATGCACCATTCGGTGC
1 CAAACTTTGAACCATGCACCATTCGGTGC
1307369 CAAACTTTGAAC
1 CAAACTTTGAAC
1307381 TTTCAACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (29 bp):
CAAACTTTGAACCATGCACCATTCGGTGC
Found at i:1309963 original size:2 final size:2
Alignment explanation
Indices: 1309958--1310044 Score: 156
Period size: 2 Copynumber: 43.5 Consensus size: 2
1309948 TCACACACAC
**
1309958 AT AT AT AT AT AT AT AT AT AT AT AT AT GG 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
1310000 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
1310042 AT A
1 AT A
1310045 AATGATTCAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1310182 original size:35 final size:35
Alignment explanation
Indices: 1310136--1310204 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1310126 TCATTATTAC
1310136 ATAATAATGTTTTACACAAATCATACAACATATAT
1 ATAATAATGTTTTACACAAATCATACAACATATAT
*
1310171 ATAATAATGTTTTACACAAATCATACAGCATATA
1 ATAATAATGTTTTACACAAATCATACAACATATA
1310205 CAAAGCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (35 bp):
ATAATAATGTTTTACACAAATCATACAACATATAT
Found at i:1328627 original size:32 final size:32
Alignment explanation
Indices: 1328566--1328627 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1328556 AGATTTTTTT
*
1328566 GGCGTCTTGCTTGGGATCTCCCGGTGTCTTCA
1 GGCGTCTTGCTTGGGATCTCCCGGCGTCTTCA
* *
1328598 GGCGTCTTGTTTGGGATCTCCCTGCGTCTT
1 GGCGTCTTGCTTGGGATCTCCCGGCGTCTT
1328628 GAGGGTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.05, C:0.27, G:0.31, T:0.37
Consensus pattern (32 bp):
GGCGTCTTGCTTGGGATCTCCCGGCGTCTTCA
Found at i:1328812 original size:22 final size:22
Alignment explanation
Indices: 1328769--1328813 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1328759 CGGATCTAGC
*
1328769 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
1328791 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
1328813 A
1 A
1328814 GTTTACTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:1329275 original size:20 final size:20
Alignment explanation
Indices: 1329208--1329383 Score: 221
Period size: 20 Copynumber: 8.7 Consensus size: 20
1329198 TAAGTTTCCA
* *
1329208 AAATCGCAACGCG-ATTCTT
1 AAATCGCAACGCGTATCCGT
* *
1329227 ACTATCGCAACGAGTATCCGT
1 A-AATCGCAACGCGTATCCGT
1329248 AAAAATCGCAACGCGTATCCGT
1 --AAATCGCAACGCGTATCCGT
*
1329270 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1329290 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
1329310 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1329330 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
1329350 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1329371 AAATCGCAACGCG
1 AAATCGCAACGCG
1329384 ATTTTTAAAG
Statistics
Matches: 138, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
19 1 0.01
20 98 0.71
21 21 0.15
22 17 0.12
23 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1329803 original size:33 final size:33
Alignment explanation
Indices: 1329764--1329834 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1329754 TTCACTTAGA
*
1329764 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
*
1329797 TTTCATTTCGCGTTACTATTCTCTCATTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
1329830 TTTCA
1 TTTCA
1329835 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
Found at i:1329940 original size:21 final size:21
Alignment explanation
Indices: 1329914--1329990 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
1329904 TGCAGAAGAG
1329914 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1329935 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
1329955 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
1329977 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1329991 TCGCAATGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1329994 original size:14 final size:14
Alignment explanation
Indices: 1329975--1330031 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1329965 GAGAAATGAA
1329975 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1329989 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1330008 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1330022 AATCGCAACG
1 AATCGCAACG
1330032 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1330009 original size:33 final size:33
Alignment explanation
Indices: 1329967--1330047 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1329957 TGCAACGAGA
*
1329967 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1330000 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1330033 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1330048 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1330065 original size:19 final size:19
Alignment explanation
Indices: 1330043--1330121 Score: 113
Period size: 19 Copynumber: 4.1 Consensus size: 19
1330033 GAAACCAAAA
*
1330043 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1330062 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1330081 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1330100 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1330120 TC
1 TC
1330122 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 37 0.70
20 16 0.30
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1330115 original size:39 final size:38
Alignment explanation
Indices: 1330043--1330121 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 38
1330033 GAAACCAAAA
**
1330043 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATAGTCATTTCGCGTTGCGATTTTCATT
* *
1330081 TCGCGTTGCGATAGTCATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATAGTCATT-TCGCGTTGCGATTTTCATT
1330120 TC
1 TC
1330122 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (38 bp):
TCGCATTGCGATAGTCATTTCGCGTTGCGATTTTCATT
Found at i:1332126 original size:14 final size:14
Alignment explanation
Indices: 1332107--1332133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1332097 AACGCGAAAC
1332107 CAAAATCGCAACGA
1 CAAAATCGCAACGA
1332121 CAAAATCGCAACG
1 CAAAATCGCAACG
1332134 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:1332130 original size:33 final size:36
Alignment explanation
Indices: 1332051--1332149 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 36
1332041 CACGAAACTT
** *
1332051 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAACCAAAATCGCAAC-AG-AACC
1332089 AAAATCGCAACGCGAAACCAAAATCGCAAC-G-A-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACAGAACC
1332122 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
1332150 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
33 29 0.50
34 1 0.02
36 1 0.02
38 27 0.47
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.07
Consensus pattern (36 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACAGAACC
Found at i:1332155 original size:19 final size:19
Alignment explanation
Indices: 1332035--1332149 Score: 132
Period size: 19 Copynumber: 6.3 Consensus size: 19
1332025 TAGTTTACTT
* *
1332035 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
1332055 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACCAAAA
*
1332074 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1332093 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1332112 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
1332126 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1332145 TCGCA
1 TCGCA
1332150 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 52 0.64
20 12 0.15
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1332167 original size:19 final size:19
Alignment explanation
Indices: 1332145--1332209 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1332135 GAAACCAAAA
1332145 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1332164 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1332180 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1332197 TCGCATTGCGATT
1 TCGCATTGCGATT
1332210 CTGTCGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1332192 original size:33 final size:33
Alignment explanation
Indices: 1332150--1332225 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
1332140 CAAAATCGCA
1332150 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1332183 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1332216 TTGCGATTTT
1 TTGCGATTTT
1332226 GGTTTCTCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1332271 original size:20 final size:19
Alignment explanation
Indices: 1332214--1332279 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1332204 GCGATTCTGT
*
1332214 CGTTGCGATTTTGGTTTCT
1 CGTTGCGATTTTGGTTTCG
*
1332233 CGTTGCAATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
1332252 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
1332272 TGTTGCGA
1 CGTTGCGA
1332280 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.11, C:0.15, G:0.27, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:1334240 original size:14 final size:14
Alignment explanation
Indices: 1334204--1334240 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1334194 GATTGTTTAA
1334204 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
1334218 ATGAATTGTAAAAG
1 TTGATTTGTAAAAG
1334232 TTGATTTGT
1 TTGATTTGT
1334241 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1334363 original size:19 final size:19
Alignment explanation
Indices: 1334347--1334458 Score: 118
Period size: 19 Copynumber: 6.4 Consensus size: 19
1334337 AAAAATGACT
1334347 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1334366 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1334380 ATCGCAATGCGAACTGAAA
1 ATCGCAATGCGAAATGAAA
*
1334399 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1334413 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1334432 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1334452 ATCGCAA
1 ATCGCAA
1334459 CGAGAGAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 4 0.05
17 4 0.05
18 1 0.01
19 30 0.39
20 16 0.21
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1334384 original size:14 final size:14
Alignment explanation
Indices: 1334365--1334419 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1334355 GCGAAATGAA
1334365 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1334379 AATCGCAATGCGAACTGAA
1 AATCGCAA--CG-A--GAG
1334398 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1334412 AATCGCAA
1 AATCGCAA
1334420 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1334389 original size:33 final size:33
Alignment explanation
Indices: 1334347--1334438 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1334337 AAAAATGACT
1334347 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1334380 ATCGCAATGCGAACTGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1334413 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1334439 TGCGGAAATG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1334495 original size:19 final size:19
Alignment explanation
Indices: 1334467--1334597 Score: 182
Period size: 20 Copynumber: 7.0 Consensus size: 19
1334457 AACGAGAGAA
*
1334467 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1334486 TCGCATTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
*
1334506 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1334522 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1334539 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1334558 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1334578 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1334598 GCGGTGCGGC
Statistics
Matches: 102, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 4 0.04
18 3 0.03
19 31 0.30
20 51 0.50
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1334510 original size:53 final size:53
Alignment explanation
Indices: 1334453--1334563 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 53
1334443 GAAATGAAAA
1334453 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTT
** * *** * **
1334506 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTT
*
1334559 CCGCA
1 TCGCA
1334564 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (53 bp):
TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:1334738 original size:23 final size:23
Alignment explanation
Indices: 1334712--1334759 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1334702 ATAAAGTACA
*
1334712 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1334735 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1334758 AT
1 AT
1334760 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Done.