Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008241.1 Hibiscus syriacus cultivar Beakdansim tig00110889_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: 1355325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1112579 original size:29 final size:28
Alignment explanation
Indices: 1112542--1112607 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
1112532 ACTAAACATT
1112542 TTATGAAATTATACAAAA-TAGAGACCCTAA
1 TTAT-AAATTA-A-AAAATTAGAGACCCTAA
*
1112572 TTATAAATTAAAAAATTGGAGACCCTAA
1 TTATAAATTAAAAAATTAGAGACCCTAA
*
1112600 CTATAAAT
1 TTATAAAT
1112608 ACAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 4 0.12
28 19 0.58
29 6 0.18
30 4 0.12
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (28 bp):
TTATAAATTAAAAAATTAGAGACCCTAA
Found at i:1113127 original size:18 final size:18
Alignment explanation
Indices: 1113099--1113149 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1113089 AGTTATATTT
*
1113099 AAAAATGAATTTAATTAA
1 AAAAATAAATTTAATTAA
*
1113117 TAAAATAAATTGT-A-TAA
1 AAAAATAAATT-TAATTAA
*
1113134 AAAAATAAAATTAATT
1 AAAAATAAATTTAATT
1113150 GTCACTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.04
17 13 0.50
18 11 0.42
19 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAAATAAATTTAATTAA
Found at i:1114093 original size:3 final size:3
Alignment explanation
Indices: 1114085--1114114 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1114075 AGTGAATAAT
1114085 TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1114115 TTTAATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1114509 original size:19 final size:19
Alignment explanation
Indices: 1114483--1114527 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1114473 ATTTAAAAAA
*
1114483 TAATAATAAATAACTTATTT
1 TAATAATAAATAA-ATATTT
*
1114503 T-ATAATATATAAATATTT
1 TAATAATAAATAAATATTT
1114521 TAATAAT
1 TAATAAT
1114528 TTAAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 15 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATAAATAAATATTT
Found at i:1115080 original size:32 final size:31
Alignment explanation
Indices: 1114986--1115084 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 31
1114976 TGATTCGATA
* * *
1114986 TTGATCCGACCTG-AAATCAACCGATCTGGTA
1 TTGA-CCGACCTGAAAATCAACCTATCTGATT
* * * *
1115017 TTGACCCAGCCCGAAAATCAA-TTGATATGATT
1 TTGACCGA-CCTGAAAATCAACCT-ATCTGATT
1115049 TTGACCTGACCTGAAAATCAACCTATCTGATT
1 TTGACC-GACCTGAAAATCAACCTATCTGATT
1115081 TTGA
1 TTGA
1115085 TCCGGCCCAA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
30 3 0.06
31 7 0.13
32 40 0.77
33 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (31 bp):
TTGACCGACCTGAAAATCAACCTATCTGATT
Found at i:1119208 original size:13 final size:14
Alignment explanation
Indices: 1119190--1119222 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1119180 ATGGAACACC
1119190 GATTTTATA-AAAT
1 GATTTTATATAAAT
1119203 GATTTTATATAAAT
1 GATTTTATATAAAT
*
1119217 TATTTT
1 GATTTT
1119223 TGTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
GATTTTATATAAAT
Found at i:1128591 original size:16 final size:16
Alignment explanation
Indices: 1128570--1128603 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1128560 ATAATATTGT
1128570 ATAAAACAT-TAATAAA
1 ATAAAACATGT-ATAAA
1128586 ATAAAACATGTATAAA
1 ATAAAACATGTATAAA
1128602 AT
1 AT
1128604 TAGTTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
ATAAAACATGTATAAA
Found at i:1142849 original size:23 final size:21
Alignment explanation
Indices: 1142838--1142884 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1142828 TTCGGTTTGC
*
1142838 AAAAAAAACCGGTTTTTTTAA
1 AAAAAAAACCGGTTTGTTTAA
1142859 AAAAAAAACCGGTTT-TTTAA
1 AAAAAAAACCGGTTTGTTTAA
1142879 AAAAAA
1 AAAAAA
1142885 CCAGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAAAAACCGGTTTGTTTAA
Found at i:1142864 original size:21 final size:20
Alignment explanation
Indices: 1142838--1142884 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
1142828 TTCGGTTTGC
1142838 AAAAAAAACCGGTTTTTTTAA
1 AAAAAAAACCGG-TTTTTTAA
1142859 AAAAAAAACCGGTTTTTTAA
1 AAAAAAAACCGGTTTTTTAA
1142879 AAAAAA
1 AAAAAA
1142885 CCAGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAAAAAACCGGTTTTTTAA
Found at i:1142936 original size:40 final size:39
Alignment explanation
Indices: 1142839--1142996 Score: 160
Period size: 39 Copynumber: 4.0 Consensus size: 39
1142829 TCGGTTTGCA
** *
1142839 AAAAAAACCGGTTTTTTT-AAAAAAAAAACCGGTTTTTT
1 AAAAAAACCGGTTTTTTTCGGATAAAAAACCGGTTTTTT
* * * *
1142877 AAAAAAAACCAGATTTTTTCGGATAAAAATCCAGTTTTTT
1 -AAAAAAACCGGTTTTTTTCGGATAAAAAACCGGTTTTTT
* * **
1142917 TAAAAAACCGGATTTTTTTCGGAT-AAAATCCGG-TTTGA
1 AAAAAAACCGG-TTTTTTTCGGATAAAAAACCGGTTTTTT
1142955 AAAAAAACCGGTTTTTTATCCGGATAAAAAACCGGTTTTTT
1 AAAAAAACCGGTTTTTT-T-CGGATAAAAAACCGGTTTTTT
1142996 A
1 A
1142997 TCCGGTTTGA
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
37 6 0.06
38 14 0.15
39 38 0.40
40 34 0.35
41 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (39 bp):
AAAAAAACCGGTTTTTTTCGGATAAAAAACCGGTTTTTT
Found at i:1142988 original size:24 final size:24
Alignment explanation
Indices: 1142955--1143041 Score: 122
Period size: 24 Copynumber: 3.5 Consensus size: 24
1142945 TCCGGTTTGA
1142955 AAAAAAACCGGTTTTTTATCCGG-
1 AAAAAAACCGGTTTTTTATCCGGT
1142978 ATAAAAAACCGGTTTTTTATCCGGTTT
1 A-AAAAAACCGGTTTTTTATCCGG--T
*
1143005 GAAAAAAACCGGTTTTTAATCCGGT
1 -AAAAAAACCGGTTTTTTATCCGGT
1143030 AAAAAAACCGGT
1 AAAAAAACCGGT
1143042 CGTTCAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
23 1 0.02
24 34 0.59
25 1 0.02
27 21 0.36
28 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (24 bp):
AAAAAAACCGGTTTTTTATCCGGT
Found at i:1143027 original size:51 final size:52
Alignment explanation
Indices: 1142944--1143041 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 52
1142934 TTCGGATAAA
*
1142944 ATCCGGTTTGAAAAAAAACCGGTTTTTTATCCGG-ATAAAAAACCGGTTTTTT
1 ATCCGGTTTGAAAAAAAACCGGTTTTTAATCCGGTA-AAAAAACCGGTTTTTT
1142996 ATCCGGTTTG-AAAAAAACCGGTTTTTAATCCGGTAAAAAAACCGGT
1 ATCCGGTTTGAAAAAAAACCGGTTTTTAATCCGGTAAAAAAACCGGT
1143042 CGTTCAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
51 33 0.75
52 11 0.25
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (52 bp):
ATCCGGTTTGAAAAAAAACCGGTTTTTAATCCGGTAAAAAAACCGGTTTTTT
Found at i:1147446 original size:16 final size:17
Alignment explanation
Indices: 1147417--1147463 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1147407 AAAATATTTT
1147417 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
* *
1147435 ATATATAA-AATATTAT
1 ATATATAATAATATAAA
1147451 ATATATATATAAT
1 ATATATA-ATAAT
1147464 CGGGGCAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:1148041 original size:12 final size:14
Alignment explanation
Indices: 1148013--1148042 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1148003 AGTAAATGAA
1148013 TATAAATATATTAT
1 TATAAATATATTAT
1148027 TATAAAATATATTAT
1 TAT-AAATATATTAT
1148042 T
1 T
1148043 TTAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 3 0.20
15 12 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATATATTAT
Found at i:1176956 original size:103 final size:103
Alignment explanation
Indices: 1176525--1176948 Score: 794
Period size: 103 Copynumber: 4.1 Consensus size: 103
1176515 GTCGAGGGTC
1176525 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1176590 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
**
1176628 TATGTGGTTTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1176693 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1176731 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1176796 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1176834 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
1176899 TTGATCCCTAGTATATGTATATAATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1176937 TATGTGGTCCTT
1 TATGTGGTCCTT
1176949 ATGGACATTA
Statistics
Matches: 313, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 313 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1177009 original size:23 final size:23
Alignment explanation
Indices: 1176964--1177009 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1176954 CATTATTACA
* *
1176964 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACAGTGCAATTATATG
* *
1176987 TGGCACTTCAGTGCAGTTATATG
1 TGGCACTACAGTGCAATTATATG
1177010 AGCTGTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTATATG
Found at i:1178150 original size:15 final size:15
Alignment explanation
Indices: 1178130--1178165 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1178120 TAAGTGGATT
*
1178130 GAAGCTTGTTTCAAG
1 GAAGCTTATTTCAAG
*
1178145 GAAGCTTATTTCAGG
1 GAAGCTTATTTCAAG
1178160 GAAGCT
1 GAAGCT
1178166 AGGTATTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (15 bp):
GAAGCTTATTTCAAG
Found at i:1180264 original size:14 final size:14
Alignment explanation
Indices: 1180245--1180273 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1180235 TGTATGAATT
1180245 TTTTAAAAATTATA
1 TTTTAAAAATTATA
1180259 TTTTAAAAATTATA
1 TTTTAAAAATTATA
1180273 T
1 T
1180274 GAAATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAAAAATTATA
Found at i:1181208 original size:27 final size:27
Alignment explanation
Indices: 1181157--1181220 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1181147 AATAAATTAT
1181157 ATATTTTTAAATGAAAATGAAAATAAA
1 ATATTTTTAAATGAAAATGAAAATAAA
* *
1181184 ATATTTTTAAAT-TAAATTAATAATAAA
1 ATATTTTTAAATGAAAATGAA-AATAAA
*
1181211 ATATATTTAA
1 ATATTTTTAA
1181221 TAAGTTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 6 0.18
27 27 0.82
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATGAAAATAAA
Found at i:1181233 original size:27 final size:25
Alignment explanation
Indices: 1181178--1181249 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
1181168 TGAAAATGAA
1181178 AATAAAATATTTTTAAATTAAATTAAT
1 AATAAAATA-TTTT-AATTAAATTAAT
* *
1181205 AATAAAATATATTTAA-TAAGTTGAT
1 AATAAAATAT-TTTAATTAAATTAAT
1181230 -ATAAAAATATTTTAAGTTAA
1 AAT-AAAATATTTTAA-TTAA
1181250 TATATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.18
25 14 0.36
26 6 0.15
27 12 0.31
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
AATAAAATATTTTAATTAAATTAAT
Found at i:1181247 original size:21 final size:22
Alignment explanation
Indices: 1181200--1181258 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 22
1181190 TTAAATTAAA
1181200 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAA-ATATTT-ATAAG
*
1181225 TTGATATAAAAATATTT-TAAG
1 TTAATATAAAAATATTTATAAG
1181246 TTAATATATAAAA
1 TTAATATA-AAAA
1181259 ATTATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 6 0.19
24 6 0.19
25 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TTAATATAAAAATATTTATAAG
Found at i:1181254 original size:23 final size:23
Alignment explanation
Indices: 1181195--1181260 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
1181185 TATTTTTAAA
*
1181195 TTAAATTAATA-ATAAAATATATT
1 TTAAGTTAATATATAAAA-ATATT
*
1181218 TAATAAGTT--GATATAAAAATATT
1 T--TAAGTTAATATATAAAAATATT
1181241 TTAAGTTAATATATAAAAAT
1 TTAAGTTAATATATAAAAAT
1181261 TATTATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 6 0.17
23 18 0.51
24 6 0.17
25 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
TTAAGTTAATATATAAAAATATT
Found at i:1182060 original size:31 final size:31
Alignment explanation
Indices: 1182022--1182089 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1182012 GGGTGAACAC
* *
1182022 ATCTTAATTAAATAAAATCAAAAGTGACCAT
1 ATCTTAATTAAATAAAAACAAAAATGACCAT
1182053 ATCTTAATTAAATAAAAACAAAAATGACCAT
1 ATCTTAATTAAATAAAAACAAAAATGACCAT
1182084 ATCTTA
1 ATCTTA
1182090 TGTTTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAATGACCAT
Found at i:1182519 original size:16 final size:15
Alignment explanation
Indices: 1182498--1182557 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
1182488 ATATATTTTT
*
1182498 ATTTTTTAGTAATTTA
1 ATTTTTTAAT-ATTTA
*
1182514 ATTTTTTAATTTTTTA
1 ATTTTTTAA-TATTTA
1182530 ATTTTTTAATATTT-
1 ATTTTTTAATATTTA
*
1182544 ATTTTTTACTATTT
1 ATTTTTTAATATTT
1182558 TTGTATAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.33
15 4 0.10
16 21 0.54
17 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
ATTTTTTAATATTTA
Found at i:1182521 original size:8 final size:8
Alignment explanation
Indices: 1182510--1182551 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
1182500 TTTTTAGTAA
1182510 TTTAATTT
1 TTTAATTT
1182518 TTTAATTT
1 TTTAATTT
1182526 TTTAATTT
1 TTTAATTT
*
1182534 TTTAA-TA
1 TTTAATTT
1182541 TTT-ATTT
1 TTTAATTT
1182548 TTTA
1 TTTA
1182552 CTATTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 8 0.27
8 21 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTAATTT
Found at i:1183682 original size:17 final size:20
Alignment explanation
Indices: 1183659--1183704 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
1183649 AAATTTTATT
1183659 TTTTAAAATTAATT-T-GAA
1 TTTTAAAATTAATTATAGAA
*
1183677 -TTTAAATTTAATTATAGAA
1 TTTTAAAATTAATTATAGAA
1183696 TTTTAAAAT
1 TTTTAAAAT
1183705 GGCATGGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 3 0.13
20 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTAAAATTAATTATAGAA
Found at i:1188753 original size:27 final size:27
Alignment explanation
Indices: 1188701--1188755 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1188691 CCGTTCAGAG
* * *
1188701 GAAGTTAGGCTGTTAGGAAGCTGTTGA
1 GAAGTTAGGCTGTTAGAAAACGGTTGA
*
1188728 GAAGTTAGTCTGTTAGAAAACGGTTGA
1 GAAGTTAGGCTGTTAGAAAACGGTTGA
1188755 G
1 G
1188756 CTTCTGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.29
Consensus pattern (27 bp):
GAAGTTAGGCTGTTAGAAAACGGTTGA
Found at i:1194497 original size:27 final size:27
Alignment explanation
Indices: 1194445--1194499 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1194435 CCGTTCAGAG
* *
1194445 GAAGTTAGGCTGTTAGGAAGATGTTGA
1 GAAGTTAGGCTGTTAGAAAGAGGTTGA
*
1194472 GAAGTTAGGCTGTTAGAAAGCGGTTGA
1 GAAGTTAGGCTGTTAGAAAGAGGTTGA
1194499 G
1 G
1194500 CTTCTGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.27
Consensus pattern (27 bp):
GAAGTTAGGCTGTTAGAAAGAGGTTGA
Found at i:1198950 original size:12 final size:12
Alignment explanation
Indices: 1198933--1198985 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
1198923 TCTTCAAAGA
1198933 AATTTTATATTT
1 AATTTTATATTT
1198945 AATTTTATA-TT
1 AATTTTATATTT
*
1198956 ATATTTGAT-TTT
1 A-ATTTTATATTT
1198968 AATTTTA-ATATT
1 AATTTTATAT-TT
1198980 AATTTT
1 AATTTT
1198986 TTAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:1199060 original size:24 final size:25
Alignment explanation
Indices: 1199009--1199080 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
1198999 ATATTAATTT
* * *
1199009 TTTTAATATTATATTATAGATATTAA
1 TTTTAATATTATTTTTTA-ATATAAA
1199035 TTTTAATATTATTTTTTAA-ATAAA
1 TTTTAATATTATTTTTTAATATAAA
*
1199059 -TTAAATATTAATTTTTTAATAT
1 TTTTAATATT-ATTTTTTAATAT
1199081 TATATTATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.20
24 13 0.32
25 3 0.08
26 16 0.40
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TTTTAATATTATTTTTTAATATAAA
Found at i:1199104 original size:65 final size:66
Alignment explanation
Indices: 1198947--1199102 Score: 263
Period size: 63 Copynumber: 2.5 Consensus size: 66
1198937 TTATATTTAA
1198947 TTTT-ATATTATATT-T-GAT-TTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1199008 T
66 T
1199009 TTTTAATATTATATTATAGATA-TTAATTTTAATATT-ATTTTTTAAATAAATTAAATATTAA-T
1 TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1199071 T
66 T
1199072 TTTTAATATTATATTATAGATATTTAATTTT
1 TTTTAATATTATATTATAGATATTTAATTTT
1199103 TATCATATAA
Statistics
Matches: 89, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
62 4 0.04
63 34 0.38
64 34 0.38
65 17 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (66 bp):
TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
T
Found at i:1199116 original size:29 final size:26
Alignment explanation
Indices: 1199028--1199117 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 26
1199018 TATATTATAG
* *
1199028 ATATTAATTTTAATATT-ATTTTTTA
1 ATATAAATTATAATATTAATTTTTTA
1199053 A-ATAAATTA-AATATTAATTTTTTA
1 ATATAAATTATAATATTAATTTTTTA
* *
1199077 ATATTATATTATAGATATTTAATTTTTATC
1 ATA-TAAATTATA-ATA-TTAATTTTT-TA
1199107 ATATAAATTAT
1 ATATAAATTAT
1199118 TTTATATATT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 6 0.11
24 15 0.28
25 2 0.04
26 6 0.11
27 1 0.02
28 3 0.06
29 16 0.30
30 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATAAATTATAATATTAATTTTTTA
Found at i:1199132 original size:63 final size:62
Alignment explanation
Indices: 1198947--1199102 Score: 212
Period size: 64 Copynumber: 2.5 Consensus size: 62
1198937 TTATATTTAA
*
1198947 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTTAATATTATATTATAGATATTAATTTTAATA-TAATTTTTT-AAT-AATTAAATATTAATTT
*
1199009 TTTTAATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTAA-TT
1 TTTTAATATTATATTATAGATATTAATTTTAATATAATTTTTT-AAT-AATTAAATATTAATTT
1199072 TTTTAATATTATATTATAGATATTTAATTTT
1 TTTTAATATTATATTATAGATA-TTAATTTT
1199103 TATCATATAA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
62 4 0.05
63 34 0.39
64 35 0.40
65 15 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (62 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATAATTTTTTAATAATTAAATATTAATTT
Found at i:1199157 original size:20 final size:19
Alignment explanation
Indices: 1199112--1199158 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1199102 TTATCATATA
1199112 AATTATTTTATATATTATT
1 AATTATTTTATATATTATT
*
1199131 AA-AATTTTATAT-TTATTTT
1 AATTATTTTATATATTA--TT
1199150 AATTATTTT
1 AATTATTTT
1199159 GATTTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 9 0.39
19 6 0.26
20 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTTTATATATTATT
Found at i:1199656 original size:31 final size:31
Alignment explanation
Indices: 1199619--1199678 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1199609 TAGTTGTATG
*
1199619 AATTATTTAAAT-TTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTT-AGTATTGCAAAACTAA
1199650 AATTATTTAAATCTTAGTATTGCAAAACT
1 AATTATTTAAATCTTAGTATTGCAAAACT
1199679 TTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTTAGTATTGCAAAACTAA
Found at i:1199836 original size:30 final size:30
Alignment explanation
Indices: 1199800--1199863 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
1199790 CTTCTGCTGT
1199800 AGATGTCTGCAGATGTGGTCCGCAGACTGC
1 AGATGTCTGCAGATGTGGTCCGCAGACTGC
1199830 AGATGTCTGCAGATGTGGTCCGCAGACTGC
1 AGATGTCTGCAGATGTGGTCCGCAGACTGC
1199860 AGAT
1 AGAT
1199864 ATTTTACATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (30 bp):
AGATGTCTGCAGATGTGGTCCGCAGACTGC
Found at i:1201385 original size:18 final size:18
Alignment explanation
Indices: 1201351--1201384 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1201341 AATTTCCTTT
*
1201351 TATTTTATATGTTTTTTG
1 TATTTTAGATGTTTTTTG
1201369 TATTTTAGAT-TTTTTT
1 TATTTTAGATGTTTTTT
1201385 TTATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TATTTTAGATGTTTTTTG
Found at i:1208989 original size:28 final size:27
Alignment explanation
Indices: 1208957--1209010 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1208947 ATAGTATATT
1208957 TTATTAAATGATGGCTTTGGATCGTGAA
1 TTATT-AATGATGGCTTTGGATCGTGAA
** *
1208985 TTATTTTTGGTGGCTTTGGATCGTGA
1 TTATTAATGATGGCTTTGGATCGTGA
1209011 TGGTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.44
Consensus pattern (27 bp):
TTATTAATGATGGCTTTGGATCGTGAA
Found at i:1210935 original size:2 final size:2
Alignment explanation
Indices: 1210928--1210972 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1210918 AAATGAAGAA
1210928 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
1210970 AT A
1 AT A
1210973 GAAAACATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1211748 original size:22 final size:22
Alignment explanation
Indices: 1211720--1211832 Score: 112
Period size: 22 Copynumber: 5.4 Consensus size: 22
1211710 TTTCATTTCG
1211720 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
1211742 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
** * *
1211761 CGTTGCGATTTTCCA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
1211781 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1211802 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1211824 CGTTGCGAT
1 CGTTGCGAT
1211833 TTTCCAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
19 21 0.28
20 12 0.16
21 2 0.03
22 39 0.53
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1211765 original size:19 final size:19
Alignment explanation
Indices: 1211741--1211788 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1211731 TCTACAGTTG
1211741 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1211760 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
1211779 TTGTTGCGAT
1 TCGTTGCGAT
1211789 AGTCTACAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1211954 original size:6 final size:6
Alignment explanation
Indices: 1211943--1211969 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1211933 GATACGTATT
1211943 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
1211970 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1212644 original size:20 final size:20
Alignment explanation
Indices: 1212621--1212672 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1212611 ACTGTAGACT
1212621 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
*
1212641 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
1212661 ATCGCAACGCGA
1 ATCGCAACGCGA
1212673 TTTTCAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:1213069 original size:24 final size:26
Alignment explanation
Indices: 1213041--1213100 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
1213031 TTTTTGAAAA
* *
1213041 TATTTTTTA-AT-TTTAAAAATAATT
1 TATTTTTTATATATTTAAAAAAAATC
1213065 TA-TTTTTATATATTTAAAAAAAATC
1 TATTTTTTATATATTTAAAAAAAATC
1213090 TATTTTTTATA
1 TATTTTTTATA
1213101 ATTACTACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 4 0.13
25 13 0.42
26 8 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTTTATATATTTAAAAAAAATC
Found at i:1220080 original size:18 final size:17
Alignment explanation
Indices: 1220011--1220080 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 17
1220001 ATATAAAGAG
1220011 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
* **
1220028 CCAGTTTAAATGGATGAA
1 CTAGTTT-AATTAATGAA
*
1220046 CTAGTTTAATTAGTGAA
1 CTAGTTTAATTAATGAA
1220063 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTAATT-AATGAA
1220081 AGATGATACT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 20 0.48
18 22 0.52
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:1220080 original size:35 final size:35
Alignment explanation
Indices: 1220011--1220080 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1220001 ATATAAAGAG
*
1220011 CTAGTTTAATTAATGAACCAGTTTAAATGGATGAA
1 CTAGTTTAATTAATGAACCAGTTTAAATGAATGAA
* * *
1220046 CTAGTTTAATTAGTGAACTAGCTTT-ATTGAATGAA
1 CTAGTTTAATTAATGAACCAG-TTTAAATGAATGAA
1220081 AGATGATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (35 bp):
CTAGTTTAATTAATGAACCAGTTTAAATGAATGAA
Found at i:1221685 original size:30 final size:30
Alignment explanation
Indices: 1221649--1221727 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
1221639 GCCCTCTTTA
1221649 ATTTTTTTTTCTATTTTTACTTTTTTT-GAT
1 ATTTTTTTTT-TATTTTTACTTTTTTTCGAT
*
1221679 ATTTTTTTGTTT-TTCTTTTCTTTTTTTCGAT
1 ATTTTTTT-TTTATT-TTTACTTTTTTTCGAT
*
1221710 TTTTTATTTTTTATTTTT
1 ATTTT-TTTTTTATTTTT
1221728 TTGATTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 2 0.05
30 20 0.48
31 15 0.36
32 5 0.12
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (30 bp):
ATTTTTTTTTTATTTTTACTTTTTTTCGAT
Found at i:1221714 original size:23 final size:22
Alignment explanation
Indices: 1221688--1221739 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1221678 TATTTTTTTG
*
1221688 TTTTTCTTTTCTTTTTTTCGATT
1 TTTTTCTTTTATTTTTTT-GATT
*
1221711 TTTTATTTTTTATTTTTTTGATT
1 TTTT-TCTTTTATTTTTTTGATT
1221734 TTTTTC
1 TTTTTC
1221740 ACTAACCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 12 0.48
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTATTTTTTTGATT
Found at i:1223066 original size:63 final size:63
Alignment explanation
Indices: 1222967--1223092 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1222957 GTGAAGGTGT
1222967 AATGGGGAATTACCATATTATAATATCACCCCCTTCAATCCTTTGTTATAACGTAACATGCAA
1 AATGGGGAATTACCATATTATAATATCACCCCCTTCAATCCTTTGTTATAACGTAACATGCAA
1223030 AATGGGGAATTACCATATTATAATATCACCCCCTTCAATCCTTTGTTATAACGTAACATGCAA
1 AATGGGGAATTACCATATTATAATATCACCCCCTTCAATCCTTTGTTATAACGTAACATGCAA
1223093 CCAAAATTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (63 bp):
AATGGGGAATTACCATATTATAATATCACCCCCTTCAATCCTTTGTTATAACGTAACATGCAA
Found at i:1236521 original size:19 final size:21
Alignment explanation
Indices: 1236494--1236548 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
1236484 AAATAATCAA
*
1236494 CAAAATCGCAACGCGA-TTT-
1 CAAATTCGCAACGCGAGTTTC
*
1236513 CAAATTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGAGTTTC
1236533 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
1236549 ACATAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 13 0.43
21 1 0.03
ACGTcount: A:0.36, C:0.29, G:0.15, T:0.20
Consensus pattern (21 bp):
CAAATTCGCAACGCGAGTTTC
Found at i:1236708 original size:13 final size:14
Alignment explanation
Indices: 1236684--1236712 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1236674 TAGGTAAACA
1236684 CGGTAGAAAAAATC
1 CGGTAGAAAAAATC
1236698 CGGTA-AAAAAATC
1 CGGTAGAAAAAATC
1236711 CG
1 CG
1236713 AATTCGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (14 bp):
CGGTAGAAAAAATC
Found at i:1237178 original size:50 final size:49
Alignment explanation
Indices: 1237119--1237217 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 49
1237109 TTGTGAAATT
1237119 CGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAACGTTGCGAAAA
1 CGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAACGTTGC-AAAA
*
1237169 CGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAATGTTGCAAAA
1 CGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAACGTTGCAAAA
1237218 TTCGTGTTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 4 0.08
50 44 0.92
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (49 bp):
CGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAACGTTGCAAAA
Found at i:1238733 original size:12 final size:12
Alignment explanation
Indices: 1238716--1238756 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1238706 TTATATACCT
1238716 TTAATTTTTGTA
1 TTAATTTTTGTA
1238728 TTAA-TTTTGTA
1 TTAATTTTTGTA
*
1238739 TAGAATTTTT-TA
1 T-TAATTTTTGTA
1238751 TTAATT
1 TTAATT
1238757 CAATCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 9 0.36
13 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTAATTTTTGTA
Found at i:1239556 original size:21 final size:21
Alignment explanation
Indices: 1239532--1239571 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1239522 AAGGCTACTG
1239532 CAGGGAATACTGCCTCTACCA
1 CAGGGAATACTGCCTCTACCA
1239553 CAGGGAATACTGCCTCTAC
1 CAGGGAATACTGCCTCTAC
1239572 TGATTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
CAGGGAATACTGCCTCTACCA
Found at i:1246392 original size:32 final size:32
Alignment explanation
Indices: 1246330--1246397 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
1246320 TTATACGATG
*
1246330 TTATTATAAAATTTATATAATATAGTATAATA
1 TTATTATAAAATTTATATAATATAATATAATA
* *
1246362 TTATTATACAAATTT-TATTAT-TAATAATAATG
1 TTATTATA-AAATTTATATAATATAAT-ATAATA
1246394 TTAT
1 TTAT
1246398 ACTGGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 3 0.10
32 22 0.71
33 6 0.19
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATTATAAAATTTATATAATATAATATAATA
Found at i:1246897 original size:108 final size:108
Alignment explanation
Indices: 1246708--1246923 Score: 333
Period size: 108 Copynumber: 2.0 Consensus size: 108
1246698 CATCGCTCAA
* * * * * *
1246708 ATGCATTGTTGAGAAAACACTGGTGAAGTACTCGAACGTCACGAGGTTGACGGAGTTGACAAAAG
1 ATGCATTGTTAAGAAAACACCGGTGAAGTACTCGAACGTCACAAGGCTAACGGAGCTGACAAAAG
* *
1246773 ATGCGCATTCTTCAATTGAAGGTTGGCCCTGATTGCACTCGCT
66 ATACACATTCTTCAATTGAAGGTTGGCCCTGATTGCACTCGCT
* * *
1246816 ATGCATTGTTAAGAAAACACCGGTTAAGTACTTGAACGTCACAAGGCTAACGGAGCTGAGAAAAG
1 ATGCATTGTTAAGAAAACACCGGTGAAGTACTCGAACGTCACAAGGCTAACGGAGCTGACAAAAG
1246881 ATACACATTCTTCAATTGAAGGTTGGCCCTGATTGCACTCGCT
66 ATACACATTCTTCAATTGAAGGTTGGCCCTGATTGCACTCGCT
1246924 GGTGTTAGCC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (108 bp):
ATGCATTGTTAAGAAAACACCGGTGAAGTACTCGAACGTCACAAGGCTAACGGAGCTGACAAAAG
ATACACATTCTTCAATTGAAGGTTGGCCCTGATTGCACTCGCT
Found at i:1247713 original size:12 final size:13
Alignment explanation
Indices: 1247689--1247717 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1247679 GAGTATCACG
1247689 AGAGAGTAAAAAA
1 AGAGAGTAAAAAA
1247702 AGAGAG-AAAAAA
1 AGAGAGTAAAAAA
1247714 AGAG
1 AGAG
1247718 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (13 bp):
AGAGAGTAAAAAA
Found at i:1254062 original size:2 final size:2
Alignment explanation
Indices: 1254055--1254103 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1254045 AAGTTTTAAT
1254055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1254097 TA TA TA T
1 TA TA TA T
1254104 TTGAATAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1254667 original size:12 final size:13
Alignment explanation
Indices: 1254650--1254680 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1254640 TATTCTTATT
1254650 AAAAAACAAA-AG
1 AAAAAACAAAGAG
1254662 AAAAAACAAAGAG
1 AAAAAACAAAGAG
1254675 AAAAAA
1 AAAAAA
1254681 AACGATGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:1257628 original size:154 final size:157
Alignment explanation
Indices: 1257348--1257659 Score: 594
Period size: 154 Copynumber: 2.0 Consensus size: 157
1257338 CAAATGCATC
1257348 GAACATAGAGTGGTGGTTAATGAGGAGGAGGAGCCGCTGTCGATTGCATCATTTCACTATCCCAG
1 GAACATAGAGTGGTGGTTAATGAGGAGGAGGAGCCGCTGTCGATTGCATCATTTCACTATCCCAG
1257413 AAGGAGTACCCAGATTGGTCCACTGCCGGATGTTGTTAAGACGAACAAAGCAGTGTAC-A-AG-A
66 AAGGAGTACCCAGATTGGTCCACTGCCGGATGTTGTTAAGACGAACAAAGCAGTGTACAAGAGTA
1257475 TGCCGCTTGAGGAGCTCCTCACACTTA
131 TGCCGCTTGAGGAGCTCCTCACACTTA
*
1257502 GAACATAGAGTGGTGGTTAATGAGGAGGAGGAGCGGCTGTCGATTGCATCATTTCACTATCCCAG
1 GAACATAGAGTGGTGGTTAATGAGGAGGAGGAGCCGCTGTCGATTGCATCATTTCACTATCCCAG
1257567 AAGGAGTACCCAGATTGGTCCACTGCCGGATGTTGTTAAGACGAACAAAGCAGTGTACAAGAGTA
66 AAGGAGTACCCAGATTGGTCCACTGCCGGATGTTGTTAAGACGAACAAAGCAGTGTACAAGAGTA
1257632 TGCCGCTTGAGGAGCTCCTCACACTTA
131 TGCCGCTTGAGGAGCTCCTCACACTTA
1257659 G
1 G
1257660 GCTTAGTCGG
Statistics
Matches: 154, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
154 122 0.79
155 1 0.01
156 2 0.01
157 29 0.19
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (157 bp):
GAACATAGAGTGGTGGTTAATGAGGAGGAGGAGCCGCTGTCGATTGCATCATTTCACTATCCCAG
AAGGAGTACCCAGATTGGTCCACTGCCGGATGTTGTTAAGACGAACAAAGCAGTGTACAAGAGTA
TGCCGCTTGAGGAGCTCCTCACACTTA
Found at i:1258538 original size:184 final size:182
Alignment explanation
Indices: 1258266--1258761 Score: 649
Period size: 182 Copynumber: 2.7 Consensus size: 182
1258256 CGCTCCATAG
* * * * * ** * *
1258266 CAATATTACAGGTACAAATATGACAAAACTGGTC-CCAAAATGACAAAACCGGTAAAACGCTACC
1 CAATATAACAGGTAAAAATATAATAAAACAGGTCTAAAAAATGACAAAACCGG-AAAAAGTTACC
*
1258330 GGATATGTGTCG--AGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAA
65 GGATATGT-T-GAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAA
* * *
1258393 GAAGTTATAACGCCTATAAAGTGTCGATACTTTAAAAAATAATATATCGATCCACAA
128 AAAGTTATAACGCCTAAAAAGTGTCGACACTTT-AAAAA-AATATATCGATCCACAA
*
1258450 CAATATAACATGTAAAAATATAATAAAACTA-GTCTAAAAAATGACAAAACCGGAAAAAGTTACC
1 CAATATAACAGGTAAAAATATAATAAAAC-AGGTCTAAAAAATGACAAAACCGGAAAAAGTTACC
* *
1258514 GGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAAA
65 GGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAA
* ** * * ** *
1258579 AGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGCTCCTTAC
130 AGTTATAACGCCTAAAAAGTGTCGACACTTTAAAAAAATATATCGATCCACAA
* * *
1258632 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAATCGGAAAAAGTTACCG
1 CAATATAACAGGTAAAAATATAATAAAACAGGTCTAAAAAATGACAAAACCGGAAAAAGTTACCG
*
1258697 GATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAAGAGAAAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTT-AAAAGAGAAAA
1258762 TCGCCCCAGT
Statistics
Matches: 275, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
181 1 0.00
182 122 0.44
183 15 0.05
184 121 0.44
185 16 0.06
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (182 bp):
CAATATAACAGGTAAAAATATAATAAAACAGGTCTAAAAAATGACAAAACCGGAAAAAGTTACCG
GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAA
GTTATAACGCCTAAAAAGTGTCGACACTTTAAAAAAATATATCGATCCACAA
Found at i:1258712 original size:182 final size:182
Alignment explanation
Indices: 1258246--1258761 Score: 687
Period size: 184 Copynumber: 2.8 Consensus size: 182
1258236 GATACAAATG
* * * * * * *
1258246 AAAAATGGATCGCTCCATAGCAATATTACAGGTACAAATATGACAAAACTGGTC-CCAAAATGAC
1 AAAAATGTATCGCTCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
* * ** *
1258310 AAAACCGGTAAAACGCTACCGGATATGTGTCGAGTGTCGATAATTTAATATAAGTATCGAAACTT
66 AAAACCGG-AAAAAGTTACCGGATATGT-TAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* * *
1258375 TCTGAATTTAAAAGAGAAGAAGTTATAACGCCTATAAAGTGTCGATACTTTAAA
129 TCTGAATTTAAAAGAGAAAAAGTTATAACGCCTAAAAAGTGTCGACACTTTAAA
* * * * * *
1258429 AAATAATATATCGATCCACAACAATATAACATGTAAAAATATAATAAAACTA-GTCTAAAAAATG
1 AAA-AATGTATCGCTCCATAACAATATAACAGGTAAAAATATGATAAAAC-AGGTCTCAAAAATG
* *
1258493 ACAAAACCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACT
64 ACAAAACCGGAAAAAGTTACCGGATATGTT-AAAGTGTCGATAATTTAATATAAGTATCGACACT
* *
1258558 TTCTGAATTTAAAAGAGAAAAAGTTATAGCGCCTAAAAAGTGTCGACACTTT-AT
128 TTCTGAATTTAAAAGAGAAAAAGTTATAACGCCTAAAAAGTGTCGACACTTTAAA
* * *
1258612 GAAAATGTATCGCTCCTTACCAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
1 AAAAATGTATCGCTCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
*
1258677 AAAATCGGAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
66 AAAACCGGAAAAAGTTACCGGATATGTT-AAAGTGTCGATAATTTAATATAAGTATCGACACTTT
1258742 CTGAATTTAAAAAGAGAAAA
130 CTGAATTT-AAAAGAGAAAA
1258762 TCGCCCCAGT
Statistics
Matches: 289, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
181 1 0.00
182 121 0.42
183 18 0.06
184 133 0.46
185 16 0.06
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGCTCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
AAAACCGGAAAAAGTTACCGGATATGTTAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
TGAATTTAAAAGAGAAAAAGTTATAACGCCTAAAAAGTGTCGACACTTTAAA
Found at i:1258922 original size:21 final size:20
Alignment explanation
Indices: 1258891--1258993 Score: 80
Period size: 21 Copynumber: 5.0 Consensus size: 20
1258881 CGCAAATCAG
1258891 TTTCTAAAATCGCAACGCGAT
1 TTTC-AAAATCGCAACGCGAT
* *
1258912 TCTTGAAAATCGCAATGCGAT
1 T-TTCAAAATCGCAACGCGAT
* * * **
1258933 AGTACAAATTCGCATTGCGAT
1 -TTTCAAAATCGCAACGCGAT
*
1258954 TTTCCAAAATCGCAACGCGAA
1 TTT-CAAAATCGCAACGCGAT
* *
1258975 TATGAAAATCGCAACGCGA
1 TTTCAAAATCGCAACGCGA
1258994 ACACATAAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
20 16 0.25
21 46 0.72
22 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (20 bp):
TTTCAAAATCGCAACGCGAT
Found at i:1259022 original size:20 final size:20
Alignment explanation
Indices: 1258960--1259209 Score: 247
Period size: 20 Copynumber: 12.5 Consensus size: 20
1258950 CGATTTTCCA
* ** *
1258960 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1258980 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1259000 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1259020 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1259040 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1259060 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1259080 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1259100 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1259120 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1259140 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
1259160 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1259180 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1259200 AAATCACAAC
1 AAATCGCAAC
1259210 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 192 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1260116 original size:12 final size:12
Alignment explanation
Indices: 1260099--1260123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1260089 ATATAATCCT
1260099 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1260111 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1260123 G
1 G
1260124 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:1262347 original size:33 final size:34
Alignment explanation
Indices: 1262296--1262531 Score: 229
Period size: 33 Copynumber: 6.8 Consensus size: 34
1262286 CGGAAATTAC
*
1262296 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
1262329 AATCCCAAC-ATGAAAATCGCAATGCGGAAATAAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
1262363 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
1262396 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAT
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
1262429 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
*
1262467 AATCGCAACGA-GATAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
1262500 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGA
1262532 TTCTCTCGTT
Statistics
Matches: 173, Mismatches: 12, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
32 1 0.01
33 94 0.54
34 30 0.17
35 7 0.04
36 4 0.02
37 3 0.02
38 34 0.20
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:1262401 original size:19 final size:19
Alignment explanation
Indices: 1262310--1262531 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
1262300 GCAACGAGAG
1262310 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1262329 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
1262343 AATCGCAATGCGGAAATAAA
1 AATCGCAATGC-GAAATGAA
*
1262363 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1262377 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1262396 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1262415 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
1262429 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1262448 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1262467 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
1262481 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1262500 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1262519 AATCGCATTGCGA
1 AATCGCAATGCGA
1262532 TTCTCTCGTT
Statistics
Matches: 171, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 41 0.24
15 3 0.02
16 7 0.04
17 6 0.04
18 4 0.02
19 98 0.57
20 12 0.07
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1262466 original size:71 final size:71
Alignment explanation
Indices: 1262310--1262531 Score: 228
Period size: 71 Copynumber: 3.2 Consensus size: 71
1262300 GCAACGAGAG
* * * **
1262310 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATAAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GATAATCGAAATGC-GAAACGAAAATCGCAATGC
*
1262372 G--A-GAG
64 GAAATGAA
* * *
1262377 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGATAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCG-AAATGCGAAACGA-A-AATCGCAATG
1262439 CGAAATGAA
63 CGAAATGAA
* *
1262448 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGAAATGCGAAACGAAAATCGCAATGCGA
1262513 AATGAA
66 AATGAA
*
1262519 AATCGCATTGCGA
1 AATCGCAATGCGA
1262532 TTCTCTCGTT
Statistics
Matches: 129, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
64 4 0.03
65 3 0.02
66 14 0.11
67 28 0.22
68 2 0.02
70 1 0.01
71 63 0.49
72 7 0.05
73 7 0.05
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGAAATGCGAAACGAAAATCGCAATGCGA
AATGAA
Found at i:1262545 original size:52 final size:52
Alignment explanation
Indices: 1262338--1262525 Score: 349
Period size: 52 Copynumber: 3.6 Consensus size: 52
1262328 AAATCCCAAC
* *
1262338 ATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1262391 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1262443 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1262495 ATGAAAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCA
1262526 TTGCGATTCT
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 117 0.88
53 16 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
Found at i:1262634 original size:52 final size:53
Alignment explanation
Indices: 1262521--1262637 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1262511 GAAATGAAAA
1262521 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1262574 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1262626 TCGCATTGCGAT
1 TCGCATTGCGAT
1262638 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1262645 original size:19 final size:19
Alignment explanation
Indices: 1262540--1262637 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1262530 GATTCTCTCG
1262540 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1262560 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1262579 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1262593 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1262612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1262631 TTGCGAT
1 TTGCGAT
1262638 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1262760 original size:13 final size:14
Alignment explanation
Indices: 1262744--1262779 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1262734 CATCAATTAC
1262744 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
1262757 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1262771 ACAAATCAA
1 ACAAATCAA
1262780 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1264734 original size:19 final size:18
Alignment explanation
Indices: 1264694--1264809 Score: 102
Period size: 19 Copynumber: 6.6 Consensus size: 18
1264684 TAGTTTACTT
*
1264694 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
1264714 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
1264733 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
1264752 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
*
1264766 TCGCAACGCGAAACGAAA
1 TCGCAACGCGAAACAAAA
1264784 T-GCAACGCG-AA-AAAA
1 TCGCAACGCGAAACAAAA
*
1264799 TCGCAATGCGA
1 TCGCAACGCGA
1264810 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 17
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.11
15 5 0.06
16 11 0.14
17 10 0.12
18 5 0.06
19 27 0.34
20 12 0.15
21 1 0.01
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:1264801 original size:33 final size:35
Alignment explanation
Indices: 1264694--1264809 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 35
1264684 TAGTTTACTT
* *
1264694 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAAC-GAAAATCGCAACGCG-AA--AAAA
* * *
1264733 TCGCAACGCGAAATGAAAATCGCAA--CGACAGAA
1 TCGCAACGCGAAACGAAAATCGCAACGCGAAAAAA
1264766 TCGCAACGCGAAACG-AAAT-GCAACGCGAAAAAA
1 TCGCAACGCGAAACGAAAATCGCAACGCGAAAAAA
*
1264799 TCGCAATGCGA
1 TCGCAACGCGA
1264810 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
31 4 0.06
32 4 0.06
33 33 0.50
35 1 0.02
36 2 0.03
38 10 0.15
39 12 0.18
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.09
Consensus pattern (35 bp):
TCGCAACGCGAAACGAAAATCGCAACGCGAAAAAA
Found at i:1264827 original size:19 final size:19
Alignment explanation
Indices: 1264805--1264933 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1264795 AAAATCGCAA
1264805 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1264824 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1264838 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1264857 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1264871 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1264890 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1264909 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1264929 TGCGA
1 TGCGA
1264934 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1264847 original size:33 final size:33
Alignment explanation
Indices: 1264805--1264896 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1264795 AAAATCGCAA
1264805 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1264838 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1264871 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1264897 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1265097 original size:93 final size:93
Alignment explanation
Indices: 1264981--1265447 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
1264971 ATGGATTGCA
1264981 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265045 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1265073 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-A-ACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265136 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1265164 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265229 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1265257 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265322 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1265350 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1265415 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1265443 TTACT
1 TTACT
1265448 AAGCAATCTA
Statistics
Matches: 371, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
91 90 0.24
92 6 0.02
93 275 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1265294 original size:184 final size:186
Alignment explanation
Indices: 1264981--1265447 Score: 904
Period size: 184 Copynumber: 2.5 Consensus size: 186
1264971 ATGGATTGCA
1264981 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265045 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1265110 ATTTCACAGTGTTAAAG-A-ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1265164 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1265229 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1265294 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1265350 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1265415 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1265448 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
183 4 0.01
184 142 0.51
185 1 0.00
186 133 0.47
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1267167 original size:14 final size:14
Alignment explanation
Indices: 1267148--1267235 Score: 68
Period size: 14 Copynumber: 5.7 Consensus size: 14
1267138 TTGAAATGAA
*
1267148 AATCGCAACGAGAT
1 AATCGCAACGAGAG
*
1267162 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1267181 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1267195 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
*
1267212 AAACGCAACGAGAG
1 AATCGCAACGAGAG
1267226 AATCGCAACG
1 AATCGCAACG
1267236 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
14 28 0.47
15 5 0.08
16 6 0.10
17 10 0.17
18 1 0.02
19 10 0.17
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1267222 original size:31 final size:32
Alignment explanation
Indices: 1267140--1267251 Score: 190
Period size: 33 Copynumber: 3.5 Consensus size: 32
1267130 TCTTTGGGTT
*
1267140 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1267173 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-AATCGCAACGAGAGAATCGCAACGC
1267206 GAAATGAAA-CGCAACGAGAGAATCGCAACGC
1 GAAATGAAATCGCAACGAGAGAATCGCAACGC
1267237 GAAATGAAATCGCAA
1 GAAATGAAATCGCAA
1267252 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
31 31 0.41
32 8 0.11
33 37 0.49
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (32 bp):
GAAATGAAATCGCAACGAGAGAATCGCAACGC
Found at i:1267287 original size:14 final size:14
Alignment explanation
Indices: 1267268--1267324 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1267258 TTTGGTTTCG
1267268 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1267282 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1267301 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1267315 CGTTGCGATT
1 CGTTGCGATT
1267325 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1267300 original size:33 final size:33
Alignment explanation
Indices: 1267252--1267332 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1267242 GAAATCGCAA
**
1267252 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1267285 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1267318 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1267333 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1267335 original size:21 final size:21
Alignment explanation
Indices: 1267309--1267384 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1267299 CGCGTTGCGA
1267309 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1267330 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
1267350 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1267371 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1267385 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1267365 original size:41 final size:41
Alignment explanation
Indices: 1267308--1267385 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1267298 TCGCGTTGCG
* *
1267308 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
1267349 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1267386 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1267370 original size:20 final size:20
Alignment explanation
Indices: 1267275--1267384 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 20
1267265 TCGCGTTGCG
1267275 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1267295 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
1267308 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1267328 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
1267349 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1267369 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1267385 CTCTTCTGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 9 0.13
20 20 0.29
21 29 0.41
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1267909 original size:20 final size:20
Alignment explanation
Indices: 1267884--1268077 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1267874 CTTTAAATAT
1267884 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1267904 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1267926 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1267945 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1267965 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1267985 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1268005 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1268025 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1268045 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1268065 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1268078 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1268071 original size:60 final size:60
Alignment explanation
Indices: 1267884--1268077 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1267874 CTTTAAATAT
**
1267884 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1267945 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1268005 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1268065 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1268078 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1268094 original size:21 final size:21
Alignment explanation
Indices: 1268064--1268146 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1268054 ATTTTCATAT
*
1268064 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1268085 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1268106 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1268127 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1268147 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1268137 original size:42 final size:43
Alignment explanation
Indices: 1268044--1268142 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1268034 ATTTATGTGT
* *
1268044 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1268085 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1268127 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1268143 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:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1268591 original size:183 final size:183
Alignment explanation
Indices: 1268283--1268655 Score: 557
Period size: 183 Copynumber: 2.0 Consensus size: 183
1268273 CGATTTTCTC
* * ** *
1268283 ATTTAAAAAAGAAAAAGTTATTCCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCA
1 ATTTAAAAAAGAAAAAGTTATACCGCCTAAAAAGTGTCGACACTTTAAAAAAATATATCGATCCA
* * * * *
1268348 TAATAATATAACATGTAAAAATATGATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCT
66 CAACAATATAACAGGTAAAAATATGATAAAACAGGTCCCAAAATTGACAAAACCAGTAAAACGAT
*
1268413 ACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGA
131 ACCGGATATATTGAAAGTGTCGATAATTTAAAATAAGTATCGAAACTTTCTGA
* * * * *
1268466 ATTTAAAATAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATATATCGATCCA
1 ATTTAAAAAAGAAAAAGTTATACCGCCTAAAAAGTGTCGACACTTTAAAAAAATATATCGATCCA
* *
1268531 CAACAATATAACAGGTAAAAATATGATAAAACAGGTCCCAAAATTGATAAAACCAGTAAAATGAT
66 CAACAATATAACAGGTAAAAATATGATAAAACAGGTCCCAAAATTGACAAAACCAGTAAAACGAT
* *
1268596 ACCGGATATGTTGAAAGTGTCGATAATTTAAAATAAGTATCGACACTTTCTGA
131 ACCGGATATATTGAAAGTGTCGATAATTTAAAATAAGTATCGAAACTTTCTGA
*
1268649 AATTAAA
1 ATTTAAA
1268656 CTAAAAAGTG
Statistics
Matches: 169, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
183 169 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (183 bp):
ATTTAAAAAAGAAAAAGTTATACCGCCTAAAAAGTGTCGACACTTTAAAAAAATATATCGATCCA
CAACAATATAACAGGTAAAAATATGATAAAACAGGTCCCAAAATTGACAAAACCAGTAAAACGAT
ACCGGATATATTGAAAGTGTCGATAATTTAAAATAAGTATCGAAACTTTCTGA
Found at i:1268911 original size:20 final size:20
Alignment explanation
Indices: 1268886--1268939 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1268876 TTACTAATAT
*
1268886 AACAGGTAAAAATATGATAA
1 AACAGGTAAAAATATGACAA
1268906 AACAGGTCTAAAAA-ATGACAA
1 AACAGG--TAAAAATATGACAA
* *
1268927 AACCGGAAAAAAT
1 AACAGGTAAAAAT
1268940 TATCGGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 5 0.18
20 6 0.21
21 11 0.39
22 6 0.21
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (20 bp):
AACAGGTAAAAATATGACAA
Found at i:1268964 original size:182 final size:181
Alignment explanation
Indices: 1268657--1269155 Score: 777
Period size: 182 Copynumber: 2.7 Consensus size: 181
1268647 GAAATTAAAC
* * * *
1268657 TAAAAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAAGTAAACATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGAT-CTTAACAATATAACAGGTAAAAATATGAT
* * * *
1268722 AAAACTGGTCTAAAAAATGACAAAATCGGGAAAAGTTATCGGATATGTTGAAAGTGTCGATAATT
65 AAAACAGGTCTAAAAAATGACAAAACCGGAAAAAATTATCGGATATGTTGAAAGTGTCGATAATT
1268787 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
* * *
1268839 TAAAAAGTGTCGACACTTTATTAAAATGTATTGATCTTTACTAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCTTAAC-AATATAACAGGTAAAAATATGAT
1268904 AAAACAGGTCTAAAAAATGACAAAACCGGAAAAAATTATCGGATATGTTGAAAGTGTCGATAATT
65 AAAACAGGTCTAAAAAATGACAAAACCGGAAAAAATTATCGGATATGTTGAAAGTGTCGATAATT
1268969 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
*
1269021 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCTAGAACAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCT-TAACAATATAACAGGTAAAAATATGAT
* * * * * *
1269086 AAATCCGATCT-CAAAATGACAAAACCGGTAAATAGA-TATCGGATATGTTGAAAGTGTCGATAC
65 AAAACAGGTCTAAAAAATGACAAAACCGG-AAA-AAATTATCGGATATGTTGAAAGTGTCGATAA
1269149 TTTAATA
128 TTTAATA
1269156 AGTACGCGTA
Statistics
Matches: 292, Mismatches: 21, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
181 20 0.07
182 268 0.92
183 4 0.01
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (181 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCTTAACAATATAACAGGTAAAAATATGATA
AAACAGGTCTAAAAAATGACAAAACCGGAAAAAATTATCGGATATGTTGAAAGTGTCGATAATTT
AATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
Found at i:1269234 original size:21 final size:21
Alignment explanation
Indices: 1269210--1269266 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1269200 TATCATATCG
*
1269210 AAAGTATTGACACTTGACATA
1 AAAGTATCGACACTTGACATA
1269231 AAAGTATCGACACTTGACATA
1 AAAGTATCGACACTTGACATA
1269252 AAAGTATCGACACTT
1 AAAGTATCGACACTT
1269267 ATGTAGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (21 bp):
AAAGTATCGACACTTGACATA
Found at i:1269582 original size:19 final size:20
Alignment explanation
Indices: 1269558--1269608 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1269548 TACTTTTAGT
1269558 TAATATTTATAGGTA-AAAA
1 TAATATTTATAGGTAGAAAA
1269577 TAATA-TTATAGGTAGAAAA
1 TAATATTTATAGGTAGAAAA
*
1269596 TGATATTT-TAGGT
1 TAATATTTATAGGT
1269609 TGTATAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.31
19 18 0.62
20 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (20 bp):
TAATATTTATAGGTAGAAAA
Found at i:1269889 original size:18 final size:18
Alignment explanation
Indices: 1269854--1269892 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1269844 TTGAAATGGT
1269854 AATTGGATTAAAACTTTA
1 AATTGGATTAAAACTTTA
*
1269872 AATT-GATTACAAATTTTA
1 AATTGGATTA-AAACTTTA
1269890 AAT
1 AAT
1269893 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTGGATTAAAACTTTA
Found at i:1270902 original size:22 final size:22
Alignment explanation
Indices: 1270852--1270906 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1270842 AATGTTTTTG
1270852 TTTT-TTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
1270874 TAATTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
1270896 CTTTTATTATA
1 -TTTTATTATA
1270907 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 3 0.11
24 15 0.54
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Found at i:1271167 original size:18 final size:18
Alignment explanation
Indices: 1271144--1271186 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1271134 TCAAGGAGTT
1271144 AGAGGAGGCA-AATGAGGC
1 AGAGGAGGCAGAA-GAGGC
*
1271162 AGAGGACGCAGAAGAGGC
1 AGAGGAGGCAGAAGAGGC
*
1271180 AGTGGAG
1 AGAGGAG
1271187 AAGGAAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.37, C:0.12, G:0.47, T:0.05
Consensus pattern (18 bp):
AGAGGAGGCAGAAGAGGC
Found at i:1271644 original size:22 final size:18
Alignment explanation
Indices: 1271595--1271633 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1271585 GAAAAAATTT
*
1271595 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1271613 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1271631 GAA
1 GAA
1271634 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1272366 original size:18 final size:18
Alignment explanation
Indices: 1272343--1272382 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1272333 TCATGTTCAT
1272343 AACTATGTGAAATTCACC
1 AACTATGTGAAATTCACC
1272361 AACTATGTGAAATTCACC
1 AACTATGTGAAATTCACC
1272379 AACT
1 AACT
1272383 GTGAGAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (18 bp):
AACTATGTGAAATTCACC
Found at i:1273149 original size:19 final size:19
Alignment explanation
Indices: 1273123--1273171 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1273113 AACTGCATGG
1273123 TTAA-TTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
1273141 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
1273160 ATAATTTTGTAT
1 TTAATTTTGTAT
1273172 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:1273755 original size:199 final size:199
Alignment explanation
Indices: 1273321--1274418 Score: 1857
Period size: 199 Copynumber: 5.5 Consensus size: 199
1273311 GTAAACTTAT
1273321 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
1273386 GGTAAATTAGCAATATATCCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTA-AAAAAGTA
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
1273450 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1273515 AAAA
196 AAAA
1273519 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
*
1273584 GGTAAATTAGAAATATAACCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
1273649 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
*
1273714 AAGA
196 AAAA
*
1273718 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * * *
1273783 TGTAAATTAGCAATATAACCGGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTA-AAGAAAGT
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAA-AAAGT
*
1273847 ATCGACTCAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
130 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
1273912 AAAAA
195 AAAAA
1273917 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
1273982 GGTAAATTAGAAATATAATCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
1274047 TTGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1274112 AAAA
196 AAAA
* *
1274116 GTGTCGATACATTTGTAACAAGTGTCGATCCC-AAAACTATCGAAAACTATAATTATAATGTAAT
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAAC-ATCGAAAACCATAATTATAATGTAAT
* *
1274180 AGGTAAATTCGCAATATAACCGGTCTAAATATACC-GATTTTTGAGAAAATC-GGTGTACAAAAA
65 AGGTAAATTAGAAATATAACCGGTCTAAATATACCAG-TTTTTGAGAAAA-CAGGTGTACAAAAA
*
1274243 GTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCA
128 GTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCA
1274308 CTAAAAA
193 CTAAAAA
* * * *
1274315 GTGTCGATACATTTATAACAATTGTCAATCCCAAAAAAATCGAAAACCATAATTATAATATAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
**
1274380 GGTAAATTA-ACAATATAATTGGTCTAAATATACCAGTTT
66 GGTAAATTAGA-AATATAACCGGTCTAAATATACCAGTTT
1274419 AAATTGAAAA
Statistics
Matches: 847, Mismatches: 44, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
198 126 0.15
199 713 0.84
200 8 0.01
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (199 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
GGTAAATTAGAAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
AAAA
Found at i:1274788 original size:15 final size:15
Alignment explanation
Indices: 1274768--1274809 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1274758 TTTCTCAAAT
*
1274768 CTCTTCTGAACCCAC
1 CTCTTCTCAACCCAC
* *
1274783 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
1274798 CTCTTCTCAACC
1 CTCTTCTCAACC
1274810 ACAACATCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.50, G:0.05, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:1277431 original size:21 final size:21
Alignment explanation
Indices: 1277407--1277449 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277397 ACAAAATGTA
1277407 TCGACACAAATAAAACAAGTG
1 TCGACACAAATAAAACAAGTG
* **
1277428 TCGATACATTTAAAACAAGTG
1 TCGACACAAATAAAACAAGTG
1277449 T
1 T
1277450 TGATCCCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (21 bp):
TCGACACAAATAAAACAAGTG
Found at i:1277720 original size:140 final size:140
Alignment explanation
Indices: 1277541--1277824 Score: 410
Period size: 140 Copynumber: 2.0 Consensus size: 140
1277531 AGAAAACATG
* ** * *
1277541 TGTACAAAAAGTATCGACACATATCTAACAAGTGTCGATACTTTTTCTCCAGACTGTATTTCAAA
1 TGTACAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGCTCCAGAATGTATTTCAAA
*
1277606 ACCAAGTGCAC-TAAAAAGTGTC-AATACATATATAACAAATGTCGATCCCAAAAACATCGAAAA
66 ACCAAGTGCACAT-AAAAGTGTCGAAT-CATATAAAACAAATGTCGATCCCAAAAACATCGAAAA
*
1277669 CCATAATTATAA
129 ACATAATTATAA
* * *
1277681 TGTACAAAATGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGA
1 TGTACAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGCTCCAGAATGTATTTCAAA
* * * *
1277746 ACCAAGTGCACATAAAAGTGTCGAATCATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAAC
66 ACCAAGTGCACATAAAAGTGTCGAATCATATAAAACAAATGTCGATCCCAAAAACATCGAAAAAC
1277811 ATAATTATAA
131 ATAATTATAA
1277821 TGTA
1 TGTA
1277825 ATAGGTAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
140 124 0.97
141 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (140 bp):
TGTACAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGCTCCAGAATGTATTTCAAA
ACCAAGTGCACATAAAAGTGTCGAATCATATAAAACAAATGTCGATCCCAAAAACATCGAAAAAC
ATAATTATAA
Found at i:1278182 original size:199 final size:198
Alignment explanation
Indices: 1277681--1278617 Score: 1269
Period size: 199 Copynumber: 4.7 Consensus size: 198
1277671 ATAATTATAA
* *
1277681 TGTACAAAATGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGA
1 TGTACAAAA-GTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAA
* * *
1277746 ACCAAGTGCACATAAAAGTGTCGA-ATCATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAA
65 ACCAAGTGCACATAAAAGTGTCGATA-CATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAA
** * **
1277810 CATAATTATAATGTAATAGGTAAATTATTTATGTAAAAGGTCTAAATATACCAGTTTTTGAGAAA
129 CATAATTATAATGTAATAGGTAAATTATCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAA
*
1277875 A-ATG
194 ATAGG
* ** * *
1277879 TGTACAAAAAGTATAGACACAAATCTAACAAGTGTCGATACTTTTTCTCCAGACTGTATTTCAAA
1 TGTAC-AAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAA
* *
1277944 ATCAAGTGCAC-TAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAC
65 ACCAAGTGCACAT-AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAA
* * *
1278008 CATAATTATAATGTATTAGGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAA
129 CATAATTATAATGTAATAGGTAAATTATCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAA
1278073 ATAGG
194 ATAGG
*
1278078 TGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAA
1 TGTACAAA-AGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAA
* * * *
1278143 ACCAAGTGCACATAAAAGGGTCGATACATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAAC
65 ACCAAGTGCACATAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAAC
*
1278208 ATAATTATAATGTAATAGGTAAATTATTC-ATGTAACCGGTCTAAATATACCAGTTTTTGAGAAA
130 ATAATTATAATGTAATAGGTAAATTA-TCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAA
1278272 ATAGG
194 ATAGG
* * * *
1278277 TGTACAAAAAGTATCGACACAAATATAACAAGTGTTGATACTTTTTCTCCATAATGTATTTCAAA
1 TGTAC-AAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAA
1278342 ACCAAGTGCAC-TAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCG-AAAA
65 ACCAAGTGCACAT-AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAA
* * *
1278405 CTATAATTATAATGTAATAGGTAAATTAAT-AATATAACCGGTCTAAATGTACCGGTTTATGAGA
129 C-ATAATTATAATGTAATAGGTAAATT-ATCAATATAACCGGTCTAAATATACCAGTTTTTGAGA
* **
1278469 AAACATA
192 AAATAGG
* * * * * * * *
1278476 TATACATGAAGTATCGACACAAATACATCAAGTTTCGATACATTTTTGTCCAGACTATATTTTAA
1 TGTACA-AAAGTATCGACACAAATAGAACAAGTGTCGATAC-TTTTTGTCCAGAATGTA-TTTCA
* *
1278541 AAACCAAGTGCACA-ACAAAGTTTCGATACATTTATAACAACTGTCGATCCCAAAAACATCGAAA
63 AAACCAAGTGCACATA-AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAA
1278605 AACATAATTATAA
127 AACATAATTATAA
1278618 CCAAATGTCT
Statistics
Matches: 655, Mismatches: 66, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
197 1 0.00
198 176 0.27
199 383 0.58
200 20 0.03
201 70 0.11
202 5 0.01
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (198 bp):
TGTACAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAA
CCAAGTGCACATAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAACA
TAATTATAATGTAATAGGTAAATTATCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAAT
AGG
Found at i:1278462 original size:398 final size:396
Alignment explanation
Indices: 1277680--1278617 Score: 1475
Period size: 398 Copynumber: 2.4 Consensus size: 396
1277670 CATAATTATA
*
1277680 ATGTACAAAATGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAG
1 ATGTACAAAA-GTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAA
1277745 AACCAAGTGCACATAAAAGTGTCGA-ATCATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAA
65 AACCAAGTGCACATAAAAGTGTCGATA-CATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAA
*
1277809 ACATAATTATAATGTAATAGGTAAATTATTTATGTAAAAGGTCTAAATATACCAGTTTTTGAGAA
129 ACATAATTATAATGTAATAGGTAAATTATTCATGTAAAAGGTCTAAATATACCAGTTTTTGAGAA
* * *
1277874 AAATGTGTACAAAAAGTATAGACACAAATCTAACAAGTGTCGATACTTTTTCTCCAGACTGTATT
194 AAAGGTGTACAAAAAGTATAGACACAAATATAACAAGTGTCGATACTTTTTCTCCAGAATGTATT
*
1277939 TCAAAATCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGA
259 TCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGA
* * *
1278004 AAACCATAATTATAATGTATTAGGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGA
324 AAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAATATACCGGTTTATGA
*
1278069 GAAAATAG
389 GAAAACAG
*
1278077 GTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAA
1 ATGTACAAA-AGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAA
*
1278142 AACCAAGTGCACATAAAAGGGTCGATACATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAA
65 AACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAA
**
1278207 CATAATTATAATGTAATAGGTAAATTATTCATGTAACCGGTCTAAATATACCAGTTTTTGAGAAA
130 CATAATTATAATGTAATAGGTAAATTATTCATGTAAAAGGTCTAAATATACCAGTTTTTGAGAAA
* * *
1278272 ATAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTTGATACTTTTTCTCCATAATGTATT
195 A-AGGTGTACAAAAAGTATAGACACAAATATAACAAGTGTCGATACTTTTTCTCCAGAATGTATT
1278337 TCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGA
259 TCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGA
* * *
1278402 AAACTATAATTATAATGTAATAGGTAAATTAATAATATAACCGGTCTAAATGTACCGGTTTATGA
324 AAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAATATACCGGTTTATGA
*
1278467 GAAAACAT
389 GAAAACAG
* * * * * * * * *
1278475 ATATACATGAAGTATCGACACAAATACATCAAGTTTCGATACATTTTTGTCCAGACTATATTTTA
1 ATGTACA-AAAGTATCGACACAAATAGAACAAGTGTCGATAC-TTTTGGTCCAGAATGTA-TTTC
* * * * *
1278540 AAAACCAAGTGCACA-ACAAAGTTTCGATACATTTATAACAACTGTCGATCCCAAAAACATCGAA
63 AAAACCAAGTGCACATA-AAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAATATCGAA
1278604 AAACATAATTATAA
127 AAACATAATTATAA
1278618 CCAAATGTCT
Statistics
Matches: 497, Mismatches: 37, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
397 186 0.37
398 222 0.45
399 16 0.03
400 73 0.15
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (396 bp):
ATGTACAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAA
ACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTGTCGATCCCGAAAATATCGAAAAAC
ATAATTATAATGTAATAGGTAAATTATTCATGTAAAAGGTCTAAATATACCAGTTTTTGAGAAAA
AGGTGTACAAAAAGTATAGACACAAATATAACAAGTGTCGATACTTTTTCTCCAGAATGTATTTC
AAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAA
ACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAATATACCGGTTTATGAGA
AAACAG
Found at i:1281536 original size:198 final size:197
Alignment explanation
Indices: 1281037--1281563 Score: 557
Period size: 198 Copynumber: 2.7 Consensus size: 197
1281027 AGTATCGACC
* * * ** * *
1281037 CCAAAAACATCG-AAACAAATAATTATAATGTAATATTTAAATTAACAATGTAACCAGTATACAT
1 CCAAAAACATCGAAAAC-GATAAATACAATGTAATAGGTAAATTTACAATGTAACCAGTATAAAT
** * * * * * *
1281101 ATACC-AATTAATTATAAAACATGTCA-ACATAAAGTATCGACACTTTTTAAGTTTGTGTCGATA
65 ATACCGGTTTTATGAGAAAATAGGTCAGA-ATAAAGTATCGACACTTTATAA-TTTGTGTCGATA
* * * *
1281164 C-TTTTTTCCAAAAGAAAGCACAAACAGGTTCACGCATAAAGTGTCGATACATTTAAAATTGTAT
128 CATTTTGTCCAAAAGAAAGCACAAACAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTGTAT
*
1281228 CGATA
193 AGATA
* * * * * * * *
1281233 TCAAAAACATCGAAACCGATAAATATAATGTAATAGGTCAATTTATAATGTAACCGGTTTAAATT
1 CCAAAAACATCGAAAACGATAAATACAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATA
*
1281298 TACCGGTTTTATGAGAAAATAGGTCAGAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACA
66 TACCGGTTTTATGAGAAAATAGGTCAGAATAAAGTATCGACACTT-TATAATTTGTGTCGATACA
* * * *
1281363 TTTTGTCCATAATGAATGC-CCAACGAGGTGCAAGAATAACGTGTCGATACATTTAAAATTGTAT
130 TTTTGTCCA-AAAGAAAGCACAAAC-AGGTGCAAGAATAAAGTGTCGATACATTTAAAATTGTAT
*
1281427 AGATC
193 AGATA
* * *
1281432 CCATAAACATC-AAAACGA-AAATTACAATGTTATAGGTAAATTTACAATGTACCCAGTATAAAT
1 CCAAAAACATCGAAAACGATAAA-TACAATGTAATAGGTAAATTTACAATGTAACCAGTATAAAT
* * *
1281495 ATGCCGGTTTTATGAGAAAATAGGTCTA-AATAATGTATCGACACCTTTATAGTTTGTGTCGATA
65 ATACCGGTTTTATGAGAAAATAGGTC-AGAATAAAGTATCGACA-CTTTATAATTTGTGTCGATA
1281559 CATTT
128 CATTT
1281564 AAATTTGCAA
Statistics
Matches: 275, Mismatches: 46, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
196 52 0.19
197 50 0.18
198 115 0.42
199 58 0.21
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (197 bp):
CCAAAAACATCGAAAACGATAAATACAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATA
TACCGGTTTTATGAGAAAATAGGTCAGAATAAAGTATCGACACTTTATAATTTGTGTCGATACAT
TTTGTCCAAAAGAAAGCACAAACAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTGTATAGA
TA
Found at i:1281666 original size:115 final size:115
Alignment explanation
Indices: 1281463--1281678 Score: 310
Period size: 115 Copynumber: 1.9 Consensus size: 115
1281453 TTACAATGTT
* * *
1281463 ATAGGTAAATTTACAATGTACCCAGTATAAATATGCCGGTTTTATGAGAAAATAGGTCTAAATAA
1 ATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCTAAATAA
* *
1281528 TGTATCGACACCTTTATAGTTTGTGTCGATACATTTAAATTTGCAATGCA
66 AGTATCGACACCTTTATAATTTGTGTCGATACATTTAAATTTGCAATGCA
* * * *
1281578 ATAGGTAAATTTGCAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTC-AGAATA
1 ATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCTA-AATA
*
1281642 AAGTATCGACA-CTTGTGTAATTTGTGTCGATACATTT
65 AAGTATCGACACCTT-TATAATTTGTGTCGATACATTT
1281679 TGTCCATAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
114 4 0.04
115 85 0.96
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (115 bp):
ATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCTAAATAA
AGTATCGACACCTTTATAATTTGTGTCGATACATTTAAATTTGCAATGCA
Found at i:1281832 original size:313 final size:312
Alignment explanation
Indices: 1281259--1281875 Score: 1108
Period size: 313 Copynumber: 2.0 Consensus size: 312
1281249 CGATAAATAT
* * * *
1281259 AATGTAATAGGTCAATTTATAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCA
1 AATGCAATAGGTAAATTTACAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTCA
1281324 GAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
66 GAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
*
1281389 GGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATAGATCCCATAAACATCAAAACGAAAAT
131 GGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATAGATCCCAAAAACATCAAAACGAAAAT
* *
1281454 TACAATGTTATAGGTAAATTTACAATGTACCCAGTATAAATATGCCGGTTTTATGAGAAAATAGG
196 TACAATGTTATAGGTAAATTTACAATGTACCCAGTATAAATATACCGATTTTATGAGAAAATAGG
*
1281519 TCTAAATAATGTATCGACACCTTTATAGTTTGTGTCGATACATTTAAATTTGC
261 TCTAAATAATATATCGACACCTTTATAGTTTGTGTCGATA-ATTTAAATTTGC
*
1281572 AATGCAATAGGTAAATTTGCAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTCA
1 AATGCAATAGGTAAATTTACAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTCA
1281637 GAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
66 GAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
* **
1281702 GGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAAACGAAAAT
131 GGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATAGATCCCAAAAACATCAAAACGAAAAT
*
1281767 TACAATGTTATAGGTAAATTTACAATGTACCCGGTATAAATATACCGATTTTATGAGAAAATAGG
196 TACAATGTTATAGGTAAATTTACAATGTACCCAGTATAAATATACCGATTTTATGAGAAAATAGG
1281832 TCTAAATAATATATCGACACCTTTATAGTTTGTGTCGATAATTT
261 TCTAAATAATATATCGACACCTTTATAGTTTGTGTCGATAATTT
1281876 TTTCCAGAAT
Statistics
Matches: 291, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
312 4 0.01
313 287 0.99
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (312 bp):
AATGCAATAGGTAAATTTACAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTCA
GAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
GGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATAGATCCCAAAAACATCAAAACGAAAAT
TACAATGTTATAGGTAAATTTACAATGTACCCAGTATAAATATACCGATTTTATGAGAAAATAGG
TCTAAATAATATATCGACACCTTTATAGTTTGTGTCGATAATTTAAATTTGC
Found at i:1281988 original size:204 final size:197
Alignment explanation
Indices: 1281571--1282017 Score: 580
Period size: 204 Copynumber: 2.2 Consensus size: 197
1281561 TTTAAATTTG
* *
1281571 CAATGCAATAGGTAAATTTGCAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTC
1 CAATGCAATAGGTAAATTTGCAATGT-ACCGGTATAAATATACCGATTTTATGAGAAAATAGGTC
*
1281636 AGAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACG
65 AGAATAAAGTATCGACACTTGTATAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACG
* * * **
1281701 AGGTGCAAGAATAACGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAAACGAAAA
130 AGATGCAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACAACGAAACGAAAA
1281766 TTA
195 TTA
** *
1281769 CAATGTTATAGGTAAATTTACAATGTACCCGGTATAAATATACCGATTTTATGAGAAAATAGGTC
1 CAATGCAATAGGTAAATTTGCAATGTA-CCGGTATAAATATACCGATTTTATGAGAAAATAGGTC
* *
1281834 TA-AATAATA-TATCGACACCTT-TATAGTTTGTGTCGATA-ATTTTTTCCAGAATGAATTAGGA
65 -AGAATAA-AGTATCGACA-CTTGTATAATTTGTGTCGATACATTTTGTCC---AT-AA-T--GA
* *
1281895 ATGCCCAACGAGATGCAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAATAAC
120 ATGCCCAACGAGATGCAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACAAC
1281960 GAAAC-AATAATTA
185 GAAACGAA-AATTA
* *
1281973 TAATGCAATAGGTAAATTTGTAATGCTACCGGTATAAATATACCG
1 CAATGCAATAGGTAAATTTGCAATG-TACCGGTATAAATATACCG
1282018 GTTAAATGCC
Statistics
Matches: 216, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
197 9 0.04
198 86 0.40
199 5 0.02
200 2 0.01
201 2 0.01
202 1 0.00
203 2 0.01
204 107 0.50
205 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (197 bp):
CAATGCAATAGGTAAATTTGCAATGTACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCA
GAATAAAGTATCGACACTTGTATAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
GATGCAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACAACGAAACGAAAAT
TA
Found at i:1282084 original size:23 final size:23
Alignment explanation
Indices: 1282034--1282078 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1282024 TGCCTATTTT
*
1282034 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1282057 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1282079 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1285730 original size:23 final size:23
Alignment explanation
Indices: 1285704--1285766 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1285694 GACATATATA
*
1285704 TGGTCATTTGGGATATTTCTACG
1 TGGTCATTCGGGATATTTCTACG
* *
1285727 TGGTCAATCGGGACATTTCTACG
1 TGGTCATTCGGGATATTTCTACG
*
1285750 TGGTCCTTCGGGATATT
1 TGGTCATTCGGGATATT
1285767 CTATATGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.38
Consensus pattern (23 bp):
TGGTCATTCGGGATATTTCTACG
Found at i:1295463 original size:24 final size:24
Alignment explanation
Indices: 1295434--1295488 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1295424 AAGACCATTG
*
1295434 GAAGAATGATTGTCCGAAGCTGAA
1 GAAGAAAGATTGTCCGAAGCTGAA
** *
1295458 GAAGAAAGATTGTTTGAATCTGAA
1 GAAGAAAGATTGTCCGAAGCTGAA
1295482 GAAGAAA
1 GAAGAAA
1295489 TGAAAAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (24 bp):
GAAGAAAGATTGTCCGAAGCTGAA
Found at i:1298846 original size:16 final size:16
Alignment explanation
Indices: 1298818--1298891 Score: 103
Period size: 16 Copynumber: 4.6 Consensus size: 16
1298808 TGAAAAATTA
*
1298818 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
1298834 GCAAAATTAAAAGTTG
1 GCAAAATTGAAAGTTG
*
1298850 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
1298866 GCAAAATTGAAATTTG
1 GCAAAATTGAAAGTTG
*
1298882 GCAAAGTTGA
1 GCAAAATTGA
1298892 CATCTTTGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:1298854 original size:32 final size:32
Alignment explanation
Indices: 1298818--1298891 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
1298808 TGAAAAATTA
1298818 GCAAAGTTGAAAGTTGGCAAAATTAAAAGTTG
1 GCAAAGTTGAAAGTTGGCAAAATTAAAAGTTG
* *
1298850 GCAAAGTTGAAAGTTGGCAAAATTGAAATTTG
1 GCAAAGTTGAAAGTTGGCAAAATTAAAAGTTG
1298882 GCAAAGTTGA
1 GCAAAGTTGA
1298892 CATCTTTGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (32 bp):
GCAAAGTTGAAAGTTGGCAAAATTAAAAGTTG
Found at i:1300155 original size:57 final size:57
Alignment explanation
Indices: 1300072--1300186 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
1300062 TAAAAGGTAA
**
1300072 TGTACTAACACATGATTTGATAATTACAATTTCACTTGAAAGTATCTACA-TTTGTAC
1 TGTACTAACACATGATTTGATAATTACAAAGTCACTTGAAAGTATCTACACTTT-TAC
*
1300129 TGTACTAACACATGATTTGTTAATTACAAAGTCACTTGAAAGTATCTACACTTTTAC
1 TGTACTAACACATGATTTGATAATTACAAAGTCACTTGAAAGTATCTACACTTTTAC
1300186 T
1 T
1300187 TGCTTGTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 51 0.94
58 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (57 bp):
TGTACTAACACATGATTTGATAATTACAAAGTCACTTGAAAGTATCTACACTTTTAC
Found at i:1305975 original size:13 final size:13
Alignment explanation
Indices: 1305957--1305996 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1305947 ATTATAATAC
1305957 TTATAATATAATT
1 TTATAATATAATT
1305970 TTATAAATATAATT
1 TTAT-AATATAATT
* *
1305984 TCATAATAAAATT
1 TTATAATATAATT
1305997 AATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TTATAATATAATT
Found at i:1305983 original size:14 final size:14
Alignment explanation
Indices: 1305957--1305989 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1305947 ATTATAATAC
1305957 TTAT-AATATAATT
1 TTATAAATATAATT
1305970 TTATAAATATAATT
1 TTATAAATATAATT
*
1305984 TCATAA
1 TTATAA
1305990 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAAATATAATT
Found at i:1307003 original size:21 final size:20
Alignment explanation
Indices: 1306973--1307034 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1306963 AGTTTGGAAA
*
1306973 TTGTAAGAGTTTGGAAACTT
1 TTGTAAGAGTTTCGAAACTT
*
1306993 TTGTAAAGAGTTTCGAAGCTT
1 TTGT-AAGAGTTTCGAAACTT
*
1307014 TTGTAAGAGTTTTGAAACTT
1 TTGTAAGAGTTTCGAAACTT
1307034 T
1 T
1307035 GCACCCTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGTAAGAGTTTCGAAACTT
Found at i:1310826 original size:12 final size:12
Alignment explanation
Indices: 1310809--1310848 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
1310799 AGCAGCCCCC
1310809 CCCCCTTAGCAG
1 CCCCCTTAGCAG
1310821 CCCCCTTAGCAG
1 CCCCCTTAGCAG
1310833 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
1310846 CCC
1 CCC
1310849 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Done.