Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005189.1 Hibiscus syriacus cultivar Beakdansim tig00011718_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: 1183632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1077839 original size:38 final size:38
Alignment explanation
Indices: 1077709--1077881 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
1077699 GAAACCAAAA
*
1077709 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1077744 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
1077777 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
1077813 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* * *
1077851 TCGTGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1077882 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
33 56 0.49
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.37
39 11 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:1079821 original size:14 final size:14
Alignment explanation
Indices: 1079802--1079837 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1079792 ATTGTTTAAT
1079802 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1079816 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1079830 TGATTTGT
1 TGATTTGT
1079838 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1080017 original size:20 final size:19
Alignment explanation
Indices: 1079944--1080027 Score: 159
Period size: 19 Copynumber: 4.4 Consensus size: 19
1079934 AAAAATGACT
1079944 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1079963 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1079982 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1080001 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1080021 ATCGCAA
1 ATCGCAA
1080028 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 48 0.75
20 16 0.25
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1080064 original size:19 final size:19
Alignment explanation
Indices: 1080036--1080238 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
1080026 AACGAGAGAA
* *
1080036 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1080055 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1080071 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1080088 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1080107 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1080123 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1080140 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1080159 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1080175 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1080192 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1080210 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1080226 TCGCATTGCGATT
1 TCGCATTGCGATT
1080239 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 19 0.12
18 3 0.02
19 67 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1080099 original size:52 final size:52
Alignment explanation
Indices: 1080036--1080210 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
1080026 AACGAGAGAA
* *
1080036 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1080088 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1080140 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1080192 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
1080211 GTTGGGATTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 103 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1080260 original size:33 final size:33
Alignment explanation
Indices: 1080042--1080252 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
1080032 AGAATCGCAA
*
1080042 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1080075 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1080113 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1080146 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1080179 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1080213 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1080246 TGCGATT
1 TGCGATT
1080253 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 71 0.48
34 29 0.20
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1082551 original size:12 final size:12
Alignment explanation
Indices: 1082534--1082558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1082524 TCTTCGGGGA
1082534 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1082546 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1082558 C
1 C
1082559 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1082767 original size:24 final size:24
Alignment explanation
Indices: 1082733--1082779 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1082723 CTGAAACATC
1082733 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1082757 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1082780 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1083489 original size:20 final size:20
Alignment explanation
Indices: 1083461--1083710 Score: 252
Period size: 20 Copynumber: 12.5 Consensus size: 20
1083451 AAATTTCAGT
* * *
1083461 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1083481 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1083501 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1083521 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1083541 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1083561 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1083581 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1083601 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1083621 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1083641 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
*
1083661 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1083681 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1083701 GTTGCGATTT
1 GTTGCGATTT
1083711 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1083727 original size:21 final size:21
Alignment explanation
Indices: 1083697--1083779 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1083687 ATTTTCATAT
*
1083697 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1083718 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1083739 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1083760 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1083780 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1083770 original size:42 final size:43
Alignment explanation
Indices: 1083677--1083775 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1083667 ATTTATGTGT
*
1083677 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
1083718 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
1083760 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1083776 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:1084212 original size:36 final size:36
Alignment explanation
Indices: 1084138--1084212 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1084128 TTTTTATATT
*
1084138 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
1084174 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1084210 TTT
1 TTT
1084213 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1092222 original size:21 final size:21
Alignment explanation
Indices: 1092196--1092260 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1092186 CTGCCATGTT
1092196 AGTACCGTGAATCGTCACGTC
1 AGTACCGTGAATCGTCACGTC
*
1092217 AGTACCGTGAATCGTCACGTT
1 AGTACCGTGAATCGTCACGTC
* *
1092238 AGTACCGTGAATCGCCATGTC
1 AGTACCGTGAATCGTCACGTC
1092259 AG
1 AG
1092261 CACTGTGGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (21 bp):
AGTACCGTGAATCGTCACGTC
Found at i:1095211 original size:34 final size:34
Alignment explanation
Indices: 1095168--1095234 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1095158 CGCTCCTACA
*
1095168 ATTATCATATATTCGAGATTGCATATTTGAAACG
1 ATTATCATATATTCGAGATTGCAGATTTGAAACG
1095202 ATTATCATATATTCGAGATTGCAGATTTGAAAC
1 ATTATCATATATTCGAGATTGCAGATTTGAAAC
1095235 TATGTTATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (34 bp):
ATTATCATATATTCGAGATTGCAGATTTGAAACG
Found at i:1095221 original size:17 final size:17
Alignment explanation
Indices: 1095168--1095221 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1095158 CGCTCCTACA
1095168 ATTATCATATATTCGAG
1 ATTATCATATATTCGAG
*
1095185 ATT-GCATAT-TT-GAAACG
1 ATTATCATATATTCG--A-G
1095202 ATTATCATATATTCGAG
1 ATTATCATATATTCGAG
1095219 ATT
1 ATT
1095222 GCAGATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
14 1 0.03
15 2 0.07
16 6 0.21
17 11 0.38
18 6 0.21
19 2 0.07
20 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (17 bp):
ATTATCATATATTCGAG
Found at i:1096469 original size:3 final size:3
Alignment explanation
Indices: 1096461--1096487 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1096451 TAATAACGAA
1096461 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1096488 CAAATTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1103897 original size:70 final size:71
Alignment explanation
Indices: 1103756--1103902 Score: 251
Period size: 70 Copynumber: 2.1 Consensus size: 71
1103746 GTGGGGCTTC
* * * *
1103756 CGATCGTAAAGTTAGTGTGGCCAAGACTATGACATTCTTTTCCAGGAATGTTCCTAGTAGTCTTC
1 CGATCATAAAGTTAGTGTGGCCAAGACTACGACAATCTTTTCCAGGAATGTTCCCAGTAGTCTTC
1103821 GTAATT
66 GTAATT
1103827 CGATCATAAAGTTAGTGTGGCCAAGACTACGACAATC-TTTCCAGGAATGTTCCCAGTAGTCTTC
1 CGATCATAAAGTTAGTGTGGCCAAGACTACGACAATCTTTTCCAGGAATGTTCCCAGTAGTCTTC
1103891 GTAATT
66 GTAATT
1103897 CGATCA
1 CGATCA
1103903 GTGGTGGATT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
70 38 0.53
71 34 0.47
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (71 bp):
CGATCATAAAGTTAGTGTGGCCAAGACTACGACAATCTTTTCCAGGAATGTTCCCAGTAGTCTTC
GTAATT
Found at i:1106356 original size:22 final size:22
Alignment explanation
Indices: 1106329--1106382 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1106319 GAGATAGACA
*
1106329 GATTTCGCCGGAGATGGGGATG
1 GATTTCGCCGGAGATGGGGACG
*
1106351 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
1106373 GATGTCGCCG
1 GATTTCGCCG
1106383 TAGAGAGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:1106537 original size:20 final size:20
Alignment explanation
Indices: 1106487--1106525 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1106477 ATATTGTGTT
1106487 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
1106507 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
1106526 TATGTGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:1106656 original size:20 final size:21
Alignment explanation
Indices: 1106607--1106660 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1106597 CGATTTACAT
1106607 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
*
1106628 ATT-GGGTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
*
1106647 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1106661 TTTGTTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:1107067 original size:21 final size:21
Alignment explanation
Indices: 1107027--1107067 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1107017 GCGATAGTGC
* *
1107027 CAACAACAACAACGGTGATAA
1 CAACAACAACAACAGCGATAA
*
1107048 CAACAACAACAATAGCGATA
1 CAACAACAACAACAGCGATA
1107068 TCAATAATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (21 bp):
CAACAACAACAACAGCGATAA
Found at i:1107268 original size:15 final size:15
Alignment explanation
Indices: 1107248--1107278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1107238 TTGATCTAAT
*
1107248 TATTATTAAAAATAA
1 TATTATAAAAAATAA
1107263 TATTATAAAAAATAA
1 TATTATAAAAAATAA
1107278 T
1 T
1107279 GTAATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTATAAAAAATAA
Found at i:1109812 original size:14 final size:15
Alignment explanation
Indices: 1109784--1109814 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1109774 AATAATTAAG
1109784 ATAATATATTTTATA
1 ATAATATATTTTATA
1109799 ATAATATA-TTTATA
1 ATAATATATTTTATA
1109813 AT
1 AT
1109815 CATTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATATATTTTATA
Found at i:1109917 original size:2 final size:2
Alignment explanation
Indices: 1109910--1109935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1109900 TTTAAAATCT
1109910 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1109936 CAACCAGGTC
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):
TA
Found at i:1110298 original size:2 final size:2
Alignment explanation
Indices: 1110291--1110329 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1110281 TAAACTATGT
1110291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1110330 GTCATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1111873 original size:2 final size:2
Alignment explanation
Indices: 1111866--1111905 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1111856 CCGACGACAA
1111866 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
1111906 TTAAATTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1113354 original size:15 final size:15
Alignment explanation
Indices: 1113334--1113364 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1113324 CTAAAACTCG
*
1113334 TACTTTAGTGGCGTT
1 TACTTTAGAGGCGTT
1113349 TACTTTAGAGGCGTT
1 TACTTTAGAGGCGTT
1113364 T
1 T
1113365 GTAAACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (15 bp):
TACTTTAGAGGCGTT
Found at i:1113422 original size:42 final size:41
Alignment explanation
Indices: 1113349--1113654 Score: 188
Period size: 42 Copynumber: 7.4 Consensus size: 41
1113339 TAGTGGCGTT
* * * **
1113349 TACTTTAGAGGCGTTTGTAA-ACAAATGCCGCTTTAGAATCG
1 TACTTTAGTGGCGTTT-TAAGAAAAACGCCGCTAAAGAATCG
* * * *
1113390 TTCTTTAGTGGTGTTTTAAGTAAAAACGCCGCTAAATACTCG
1 TACTTTAGTGGCGTTTTAAG-AAAAACGCCGCTAAAGAATCG
* * * *
1113432 TACTTTAGTGGCGTTTTTAGACAAACGCCGCTAAA-ACCTAG
1 TACTTTAGTGGCGTTTTAAGAAAAACGCCGCTAAAGA-ATCG
* * *** * * *
1113473 TACTTTAGTTGCTTTTTTTTACAAACGCCGCTAAATACTCG
1 TACTTTAGTGGCGTTTTAAGAAAAACGCCGCTAAAGAATCG
* * * **
1113514 TACTTTAGTGGTGTTTTTAGACAAAACGCCGCTAAA-ACCTAA
1 TACTTTAGTGGCGTTTTAAGA-AAAACGCCGCTAAAGA-ATCG
* * * * * * *
1113556 TACTTTAGCGGCGTTTT-TGACAAACGTCGCTAAATACTTG
1 TACTTTAGTGGCGTTTTAAGAAAAACGCCGCTAAAGAATCG
* * **
1113596 TACTTTAGTGGCGTTTTAAGTAAAAACGCTGCTAAATACGCG
1 TACTTTAGTGGCGTTTTAAG-AAAAACGCCGCTAAAGAATCG
*
1113638 TACATTAGTGGCGTTTT
1 TACTTTAGTGGCGTTTT
1113655 TATGTATAAA
Statistics
Matches: 214, Mismatches: 42, Indels: 17
0.78 0.15 0.06
Matches are distributed among these distances:
40 34 0.16
41 85 0.40
42 95 0.44
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTAAGAAAAACGCCGCTAAAGAATCG
Found at i:1113522 original size:82 final size:81
Alignment explanation
Indices: 1113413--1113631 Score: 312
Period size: 82 Copynumber: 2.7 Consensus size: 81
1113403 TTTTAAGTAA
*
1113413 AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAGACAAACGCCGCTAAAACCTAGTACTT
1 AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAGACAAACGCCGCTAAAACCTAATACTT
** * *
1113478 TAGTTGCTTTTTTTTAC
66 TAGCGGC-GTTTTTGAC
*
1113495 AAACGCCGCTAAATACTCGTACTTTAGTGGTGTTTTTAGACAAAACGCCGCTAAAACCTAATACT
1 AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAGAC-AAACGCCGCTAAAACCTAATACT
1113560 TTAGCGGCGTTTTTGAC
65 TTAGCGGCGTTTTTGAC
* * * * *
1113577 AAACGTCGCTAAATACTTGTACTTTAGTGGCGTTTTAAGTAAAAACGCTGCTAAA
1 AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAG-ACAAACGCCGCTAAA
1113632 TACGCGTACA
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
82 94 0.76
83 29 0.24
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (81 bp):
AAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAGACAAACGCCGCTAAAACCTAATACTT
TAGCGGCGTTTTTGAC
Found at i:1113569 original size:124 final size:124
Alignment explanation
Indices: 1113387--1113669 Score: 333
Period size: 124 Copynumber: 2.3 Consensus size: 124
1113377 CGCTTTAGAA
* * ** *
1113387 TCGTTCTTTAGTGGTGTTTTAAGTAAAAACGCCGCTAAATACTCGTACTTTAGTGGCGTTTTTAG
1 TCGTACTTTAGTGGTGTTTTTAGTAAAAACGCCGCTAAATACTAATACTTTAGCGGCGTTTTT-G
* *** *
1113452 ACAAACGCCGCTAAA-ACCTAGTACTTTAGTTGC-TTTTTTTTACAAACGCCGCTAAATAC
65 ACAAACGCCGCTAAATA-CTAGTACTTTAGTGGCGTTTTAAGTAAAAACGCCGCTAAATAC
1113511 TCGTACTTTAGTGGTGTTTTTAG-ACAAAACGCCGCTAAA-ACCTAATACTTTAGCGGCGTTTTT
1 TCGTACTTTAGTGGTGTTTTTAGTA-AAAACGCCGCTAAATA-CTAATACTTTAGCGGCGTTTTT
* * *
1113574 GACAAACGTCGCTAAATACTTGTACTTTAGTGGCGTTTTAAGTAAAAACGCTGCTAAATAC
64 GACAAACGCCGCTAAATACTAGTACTTTAGTGGCGTTTTAAGTAAAAACGCCGCTAAATAC
* * * *
1113635 GCGTACATTAGTGGCGTTTTTATGTATAAAC-CCGC
1 TCGTACTTTAGTGGTGTTTTTA-GTAAAAACGCCGC
1113670 AAGTTTATAT
Statistics
Matches: 136, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
123 31 0.23
124 99 0.73
125 5 0.04
126 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (124 bp):
TCGTACTTTAGTGGTGTTTTTAGTAAAAACGCCGCTAAATACTAATACTTTAGCGGCGTTTTTGA
CAAACGCCGCTAAATACTAGTACTTTAGTGGCGTTTTAAGTAAAAACGCCGCTAAATAC
Found at i:1117626 original size:43 final size:42
Alignment explanation
Indices: 1117536--1117904 Score: 389
Period size: 43 Copynumber: 8.6 Consensus size: 42
1117526 TAGATTTAAC
*
1117536 CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
1 CTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * ***
1117578 CTATAGATCTAATCTTTTGCGGCTTTTGTATCCAAAAACGATA
1 CTATAGATCTAACCTTTTGCGGCGTTTGT-TCCAAAAACGCCG
*
1117621 CTATAGATC-AGACCTTTTGCGGCGTTTGTTCAAAAAACGCCG
1 CTATAGATCTA-ACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* ** * * *
1117663 CTATAGATCTGACCTTTTGCGGCGTTTGTTCTGAAAATGTCA
1 CTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * *
1117705 CTATAGATATCGACCTTTTGCGGCGTTTGTTCCGAAAACGCCG
1 CTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * * * *
1117748 CTATAGGTCTCGACCTTTTGCGGCGATTGTTCAAAAAACGTCG
1 CTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * *
1117791 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGTCG
1 CTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * *
1117834 CTATAGATCTCGACATTTTGCGGTGTTTGTTCCAAAAACGCCG
1 CTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * * *
1117877 CGATATATCTTGACCTATTGCGGCGTTT
1 CTATAGATC-TAACCTTTTGCGGCGTTT
1117905 TTTTGTTCTC
Statistics
Matches: 282, Mismatches: 40, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
42 80 0.28
43 201 0.71
44 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (42 bp):
CTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
Found at i:1117680 original size:85 final size:85
Alignment explanation
Indices: 1117536--1117873 Score: 441
Period size: 85 Copynumber: 4.0 Consensus size: 85
1117526 TAGATTTAAC
* * * *
1117536 CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-AATCTTTTGCGG
1 CTATAGATCAGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
*
1117600 CTTTTGTATCCAAAAACGAT-A
66 CGTTTGT-TCCAAAAACG-TCA
1117621 CTATAGATCAGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACCTTTTGCGG
1 CTATAGATCAGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
** *
1117685 CGTTTGTTCTGAAAATGTCA
66 CGTTTGTTCCAAAAACGTCA
** *
1117705 CTATAGAT-ATCGACCTTTTGCGGCGTTTGTTCCGAAAACGCCGCTATAGGTCTCGACCTTTTGC
1 CTATAGATCA--GACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTGC
* * *
1117769 GGCGATTGTTCAAAAAACGTCG
64 GGCGTTTGTTCCAAAAACGTCA
* * *
1117791 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGTCGCTATAGATCTCGACATTTTGCG
1 CTATAGATC-AGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTGCG
*
1117856 GTGTTTGTTCCAAAAACG
65 GCGTTTGTTCCAAAAACG
1117874 CCGCGATATA
Statistics
Matches: 222, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
83 2 0.01
84 16 0.07
85 105 0.47
86 99 0.45
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (85 bp):
CTATAGATCAGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
CGTTTGTTCCAAAAACGTCA
Found at i:1117807 original size:86 final size:85
Alignment explanation
Indices: 1117536--1117904 Score: 465
Period size: 86 Copynumber: 4.3 Consensus size: 85
1117526 TAGATTTAAC
* * *
1117536 CTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTAATCTTTTGCGG
1 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGG
*
1117600 CTTTTGTATCCAAAAACGAT-A
66 CGTTTGT-TCCAAAAACG-TCA
*
1117621 CTATAGATC-AGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGG
1 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGG
** *
1117685 CGTTTGTTCTGAAAATGTCA
66 CGTTTGTTCCAAAAACGTCA
* ** *
1117705 CTATAGATATCGACCTTTTGCGGCGTTTGTTCCGAAAACGCCGCTATAGGTCTCGACCTTTTGCG
1 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACCTTTTGCG
* * *
1117770 GCGATTGTTCAAAAAACGTCG
65 GCGTTTGTTCCAAAAACGTCA
* *
1117791 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGTCGCTATAGATCTCGACATTTTGCG
1 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACCTTTTGCG
* * *
1117856 GTGTTTGTTCCAAAAACGCCG
65 GCGTTTGTTCCAAAAACGTCA
* * * *
1117877 CGATATATCTTGACCTATTGCGGCGTTT
1 CTATAGATCTCGACCTTTTGCGGCGTTT
1117905 TTTTGTTCTC
Statistics
Matches: 249, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
83 1 0.00
84 16 0.06
85 105 0.42
86 127 0.51
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (85 bp):
CTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGG
CGTTTGTTCCAAAAACGTCA
Found at i:1118861 original size:32 final size:32
Alignment explanation
Indices: 1118824--1118884 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1118814 TTTTGGTCGG
*
1118824 TTTTAGTACATAAATTATCAGTTTTAGTCTAT
1 TTTTAGTACATAAACTATCAGTTTTAGTCTAT
1118856 TTTTAGTACATAAACTATCAGTTTTAGTC
1 TTTTAGTACATAAACTATCAGTTTTAGTC
1118885 CGTTATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (32 bp):
TTTTAGTACATAAACTATCAGTTTTAGTCTAT
Found at i:1122245 original size:8 final size:8
Alignment explanation
Indices: 1122234--1122281 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
1122224 TCTATCTATC
1122234 TATATGTA
1 TATATGTA
1122242 TATATGTA
1 TATATGTA
*
1122250 TATATATA
1 TATATGTA
***
1122258 TCCGTGTA
1 TATATGTA
1122266 TATATGTA
1 TATATGTA
*
1122274 TGTATGTA
1 TATATGTA
1122282 AGCTTGATTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (8 bp):
TATATGTA
Found at i:1122277 original size:12 final size:12
Alignment explanation
Indices: 1122236--1122278 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1122226 TATCTATCTA
1122236 TATGTATATATG
1 TATGTATATATG
* *
1122248 TATATATATATC
1 TATGTATATATG
**
1122260 CGTGTATATATG
1 TATGTATATATG
1122272 TATGTAT
1 TATGTAT
1122279 GTAAGCTTGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (12 bp):
TATGTATATATG
Found at i:1126016 original size:21 final size:21
Alignment explanation
Indices: 1125902--1126016 Score: 76
Period size: 20 Copynumber: 5.6 Consensus size: 21
1125892 GCGAAATAAC
**
1125902 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1125922 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
1125942 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* *
1125963 AATCGCAATGCGATTTT-CAT
1 AATCGCAACGCGATTTTCCAG
* **
1125983 ATTCGCATTGCGATTTTCCAG
1 AATCGCAACGCGATTTTCCAG
1126004 AATCGCAACGCGA
1 AATCGCAACGCGA
1126017 ATATGAAAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
19 1 0.01
20 40 0.56
21 29 0.40
22 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1126029 original size:20 final size:20
Alignment explanation
Indices: 1126004--1126156 Score: 75
Period size: 20 Copynumber: 7.7 Consensus size: 20
1125994 GATTTTCCAG
* *
1126004 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1126024 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1126044 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1126064 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1126084 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1126104 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1126124 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1126144 AATCGCAACGCGA
1 AATCGCAACGCGA
1126157 TTTTTAAAGC
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 117 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1126052 original size:40 final size:40
Alignment explanation
Indices: 1126004--1126155 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 40
1125994 GATTTTCCAG
*
1126004 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
1126044 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
1126084 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * *
1126124 TATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
1126156 ATTTTTAAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 98 0.98
41 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:1126087 original size:60 final size:59
Alignment explanation
Indices: 1126004--1126156 Score: 207
Period size: 60 Copynumber: 2.6 Consensus size: 59
1125994 GATTTTCCAG
* ** *
1126004 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTA
* * * *
1126064 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTA
*
1126124 TATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1126157 TTTTTAAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 79 0.96
61 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (59 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTA
Found at i:1126575 original size:33 final size:33
Alignment explanation
Indices: 1126536--1126606 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1126526 TTCACTTAGA
1126536 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1126569 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1126602 TTTCA
1 TTTCA
1126607 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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1126712 original size:21 final size:20
Alignment explanation
Indices: 1126686--1126792 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
1126676 TGCAGAAGAG
1126686 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1126707 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1126727 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1126749 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1126763 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1126782 TCGCAACGAGA
1 TCGCAACGAGA
1126793 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1126766 original size:14 final size:14
Alignment explanation
Indices: 1126747--1126803 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1126737 GAAAAATGAA
1126747 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1126761 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1126780 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1126794 AATCGCAACG
1 AATCGCAACG
1126804 CGAAACAAAA
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:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1126778 original size:33 final size:33
Alignment explanation
Indices: 1126740--1126819 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1126730 GCAACGAGAA
1126740 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1126773 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1126806 AAACAAAAATCGCA
1 AAATGAAAATCGCA
1126820 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1126837 original size:19 final size:19
Alignment explanation
Indices: 1126815--1126942 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
1126805 GAAACAAAAA
*
1126815 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1126834 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1126848 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1126867 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1126881 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1126901 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1126921 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1126941 TC
1 TC
1126943 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.24
16 5 0.06
17 5 0.06
19 22 0.26
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1126856 original size:14 final size:14
Alignment explanation
Indices: 1126837--1126893 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1126827 TTTCATTTCG
1126837 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1126851 CGTTGCGATTTTAATTTCG
1 CGTTGCGA---T--TCTCT
1126870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1126884 CGTTGCGATT
1 CGTTGCGATT
1126894 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
16 1 0.03
17 1 0.03
19 11 0.32
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1126862 original size:33 final size:33
Alignment explanation
Indices: 1126820--1126942 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
1126810 AAAAATCGCA
1126820 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1126853 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1126886 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1126927 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1126943 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 43 0.54
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1126904 original size:21 final size:21
Alignment explanation
Indices: 1126878--1126942 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1126868 CGCGTTGCGA
1126878 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1126899 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1126919 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1126940 TTC
1 TTC
1126943 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1126939 original size:20 final size:20
Alignment explanation
Indices: 1126877--1126940 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1126867 TCGCGTTGCG
1126877 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1126897 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1126918 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1126938 ATT
1 ATT
1126941 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1128785 original size:93 final size:93
Alignment explanation
Indices: 1128626--1129034 Score: 809
Period size: 93 Copynumber: 4.4 Consensus size: 93
1128616 TAGATTGCTT
*
1128626 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1128691 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1128719 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1128784 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1128812 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1128877 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1128905 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1128970 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1128998 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1129035 AATACCCTGA
Statistics
Matches: 315, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 315 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1129169 original size:14 final size:14
Alignment explanation
Indices: 1129150--1129206 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1129140 CGAAACTTAA
1129150 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1129164 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1129183 AATCGCAACGACAG
1 AATCGCAACGAGAG
1129197 AATCGCAACG
1 AATCGCAACG
1129207 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1129188 original size:19 final size:18
Alignment explanation
Indices: 1129164--1129255 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
1129154 GCAACGAGAG
1129164 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
1129183 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
1129197 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
1129216 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
1129230 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
1129249 AATCGCA
1 AATCGCA
1129256 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:1129190 original size:33 final size:33
Alignment explanation
Indices: 1129132--1129255 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1129122 TAGTTTACTT
* * *
1129132 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
1129166 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
1129199 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
1129232 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1129256 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:1129232 original size:14 final size:14
Alignment explanation
Indices: 1129181--1129239 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1129171 ACGCGAAATG
1129181 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1129195 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1129214 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1129228 AAAATCGCAACG
1 AAAATCGCAACG
1129240 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1129273 original size:19 final size:19
Alignment explanation
Indices: 1129251--1129423 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1129241 GAAACCAAAA
*
1129251 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1129270 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1129284 TCTCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1129303 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1129319 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1129336 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1129355 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1129374 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1129393 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1129413 TCGTGTTGCGA
1 TCGCGTTGCGA
1129424 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
16 7 0.06
17 7 0.06
19 82 0.65
20 12 0.10
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1129325 original size:14 final size:14
Alignment explanation
Indices: 1129273--1129329 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1129263 TTTCATTTCG
*
1129273 CGTTGCGATTCTCT
1 CGTTGCGATTCTGT
*
1129287 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
1129304 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
1129320 CGTTGCGATT
1 CGTTGCGATT
1129330 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 21 0.60
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.21, G:0.28, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:1129343 original size:52 final size:54
Alignment explanation
Indices: 1129287--1129423 Score: 188
Period size: 57 Copynumber: 2.5 Consensus size: 54
1129277 GCGATTCTCT
*
1129287 CGTTGCGATTTTGGTTTCGCGTTGCGATTCT-G-TCGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
*
1129339 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGG--T-TCGTTGCGATTCTCATTTCG
* *
1129396 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-GGTTTCGCGTTGCGA
1129424 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
52 30 0.40
53 1 0.01
57 31 0.41
58 13 0.17
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (54 bp):
CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
Found at i:1129381 original size:38 final size:37
Alignment explanation
Indices: 1129251--1129423 Score: 164
Period size: 33 Copynumber: 4.8 Consensus size: 37
1129241 GAAACCAAAA
* **
1129251 TCGCATTGCGATTTTCATTTCGCGTTGCGATTC----
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTGTT
*
1129284 TCTCGTTGCGATTTTGGTTTCGCGTTGCGATTCTG--
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTGTT
** *
1129319 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCT-GTT
* *
1129355 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCT-GTT
* *
1129393 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT-GGTTTCGCGTTGCGA
1129424 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
33 57 0.49
34 1 0.01
35 1 0.01
36 1 0.01
38 44 0.38
39 12 0.10
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (37 bp):
TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTCTGTT
Found at i:1129900 original size:21 final size:21
Alignment explanation
Indices: 1129876--1129942 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1129866 TCATTCCTCG
*
1129876 AGAGTCCACTCCCACCGTTCA
1 AGAGTCCACTCCCACCATTCA
* ** * *
1129897 AGAGGCCACTGTCATCATTGA
1 AGAGTCCACTCCCACCATTCA
1129918 AGAGGTCC-CTCCCACCATTCA
1 AGA-GTCCACTCCCACCATTCA
1129939 AGAG
1 AGAG
1129943 CCCGATTTAC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.88
22 3 0.09
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCACTCCCACCATTCA
Found at i:1131364 original size:14 final size:14
Alignment explanation
Indices: 1131345--1131380 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1131335 ATTGTTTAAT
1131345 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1131359 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1131373 TGATTTGT
1 TGATTTGT
1131381 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1131495 original size:19 final size:19
Alignment explanation
Indices: 1131471--1131558 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1131461 GCATTATGTT
*
1131471 GAAATGAAAATCACAATGC
1 GAAATGAAAATCGCAATGC
1131490 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1131507 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1131523 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1131542 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1131559 CGAGAGAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 16 0.27
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1131590 original size:53 final size:53
Alignment explanation
Indices: 1131471--1131577 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
1131461 GCATTATGTT
*
1131471 GAAATGAAAATCACAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1131523 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1131576 GA
1 GA
1131578 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 18 0.34
53 35 0.66
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:1131595 original size:19 final size:19
Alignment explanation
Indices: 1131567--1131756 Score: 221
Period size: 19 Copynumber: 10.7 Consensus size: 19
1131557 AACGAGAGAA
*
1131567 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1131586 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1131605 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1131622 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1131639 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1131655 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1131672 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1131691 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1131710 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
1131728 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1131744 TCGCATTGCGATT
1 TCGCATTGCGATT
1131757 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 7, Indels: 34
0.78 0.04 0.18
Matches are distributed among these distances:
14 22 0.15
16 15 0.10
17 14 0.10
18 5 0.03
19 66 0.45
20 25 0.17
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1131630 original size:14 final size:14
Alignment explanation
Indices: 1131611--1131665 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1131601 CATTTCCGCA
1131611 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1131625 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1131642 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1131658 TTGCGATT
1 TTGCGATT
1131666 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1131698 original size:105 final size:105
Alignment explanation
Indices: 1131567--1131770 Score: 372
Period size: 105 Copynumber: 1.9 Consensus size: 105
1131557 AACGAGAGAA
1131567 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
1131632 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * * *
1131672 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGAT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
1131737 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1131771 GTAATTTCCG
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (105 bp):
TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1131778 original size:33 final size:33
Alignment explanation
Indices: 1131591--1131770 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
1131581 TCATTTCGCA
1131591 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1131625 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1131658 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
1131694 CATTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1131730 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1131763 TTGCGATT
1 TTGCGATT
1131771 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 8, Indels: 13
0.86 0.05 0.08
Matches are distributed among these distances:
33 66 0.50
34 29 0.22
35 3 0.02
36 7 0.05
37 2 0.02
38 15 0.11
39 10 0.08
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1134286 original size:24 final size:24
Alignment explanation
Indices: 1134252--1134298 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1134242 CTGAAACATC
1134252 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1134276 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1134299 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1135019 original size:20 final size:20
Alignment explanation
Indices: 1134991--1135239 Score: 261
Period size: 20 Copynumber: 12.4 Consensus size: 20
1134981 AAATTTCAGT
* * * *
1134991 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1135011 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1135031 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1135051 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1135071 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1135091 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1135111 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1135131 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1135151 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1135171 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1135191 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1135211 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1135231 GTTGCGATT
1 GTTGCGATT
1135240 CTTGAAAATC
Statistics
Matches: 199, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 193 0.97
21 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1135292 original size:21 final size:20
Alignment explanation
Indices: 1135207--1135303 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
1135197 ATTTATGTGT
* *
1135207 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
1135227 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** * * *
1135248 TCGCAATGCGAATATGAAAA
1 TCGCGTTGCGATTTTCAAAA
*
1135268 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
1135289 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1135304 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.52
21 30 0.48
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:1146752 original size:12 final size:13
Alignment explanation
Indices: 1146729--1146766 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1146719 ATATTCAAAT
1146729 GAAAATATTTATA
1 GAAAATATTTATA
*
1146742 TAAAA-ATTTATA
1 GAAAATATTTATA
1146754 GAAAATATATTAT
1 GAAAATAT-TTAT
1146767 TTTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 6 0.29
14 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (13 bp):
GAAAATATTTATA
Found at i:1150958 original size:20 final size:20
Alignment explanation
Indices: 1150935--1150972 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1150925 AACACAGGTT
1150935 TCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAACGCGAAAG
1150955 TCAAAATCGCAACGCGAA
1 TCAAAATCGCAACGCGAA
1150973 TTACCGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (20 bp):
TCAAAATCGCAACGCGAAAG
Found at i:1151240 original size:20 final size:20
Alignment explanation
Indices: 1151215--1151307 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
1151205 TTTTCCAAAT
1151215 TCGCAACGCGAATA-GTTAAA
1 TCGCAACGCGAATATG-TAAA
** *
1151235 TCGCAACGATAATATGTAAT
1 TCGCAACGCGAATATGTAAA
* * *
1151255 TCTCAATGCGAATAGGTAAA
1 TCGCAACGCGAATATGTAAA
**
1151275 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
1151295 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1151308 TCTCCAAATT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1151256 original size:40 final size:40
Alignment explanation
Indices: 1151212--1151307 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1151202 CGATTTTCCA
*
1151212 AATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
* *
1151252 AATTCTCAATGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
1151292 AAATCGCAACGCGAAT
1 AATTCGCAACGCGAAT
1151308 TCTCCAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:1151526 original size:146 final size:146
Alignment explanation
Indices: 1151279--1151569 Score: 485
Period size: 146 Copynumber: 2.0 Consensus size: 146
1151269 GGTAAATCGC
*
1151279 AACGATAATATGTAAATCGCAACGCGAATTCTCCAAATTAGCAACTCGAATTTTACAACGCTAAT
1 AACGATAATATGTAAATCGCAACGCGAATTCTCCAAATTAGCAACTCGAATTTCACAACGCTAAT
* *
1151344 TACCGATATAGGTAATTAGCGTTGCGAAAACAAAATTCGCGTTGCGATTTTCTAAATTTGCAACG
66 TACCGATATAGGTAATTAGCGTTGCGAAAACAAAATTCGCGTTGCGATTTTCCAAATTCGCAACG
1151409 CGAAAGTCAAATTCGA
131 CGAAAGTCAAATTCGA
* *
1151425 AACGATAATATGTAAATCGCAACGCGAATTCTCCAAATTCGCAACTCGAATTTCGCAAC-CTTAA
1 AACGATAATATGTAAATCGCAACGCGAATTCTCCAAATTAGCAACTCGAATTTCACAACGC-TAA
* ** *
1151489 TTACCGATGTAGGTAATTAGCGTTGCGAAAATGAAATTCGCGTTGCGATTTTCCAAATTCGTAAC
65 TTACCGATATAGGTAATTAGCGTTGCGAAAACAAAATTCGCGTTGCGATTTTCCAAATTCGCAAC
1151554 GCGAAAGTCAAATTCG
130 GCGAAAGTCAAATTCG
1151570 CGTCGAGTTG
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
145 1 0.01
146 134 0.99
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (146 bp):
AACGATAATATGTAAATCGCAACGCGAATTCTCCAAATTAGCAACTCGAATTTCACAACGCTAAT
TACCGATATAGGTAATTAGCGTTGCGAAAACAAAATTCGCGTTGCGATTTTCCAAATTCGCAACG
CGAAAGTCAAATTCGA
Found at i:1158730 original size:31 final size:31
Alignment explanation
Indices: 1158692--1158801 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 31
1158682 AGTTTACCCT
1158692 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** ** **
1158723 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGA
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT--A
*
1158761 AGTGTCCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
1158792 AGTGACCAAA
1 AGTGACCAAA
1158802 TAGTTTACCC
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
31 20 0.34
32 6 0.10
33 3 0.05
34 5 0.09
35 5 0.09
36 3 0.05
37 6 0.10
38 10 0.17
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:1161204 original size:7 final size:7
Alignment explanation
Indices: 1161192--1161220 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1161182 TTAAATCATC
1161192 AATATAA
1 AATATAA
1161199 AATATAA
1 AATATAA
1161206 AATATAA
1 AATATAA
1161213 AATATAA
1 AATATAA
1161220 A
1 A
1161221 GAAAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATATAA
Found at i:1164095 original size:24 final size:24
Alignment explanation
Indices: 1164068--1164153 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
1164058 CCTAAAAATC
1164068 CAAAGAGATAATTCCTAATAAA-TG
1 CAAA-AGATAATTCCTAATAAATTG
* *
1164092 C-AAAGATAAATT-GTAAAGAAATTG
1 CAAAAGAT-AATTCCT-AATAAATTG
1164116 CAAAAGATAATTCCTAATAAATTG
1 CAAAAGATAATTCCTAATAAATTG
1164140 CAAAAGATAATTCC
1 CAAAAGATAATTCC
1164154 CTTAATTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.09
23 11 0.21
24 30 0.57
25 7 0.13
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (24 bp):
CAAAAGATAATTCCTAATAAATTG
Found at i:1164980 original size:16 final size:16
Alignment explanation
Indices: 1164959--1164989 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1164949 AGGATTAATA
1164959 AAGGGAAGATAAAATC
1 AAGGGAAGATAAAATC
1164975 AAGGGAAGATAAAAT
1 AAGGGAAGATAAAAT
1164990 TAAAGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.26, T:0.13
Consensus pattern (16 bp):
AAGGGAAGATAAAATC
Found at i:1165359 original size:7 final size:7
Alignment explanation
Indices: 1165347--1165380 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1165337 TATTGTAATT
1165347 ATAAAAA
1 ATAAAAA
1165354 AT-AAAA
1 ATAAAAA
1165360 AT-AAAA
1 ATAAAAA
1165366 ATAAAAA
1 ATAAAAA
1165373 ATAAAAA
1 ATAAAAA
1165380 A
1 A
1165381 GTGTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:1165365 original size:5 final size:6
Alignment explanation
Indices: 1165350--1165379 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1165340 TGTAATTATA
1165350 AAAAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA
1165380 AGTGTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:1165365 original size:13 final size:12
Alignment explanation
Indices: 1165350--1165379 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1165340 TGTAATTATA
1165350 AAAAATAAAAAT
1 AAAAATAAAAAT
1165362 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
1165375 AAAAA
1 AAAAA
1165380 AGTGTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:1169166 original size:29 final size:29
Alignment explanation
Indices: 1169132--1169190 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1169122 CCTAAATTAA
1169132 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1169161 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1169190 T
1 T
1169191 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1173790 original size:29 final size:29
Alignment explanation
Indices: 1173756--1173813 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1173746 CCTAAATTAA
1173756 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1173785 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1173814 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1174476 original size:25 final size:26
Alignment explanation
Indices: 1174439--1174504 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 26
1174429 ACTACCATTA
1174439 TAGC-TTTACTAAGCTTTCACTATATC
1 TAGCATTT-CTAAGCTTTCACTATATC
1174465 TAG-ATTTCTAAGC-TTCACTATATC
1 TAGCATTTCTAAGCTTTCACTATATC
*
1174489 TAGCTTTTCTAAGCTT
1 TAGCATTTCTAAGCTT
1174505 GTGGTCGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 14 0.39
25 15 0.42
26 7 0.19
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (26 bp):
TAGCATTTCTAAGCTTTCACTATATC
Found at i:1174575 original size:2 final size:2
Alignment explanation
Indices: 1174556--1174631 Score: 104
Period size: 2 Copynumber: 39.5 Consensus size: 2
1174546 CCAATCATAC
* * *
1174556 AT AT AC AT AT AT AC AT AT AT AC AT AT AT AT A- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1174596 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1174632 AACAAAACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
1 3 0.05
2 62 0.95
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1175233 original size:85 final size:85
Alignment explanation
Indices: 1175091--1175247 Score: 262
Period size: 85 Copynumber: 1.8 Consensus size: 85
1175081 CCTAACACAC
* * *
1175091 CCTTTTATAGCCAAGTTACCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATT-AATCTATA
1 CCTTTTATAGCCAAGTTACCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATA
1175155 TTTAATTGGAATTTAATAAT
66 TTTAATTGGAATTTAATAAT
*
1175175 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTA-CCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1175240 ATTTAATT
65 ATTTAATT
1175248 AATTGAAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 17 0.25
85 35 0.52
86 15 0.22
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.46
Consensus pattern (85 bp):
CCTTTTATAGCCAAGTTACCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTGGAATTTAATAAT
Done.