Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008100.1 Hibiscus syriacus cultivar Beakdansim tig00110630_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: 1372717
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 6 of 7
Found at i:1073451 original size:22 final size:22
Alignment explanation
Indices: 1073413--1073492 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
1073403 AATTTAAAAA
*
1073413 AATATTATTT-AAATAATAATT
1 AATATTATTTAAAATAATAAAT
*
1073434 AATATTATTTAAAATAATAACT
1 AATATTATTTAAAATAATAAAT
* * *
1073456 AATATGATTTTAAATATTAAAT
1 AATATTATTTAAAATAATAAAT
1073478 -A-ATTACTTTAAAATA
1 AATATTA-TTTAAAATA
1073493 TTTTTATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.06
21 19 0.38
22 28 0.56
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (22 bp):
AATATTATTTAAAATAATAAAT
Found at i:1074136 original size:36 final size:37
Alignment explanation
Indices: 1074073--1074143 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
1074063 CTTATACTAC
*
1074073 ATTTTTAAAAAAACACATAAATGTTAATACTATTAATA
1 ATTTTTAAAAAAACACATAAATATTAATA-TATTAATA
*
1074111 ATTTTTTAAAAAA-A-ATAAATATTAATATATTAA
1 ATTTTTAAAAAAACACATAAATATTAATATATTAA
1074144 ATTTTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.19
36 12 0.39
37 1 0.03
38 12 0.39
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (37 bp):
ATTTTTAAAAAAACACATAAATATTAATATATTAATA
Found at i:1075144 original size:6 final size:6
Alignment explanation
Indices: 1075135--1075204 Score: 106
Period size: 6 Copynumber: 11.5 Consensus size: 6
1075125 TATTACTATT
*
1075135 ACCACG ACCACG GCCACG ACCACG ACCACG ACCACG ACCACG ACC-CGAG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC--G
1075184 ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACC
1075205 CGAGACGAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
5 1 0.02
6 53 0.90
7 4 0.07
8 1 0.02
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1075192 original size:25 final size:25
Alignment explanation
Indices: 1075135--1075210 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
1075125 TATTACTATT
*
1075135 ACCACGACCACGGCCACGA-CC-ACG
1 ACCACGACCACGACCACGACCCGA-G
1075159 ACCACGACCACGACCACGACCCGAG
1 ACCACGACCACGACCACGACCCGAG
1075184 ACCACGACCACGACCACGACCCGAG
1 ACCACGACCACGACCACGACCCGAG
1075209 AC
1 AC
1075211 GAGACGGCGG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 18 0.37
25 30 0.61
26 1 0.02
ACGTcount: A:0.32, C:0.49, G:0.20, T:0.00
Consensus pattern (25 bp):
ACCACGACCACGACCACGACCCGAG
Found at i:1086378 original size:114 final size:113
Alignment explanation
Indices: 1086250--1086503 Score: 252
Period size: 114 Copynumber: 2.2 Consensus size: 113
1086240 AAAACAGTTA
** ** * *
1086250 TTGAAAACGTATAATATATATTTTTTTGAAAA-AAATGGTTTTTGA-AAATATATATAATATGGT
1 TTGAAAATATATAATATATATTTTTTTGAAAACAAATGGAATAT-ATAAATATATATAATATAGT
*
1086313 TTTGAAAATACGATTTAAAAACATATAT-TATATA-ATTTTGAAAATATTT
65 TTTGAAAAT--GATTTAAAAACATATATATATATAGATTTTAAAAATATTT
* * ** * *
1086362 TTGAAAACATATATAATATATA-GTTTTCGAAAACATTTTGAATATATATATATATATAATATAG
1 TTG-AAA-ATATATAATATATATTTTTTTGAAAACAAATGGAATATATAAATATATATAATATAG
* * *
1086426 TTTTTAAAATGTTTTAAAAACATATATAATATATAGTTTTTAAAAATATTT
64 TTTTGAAAATGATTTAAAAACATATAT-ATATATAGATTTTAAAAATATTT
1086477 TTGAAAATATAT--TATATAGTTTTTTTG
1 TTGAAAATATATAATATATA-TTTTTTTG
1086504 TTAATATATT
Statistics
Matches: 115, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
111 6 0.05
112 19 0.17
113 24 0.21
114 50 0.43
115 16 0.14
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (113 bp):
TTGAAAATATATAATATATATTTTTTTGAAAACAAATGGAATATATAAATATATATAATATAGTT
TTGAAAATGATTTAAAAACATATATATATATAGATTTTAAAAATATTT
Found at i:1086405 original size:26 final size:25
Alignment explanation
Indices: 1086347--1086410 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
1086337 ATATTATATA
*
1086347 ATTTTGAA-A-ATATTTTTGAAAAC
1 ATTTTGAATATATATTTTCGAAAAC
*
1086370 ATATAT-AATATATAGTTTTCGAAAAC
1 AT-TTTGAATATATA-TTTTCGAAAAC
1086396 ATTTTGAATATATAT
1 ATTTTGAATATATAT
1086411 ATATATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 6 0.18
26 20 0.61
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTTGAATATATATTTTCGAAAAC
Found at i:1086451 original size:34 final size:34
Alignment explanation
Indices: 1086413--1086500 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 34
1086403 ATATATATAT
*
1086413 ATATATAATATAGTTTTT-AAAATGTTTTAAAAA
1 ATATATAATATAGTTTTTAAAAATATTTTAAAAA
**
1086446 CATATATAATATATAGTTTTTAAAAATATTTTTGAAA
1 -ATATAT-A-ATATAGTTTTTAAAAATATTTTAAAAA
*
1086483 ATATATTATATAGTTTTT
1 ATATATAATATAGTTTTT
1086501 TTGTTAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 17 0.36
35 1 0.02
36 17 0.36
37 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (34 bp):
ATATATAATATAGTTTTTAAAAATATTTTAAAAA
Found at i:1086461 original size:77 final size:78
Alignment explanation
Indices: 1086335--1086494 Score: 216
Period size: 77 Copynumber: 2.1 Consensus size: 78
1086325 ATTTAAAAAC
* * * *
1086335 ATATATTATATAATTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTCGAAAACA-TT
1 ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT
*
1086399 TTGAATATATATAT
66 TTGAAAATATAT-T
* * * *
1086413 ATATATAATATAGTTTTTAAAAT-GTTTTAAAAACATATATAATATATAGTTTTTAAAAATATTT
1 ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT
1086477 TTGAAAATATATT
66 TTGAAAATATATT
1086490 ATATA
1 ATATA
1086495 GTTTTTTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
77 39 0.54
78 33 0.46
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (78 bp):
ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT
TTGAAAATATATT
Found at i:1086494 original size:36 final size:38
Alignment explanation
Indices: 1086188--1086494 Score: 196
Period size: 36 Copynumber: 8.2 Consensus size: 38
1086178 TTTATAACAA
*
1086188 TATAGTATAGTTTTTGAAAATATTTTCT-AAAAGCGTATA-
1 TATA-TATAGTTTTTGAAAATATTTT-TGAAAA-CATATAT
* * * * *
1086227 -ACATATAGTTTTT-AAAACAGTTATTGAAAACGTATAA
1 TATATATAGTTTTTGAAAATA-TTTTTGAAAACATATAT
* * *
1086264 TATATAT-TTTTTTGAAAAAAATGGTTTTTGAAAATATATA-
1 TATATATAGTTTTTG---AAAAT-ATTTTTGAAAACATATAT
* ** *
1086304 TA-ATAT-GGTTTTGAAAATACGATTTAAAAACATATAT
1 TATATATAGTTTTTGAAAATA-TTTTTGAAAACATATAT
1086341 TATATA-A--TTTTGAAAATATTTTTGAAAACATATAT
1 TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT
* * * *
1086376 AATATATAGTTTTCGAAAACA-TTTTGAATATATATATAT
1 TATATATAGTTTTTGAAAATATTTTTGAA-A-ACATATAT
* *
1086415 ATATAATATAGTTTTT-AAAAT-GTTTTAAAAACATATAT
1 -TAT-ATATAGTTTTTGAAAATATTTTTGAAAACATATAT
* *
1086453 AATATATAGTTTTTAAAAATATTTTTG-AAA-ATATAT
1 TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT
1086489 TATATA
1 TATATA
1086495 GTTTTTTTGT
Statistics
Matches: 212, Mismatches: 33, Indels: 49
0.72 0.11 0.17
Matches are distributed among these distances:
35 19 0.09
36 63 0.30
37 41 0.19
38 31 0.15
39 17 0.08
40 14 0.07
41 27 0.13
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (38 bp):
TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT
Found at i:1086519 original size:3 final size:3
Alignment explanation
Indices: 1086513--1086598 Score: 77
Period size: 3 Copynumber: 26.7 Consensus size: 3
1086503 GTTAATATAT
1086513 TTA TTA TTA TTA TTA TTCA TTA -TA TTTA TTTA TTA TATA TTA TATA
1 TTA TTA TTA TTA TTA TT-A TTA TTA -TTA -TTA TTA T-TA TTA T-TA
*
1086559 TTA TTA TTA TTCA TTA -TA TTTA TTT TTA GTTA TTA TTA TT
1 TTA TTA TTA TT-A TTA TTA -TTA TTA TTA -TTA TTA TTA TT
1086599 TCTTTTAGGG
Statistics
Matches: 72, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
2 4 0.06
3 45 0.62
4 23 0.32
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1086547 original size:20 final size:20
Alignment explanation
Indices: 1086522--1086583 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1086512 TTTATTATTA
1086522 TTATTATTCATTATATTTAT
1 TTATTATTCATTATATTTAT
1086542 TTATTATAT-ATTATATATTA-
1 TTATTAT-TCATTATAT-TTAT
1086562 TTATTATTCATTATATTTAT
1 TTATTATTCATTATATTTAT
1086582 TT
1 TT
1086584 TTAGTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.11
20 30 0.79
21 4 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTCATTATATTTAT
Found at i:1086553 original size:40 final size:38
Alignment explanation
Indices: 1086507--1086598 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 38
1086497 TTTTTTGTTA
1086507 ATATATTTATTATTATTATTATTCATTATATTTATTTATT
1 ATATA-TTATTATTATTATTATTCATTATATTTATTT-TT
1086547 ATATATTATATATTATTATTATTCATTATATTTATTTTT
1 ATATATTAT-TATTATTATTATTCATTATATTTATTTTT
1086586 AGT-TATTATTATT
1 A-TATATTATTATT
1086599 TCTTTTAGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 4 0.08
39 13 0.26
40 33 0.66
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (38 bp):
ATATATTATTATTATTATTATTCATTATATTTATTTTT
Found at i:1086581 original size:13 final size:13
Alignment explanation
Indices: 1086507--1086598 Score: 86
Period size: 13 Copynumber: 7.0 Consensus size: 13
1086497 TTTTTTGTTA
1086507 ATATATTTATTATT
1 ATATA-TTATTATT
1086521 AT-TATTATTCATT
1 ATATATTATT-ATT
1086534 ATAT-TTATTTATT
1 ATATATTA-TTATT
1086547 ATATATTATATATT
1 ATATATTAT-TATT
1086561 AT-TATTATTCATT
1 ATATATTATT-ATT
*
1086574 ATAT-TTATTTTT
1 ATATATTATTATT
1086586 AGT-TATTATTATT
1 A-TATATTATTATT
1086599 TCTTTTAGGG
Statistics
Matches: 67, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
12 10 0.15
13 42 0.63
14 15 0.22
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (13 bp):
ATATATTATTATT
Found at i:1087481 original size:17 final size:18
Alignment explanation
Indices: 1087450--1087484 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1087440 AGAGTTGAGA
1087450 GGTTTTTTAGAGGTTTGG
1 GGTTTTTTAGAGGTTTGG
*
1087468 GGTTTTTTTG-GGTTTGG
1 GGTTTTTTAGAGGTTTGG
1087485 TTAAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54
Consensus pattern (18 bp):
GGTTTTTTAGAGGTTTGG
Found at i:1087869 original size:29 final size:28
Alignment explanation
Indices: 1087817--1087874 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1087807 TTACTCTAAA
* * *
1087817 AAATTAACATTTTTCTTTGTTTTTCTTT
1 AAATTAACATTTTTCTATCTTTTTATTT
1087845 AAATTAACATTTTTCTCATCTTTTTATTT
1 AAATTAACATTTTTCT-ATCTTTTTATTT
1087874 A
1 A
1087875 TTTATTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (28 bp):
AAATTAACATTTTTCTATCTTTTTATTT
Found at i:1087962 original size:11 final size:11
Alignment explanation
Indices: 1087948--1087994 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1087938 TTTCTTAACC
1087948 TTTTTATTTAT
1 TTTTTATTTAT
1087959 TTTTTATTTCA-
1 TTTTTATTT-AT
*
1087970 TATTTATTTAT
1 TTTTTATTTAT
*
1087981 TTATT-TTTAT
1 TTTTTATTTAT
1087991 TTTT
1 TTTT
1087995 ACGATCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.30
11 20 0.67
12 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:1087991 original size:18 final size:17
Alignment explanation
Indices: 1087948--1087992 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
1087938 TTTCTTAACC
1087948 TTTTTATTTATTTTTTA
1 TTTTTATTTATTTTTTA
*
1087965 TTTCATATTTATTTATTTA
1 TTT-TTATTTATTT-TTTA
1087984 TTTTTATTT
1 TTTTTATTT
1087993 TTACGATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 14 0.58
19 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTATTTTTTA
Found at i:1092249 original size:46 final size:46
Alignment explanation
Indices: 1092191--1092286 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
1092181 ATTATTCTTT
* * *
1092191 ATTTTCATTTATAACATTCATCCATGTTTATAATGCA-CCATTATGC
1 ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCA-TATGC
* * **
1092237 ATTTTCAGTTATAGCATACTTTTATGTTGATAATGCACCCATATGC
1 ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCATATGC
1092283 ATTT
1 ATTT
1092287 CAACTATGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 39 0.93
47 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (46 bp):
ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCATATGC
Found at i:1092349 original size:45 final size:45
Alignment explanation
Indices: 1092266--1092384 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 45
1092256 TTTTATGTTG
* * * *
1092266 ATAATGCACCCATATGCATT-TCAACTATGACACACTTTCATTCCA
1 ATAATGCACCCATATGCATTAT-TATTTTGACACACTTTCATTACA
* *
1092311 ATAATGCACCCATATGCATTATTATTTTGGCATC-CTTTCATTACG
1 ATAATGCACCCATATGCATTATTATTTTGACA-CACTTTCATTACA
*
1092356 GTAATGCACCCATATGCATTATTATTTTG
1 ATAATGCACCCATATGCATTATTATTTTG
1092385 TTCATTCGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 63 0.97
46 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATTATTTTGACACACTTTCATTACA
Found at i:1095673 original size:45 final size:45
Alignment explanation
Indices: 1095622--1095919 Score: 384
Period size: 45 Copynumber: 6.6 Consensus size: 45
1095612 ATTTATGTTG
* * * **
1095622 ATAATGCACCCATATGCATT-TCAACTATGAAATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTAT-TATTTTGGCATCCTTTCATGCCA
*
1095667 ATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCA
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
* * * * *
1095712 ATAATGCACCCATATTCTTTATTATTTTGGGATACTTTCATGCTA
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
* * * *
1095757 ATAATGCACCTATATTCATTATTATTTTGGCATCCTTTCATGTCG
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
*
1095802 ATAATGCACCTATATG-ATTATTATTTTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
* * * *
1095846 ATAATGCACCTATCTGCATTATTATTTTGGTATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
*
1095891 ATAATGCACCCATATTCATTATTATTTTG
1 ATAATGCACCCATATGCATTATTATTTTG
1095920 TTCATTCGTT
Statistics
Matches: 223, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
44 41 0.18
45 181 0.81
46 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA
Found at i:1095868 original size:134 final size:135
Alignment explanation
Indices: 1095653--1095919 Score: 410
Period size: 134 Copynumber: 2.0 Consensus size: 135
1095643 CAACTATGAA
1095653 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG
* * * *
1095718 CACCCATATTCTTTATTATTTTGGGATACTTTCATGCTAATAATGCACCTATATTCATTATTATT
66 CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT
1095783 TTGGC
131 TTGGC
* * * *
1095788 ATCCTTTCATGTCGATAATGCACCTATATG-ATTATTATTTTGGCATCCTTTCATGCCAATAATG
1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG
* * * * *
1095852 CACCTATCTGCATTATTATTTTGGTATCCTTTCATGCCGATAATGCACCCATATTCATTATTATT
66 CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT
1095917 TTG
131 TTG
1095920 TTCATTCGTT
Statistics
Matches: 119, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
134 92 0.77
135 27 0.23
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (135 bp):
ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG
CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT
TTGGC
Found at i:1096348 original size:22 final size:21
Alignment explanation
Indices: 1096306--1096376 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 21
1096296 TGGCTCTTCA
*
1096306 GTATCGATAC-CCATACCATG
1 GTATCGATACTCCATACTATG
1096326 GTATCGATACTACCATACTATG
1 GTATCGATACT-CCATACTATG
* *
1096348 GTACCGATACT--ATGCTATG
1 GTATCGATACTCCATACTATG
1096367 GTATCGATAC
1 GTATCGATAC
1096377 CATTTTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 16 0.36
20 10 0.22
22 19 0.42
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCATACTATG
Found at i:1099358 original size:35 final size:35
Alignment explanation
Indices: 1099265--1099497 Score: 161
Period size: 36 Copynumber: 6.4 Consensus size: 35
1099255 AAAAAACCAG
* **
1099265 TTTTTGAAAATATATATAATATGGTTTTGAAAATA
1 TTTTTGAAAACATATATAATATAATTTTGAAAATA
** * *
1099300 CGATTTAAAAACATATATTATATAATTTTGAAAATA
1 -TTTTTGAAAACATATATAATATAATTTTGAAAATA
*
1099336 TTTTTGAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAACATATATAATATA-A--TTTTGAAAATA
* *
1099374 -TTTTGAATATATATATATAATATATATAGTTTTTAAAAT-
1 TTTTTGAA-A-ACATATAT-A-ATATA-A-TTTTGAAAATA
* * *
1099413 GTTTTAAAAACATATATTATATATAGTTTTGAAAATA
1 TTTTTGAAAACATATA-TA-ATATAATTTTGAAAATA
* *
1099450 TTTTTG-AAA-ATATATTATATAGTTTTGAAAA-A
1 TTTTTGAAAACATATATAATATAATTTTGAAAATA
1099482 TGGGTTTTGAAAACAT
1 T---TTTTGAAAACAT
1099498 TTTGGAAATT
Statistics
Matches: 159, Mismatches: 23, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
32 2 0.01
33 15 0.09
34 1 0.01
35 29 0.18
36 44 0.28
37 13 0.08
38 24 0.15
39 9 0.06
40 15 0.09
41 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (35 bp):
TTTTTGAAAACATATATAATATAATTTTGAAAATA
Found at i:1099382 original size:26 final size:25
Alignment explanation
Indices: 1099324--1099387 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1099314 ATATTATATA
1099324 ATTTTGAA-A-ATATTTTTGAAAAC
1 ATTTTGAATATATATTTTTGAAAAC
*
1099347 ATATAT-AATATATAGTTTTTGAAAAC
1 AT-TTTGAATATATA-TTTTTGAAAAC
1099373 ATTTTGAATATATAT
1 ATTTTGAATATATAT
1099388 ATATAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 6 0.18
26 21 0.62
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (25 bp):
ATTTTGAATATATATTTTTGAAAAC
Found at i:1099439 original size:77 final size:79
Alignment explanation
Indices: 1099318--1099470 Score: 213
Period size: 77 Copynumber: 2.0 Consensus size: 79
1099308 AAACATATAT
* * *
1099318 TATATAATTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTTGAAAACA-TTTTGAAT
1 TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAG-TTTTGAAAACATTTTTGAAA
1099382 ATATA-TATATAATA
65 ATATATTATATAATA
* * * *
1099396 TATATAGTTTTTAAAAT-GTTTTAAAAACATATATTATATATAGTTTTGAAAATATTTTTGAAAA
1 TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1099460 TATATTATATA
66 TATATTATATA
1099471 GTTTTGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 10 0.15
77 35 0.53
78 21 0.32
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (79 bp):
TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAA
TATATTATATAATA
Found at i:1099522 original size:3 final size:3
Alignment explanation
Indices: 1099516--1099587 Score: 71
Period size: 3 Copynumber: 23.7 Consensus size: 3
1099506 TTTTTTTTTG
1099516 TTA TTA TATA TTA TTCA TTA -TA TTTA TTA -TA TATA TTA TTA TTA -TA
1 TTA TTA T-TA TTA TT-A TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA
1099562 TTA TTA -TA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TT
1099588 TCTTTTAGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
2 8 0.13
3 38 0.63
4 14 0.23
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1099546 original size:23 final size:23
Alignment explanation
Indices: 1099516--1099588 Score: 96
Period size: 23 Copynumber: 3.1 Consensus size: 23
1099506 TTTTTTTTTG
1099516 TTATTATATATTATTCATTA-TAT
1 TTATTATATATTATT-ATTATTAT
1099539 TTATTATATA-TATTATTATTAT
1 TTATTATATATTATTATTATTAT
1099561 ATTATTATATTATTATTTATTATTAT
1 -TTATTATA-TATTA-TTATTATTAT
1099587 TT
1 TT
1099589 CTTTTAGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.09
22 7 0.16
23 18 0.40
24 2 0.04
25 4 0.09
26 10 0.22
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTATATATTATTATTATTAT
Found at i:1099587 original size:13 final size:13
Alignment explanation
Indices: 1099516--1099586 Score: 87
Period size: 13 Copynumber: 5.5 Consensus size: 13
1099506 TTTTTTTTTG
1099516 TTATTATATATTA
1 TTATTATATATTA
1099529 TTCATTATAT-TTA
1 TT-ATTATATATTA
1099542 TTA-TATATATTA
1 TTATTATATATTA
1099554 TTATTATATTATTA
1 TTATTATA-TATTA
1099568 -TATTAT-TATTTA
1 TTATTATATA-TTA
1099580 TTATTAT
1 TTATTAT
1099587 TTCTTTTAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.13
12 10 0.19
13 23 0.44
14 12 0.23
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATATATTA
Found at i:1104670 original size:93 final size:92
Alignment explanation
Indices: 1104535--1104719 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 92
1104525 TTCCATATTA
1104535 GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG
1 GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG
1104600 GATCGGGTCCTCCCATTTATACTTTTC
66 GATCGGGTCCTCCCATTTATACTTTTC
1104627 GCACCCCAAATATGTTTTAGGCCTTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGG
1 GCACCCCAAATATGTTTTAGGCC-TTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGG
1104692 GGATCGGGTCCTCCCATTTATACTTTTC
65 GGATCGGGTCCTCCCATTTATACTTTTC
1104720 TCGAAGAATC
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 23 0.25
93 69 0.75
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (92 bp):
GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG
GATCGGGTCCTCCCATTTATACTTTTC
Found at i:1107477 original size:25 final size:25
Alignment explanation
Indices: 1107442--1107501 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
1107432 AGGTTTTGCT
*
1107442 CCTTAAACCCGCTAGGAGCTCCGCC
1 CCTTAACCCCGCTAGGAGCTCCGCC
1107467 CCTTAACCCCGCTAGGAGCTCCGCC
1 CCTTAACCCCGCTAGGAGCTCCGCC
1107492 CCTTGAACCC
1 CCTT-AACCC
1107502 TTAGTAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 28 0.85
26 5 0.15
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.17
Consensus pattern (25 bp):
CCTTAACCCCGCTAGGAGCTCCGCC
Found at i:1107631 original size:35 final size:36
Alignment explanation
Indices: 1107585--1107653 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
1107575 TTGATATGAA
1107585 CATTATTTGACATGCATGGTT-TAGCCCCATATTTG
1 CATTATTTGACATGCATGGTTATAGCCCCATATTTG
1107620 CATTATTTGACATGCATGGTTATAGCCCCATATT
1 CATTATTTGACATGCATGGTTATAGCCCCATATT
1107654 GCAATGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
CATTATTTGACATGCATGGTTATAGCCCCATATTTG
Found at i:1108109 original size:182 final size:184
Alignment explanation
Indices: 1107801--1108166 Score: 709
Period size: 182 Copynumber: 2.0 Consensus size: 184
1107791 GATTAACAAA
1107801 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG
1 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG
*
1107866 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGCATTTCCTTACTGTTTTATATCTATAT
66 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT
1107931 TGTATGTGATGC-ATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT
131 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT
1107984 AAATGTGAAGATGCTTGAGAAGCAATCTTTGT-ATTAAGATTCGAGATTCTCCAATTGGCTTGGG
1 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG
1108048 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT
66 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT
1108113 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT
131 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT
1108167 TAAGGGCCTA
Statistics
Matches: 181, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 108 0.60
183 73 0.40
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (184 bp):
AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG
ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT
TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT
Found at i:1111944 original size:34 final size:34
Alignment explanation
Indices: 1111901--1112001 Score: 175
Period size: 34 Copynumber: 3.0 Consensus size: 34
1111891 GGTTTCTGTC
*
1111901 TATGAGACATTGTATTTCTCTTTCGAAGGAAATG
1 TATGAGACATAGTATTTCTCTTTCGAAGGAAATG
*
1111935 TATGAGACATGGTATTTCTCTTTCGAAGGAAATG
1 TATGAGACATAGTATTTCTCTTTCGAAGGAAATG
*
1111969 TATGAGACATAGTATTTCTCTTTAGAAGGAAAT
1 TATGAGACATAGTATTTCTCTTTCGAAGGAAAT
1112002 TTATCCTTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (34 bp):
TATGAGACATAGTATTTCTCTTTCGAAGGAAATG
Found at i:1113712 original size:2 final size:2
Alignment explanation
Indices: 1113705--1113744 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1113695 TGTATCGTTA
1113705 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
1113745 GCACGTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1115302 original size:87 final size:89
Alignment explanation
Indices: 1115131--1115302 Score: 296
Period size: 89 Copynumber: 2.0 Consensus size: 89
1115121 TCCCGAATAT
*
1115131 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG
1115196 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
1115220 TTAAATTCTAATTAATT-AATATAGATTTAATTAATTTGAAATAATAAAA-C-CTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTA
*
1115282 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
1115303 GTGCGTTGGG
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
87 32 0.40
88 1 0.01
89 39 0.49
90 8 0.10
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:1126294 original size:35 final size:36
Alignment explanation
Indices: 1126226--1126296 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
1126216 AATTTAAAAT
*
1126226 GGGTATTTTTCAAATACAACTGTCCCACAAAACATC
1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
* *
1126262 GGGTGTTTTTCAAATA-AATTGCCCCACAAAACATC
1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
1126297 AAGTGCAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (36 bp):
GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
Found at i:1126855 original size:63 final size:63
Alignment explanation
Indices: 1126756--1126901 Score: 240
Period size: 63 Copynumber: 2.3 Consensus size: 63
1126746 TTGACGAGGA
* * *
1126756 AGATCATTCAACAAATCT-ATTCCAATACAGTTTGATGGGGAAGATCATTCAAAAAGTATTTGT
1 AGATCACTCAACAAAT-TGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
1126819 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
1 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
*
1126882 AAATCACTCAACAAATTGAT
1 AGATCACTCAACAAATTGAT
1126902 GAGGAAGATC
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 1 0.01
63 77 0.99
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (63 bp):
AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
Found at i:1128737 original size:18 final size:18
Alignment explanation
Indices: 1128714--1128771 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1128704 ACCGGTCACA
1128714 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1128732 ACCCGA-CCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1128749 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1128767 ACCCG
1 ACCCG
1128772 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 16 0.43
18 21 0.57
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1128781 original size:7 final size:8
Alignment explanation
Indices: 1128758--1128792 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
1128748 TACCCGACCC
1128758 GACCCGTT
1 GACCCGTT
1128766 GACCCGTT
1 GACCCGTT
1128774 GA-CCGTT
1 GACCCGTT
1128781 GACCCGTT
1 GACCCGTT
1128789 GACC
1 GACC
1128793 GGAGTTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1128781 original size:15 final size:15
Alignment explanation
Indices: 1128761--1128793 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1128751 CCGACCCGAC
1128761 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1128776 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1128791 CCG
1 CCG
1128794 GAGTTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.36, G:0.27, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1131751 original size:18 final size:18
Alignment explanation
Indices: 1131728--1131798 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
1131718 ACCGGTCACA
1131728 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1131746 ACCCGA-CCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
1131762 ----TACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1131776 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1131794 ACCCG
1 ACCCG
1131799 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 1 0.02
13 10 0.23
17 10 0.23
18 23 0.52
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1131768 original size:30 final size:31
Alignment explanation
Indices: 1131732--1131798 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
1131722 GTCACAACCC
1131732 GACCCGACCCGTTGACCCGA-CCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
1131762 TACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1131793 GACCCG
1 GACCCG
1131799 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1131798 original size:13 final size:13
Alignment explanation
Indices: 1131732--1131785 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
1131722 GTCACAACCC
1131732 GACCCGACCCGTT
1 GACCCGACCCGTT
1131745 GACCCGACCGACCCGTT
1 GA--C--CCGACCCGTT
*
1131762 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1131775 TACCCGACCCG
1 GACCCGACCCG
1131786 ACCCGTTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 23 0.64
15 2 0.06
17 11 0.31
ACGTcount: A:0.17, C:0.48, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1131808 original size:7 final size:7
Alignment explanation
Indices: 1131788--1131819 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1131778 CCGACCCGAC
1131788 CCGTTGA
1 CCGTTGA
1131795 CCCGTTGA
1 -CCGTTGA
1131803 CCGTTGA
1 CCGTTGA
1131810 CCGTTGA
1 CCGTTGA
1131817 CCG
1 CCG
1131820 GAGTTGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1133577 original size:30 final size:30
Alignment explanation
Indices: 1133533--1133607 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
1133523 GCACAAACTT
1133533 AAACATAAAGGACTAAAATA-ATAAAAATAG
1 AAACATAAAGGACTAAAATAGA-AAAAATAG
*
1133563 AAAC-TAAAGGGACTAAAATAGAAAAATTAG
1 AAACATAAA-GGACTAAAATAGAAAAAATAG
*
1133593 AAACTTAAAGGACTA
1 AAACATAAAGGACTA
1133608 TACATTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 4 0.10
30 32 0.78
31 5 0.12
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.17
Consensus pattern (30 bp):
AAACATAAAGGACTAAAATAGAAAAAATAG
Found at i:1134870 original size:9 final size:8
Alignment explanation
Indices: 1134848--1134895 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
1134838 GTAAATTGTA
1134848 AATAAAAT
1 AATAAAAT
1134856 ATATAATAAT
1 A-ATAA-AAT
1134866 AATAATAAT
1 AATAA-AAT
1134875 AATAAAAT
1 AATAAAAT
1134883 -ATAAAA-
1 AATAAAAT
1134889 AATAAAA
1 AATAAAA
1134896 AAAAGACTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 12 0.32
8 4 0.11
9 17 0.46
10 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:1135301 original size:134 final size:134
Alignment explanation
Indices: 1135128--1135377 Score: 349
Period size: 134 Copynumber: 1.9 Consensus size: 134
1135118 GAGTTCTTTT
* *
1135128 CATCTTTAGGAAGGGTGATAACTCGATTCTTACGCGATGAAGACAGCTGGTTATCTAGGGGTGAC
1 CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
* * * *
1135193 ACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT
66 ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT
1135258 TGGC
131 TGGC
* * * * * *
1135262 CATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGACGACGGCAGGTTATCTATGGTTGA
1 CATCTTTAGGAAG-GGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGA
* * *
1135326 CACAGCTCCTACGTTATAAGGAGGTATAGTCAGGGGATGACATGGTTCCTAC
65 CACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTAC
1135378 AGAATGAGGA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
133 2 0.02
134 98 0.98
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (134 bp):
CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT
TGGC
Found at i:1135385 original size:134 final size:134
Alignment explanation
Indices: 1135128--1135405 Score: 344
Period size: 134 Copynumber: 2.1 Consensus size: 134
1135118 GAGTTCTTTT
* *
1135128 CATCTTTAGGAAGGGTGATAACTCGATTCTTACGCGATGAAGACAGCTGGTTATCTAGGGGTGAC
1 CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
* * * * * * *
1135193 ACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT
66 ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTAATGAGGACGAT
*
1135258 TGGC
131 TGAC
* * * * * *
1135262 CATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGACGACGGCAGGTTATCTATGGTTGA
1 CATCTTTAGGAAG-GGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGA
* * *
1135326 CACAGCTCCTACGTTATAAGGAGGTATAGTCAGGGGATGACATGGTTCCTACAG-AATGAGGACG
65 CACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTAC-GTAATGAGGACG
1135390 ATTGAC
129 ATTGAC
*
1135396 CATCCTTAGG
1 CATCTTTAGG
1135406 GATTATGGTT
Statistics
Matches: 122, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
133 2 0.02
134 119 0.98
135 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTAATGAGGACGAT
TGAC
Found at i:1135453 original size:28 final size:28
Alignment explanation
Indices: 1135421--1135509 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
1135411 TGGTTTCAGG
1135421 AGAAACCAACTCAAAGATTTGTTTCAAA
1 AGAAACCAACTCAAAGATTTGTTTCAAA
* *
1135449 AGAAA-CATACTTAAAGATTTATTTCAAGA
1 AGAAACCA-ACTCAAAGATTTGTTTCAA-A
*
1135478 A-AAACAAACTCAAAGATGATGTGTTTCAAA
1 AGAAACCAACTCAAAGAT--T-TGTTTCAAA
1135508 AG
1 AG
1135510 CAACTGTCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.04
28 34 0.69
29 3 0.06
30 3 0.06
31 7 0.14
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26
Consensus pattern (28 bp):
AGAAACCAACTCAAAGATTTGTTTCAAA
Found at i:1135591 original size:63 final size:67
Alignment explanation
Indices: 1135469--1135597 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 67
1135459 TTAAAGATTT
* *
1135469 ATTTCAAGAAAAACAAACTCAAAGATGATGTGTTTCAAAAGCAACTGTCTCAAAAGAGACAAAAT
1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
1135534 TC
66 TC
* * * **
1135536 ATTTCAAGAGAAAC-GACTCAAAGATGA-CT-TTT-AAAGGAAACTGTCTCAAGCGAGACAAAAT
1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
1135597 T
66 T
1135598 TTTTTTAAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 26 0.47
64 3 0.05
65 1 0.02
66 12 0.22
67 13 0.24
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (67 bp):
ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
TC
Found at i:1135674 original size:66 final size:63
Alignment explanation
Indices: 1135511--1135675 Score: 159
Period size: 66 Copynumber: 2.6 Consensus size: 63
1135501 TTTCAAAAGC
*
1135511 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGAGAAACGACTCAAAGATGACTTTTAAAGGA
1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATGACTTTTAAAGGA
** ** * * ** * ** **
1135574 AACTGTCTCAAGCGAGACAAAATTTTTTTTAAGGGAAGCGTTTTTAAAGATCGGTGTTTTATGGG
1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACG-ACTCAAAGAT--GACTTTTAAAGG
1135639 A
63 A
* *
1135640 AACTGTCTCAAATGAGACAAAATTCGTTTCAAGGGA
1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGA
1135676 CATGATCTCA
Statistics
Matches: 80, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
63 33 0.41
64 7 0.09
66 40 0.50
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (63 bp):
AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATGACTTTTAAAGGA
Found at i:1136028 original size:28 final size:28
Alignment explanation
Indices: 1135967--1136020 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1135957 AGAGAAATAA
* *
1135967 ACTCAAAGATTTTTTTCAAAAGGAACAG
1 ACTCAAAGATTTGTTTCAAAAGAAACAG
*
1135995 ACTCAAAGATTTGTTTCAAGAGAAAC
1 ACTCAAAGATTTGTTTCAAAAGAAAC
1136021 TGTCTCAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATTTGTTTCAAAAGAAACAG
Found at i:1136284 original size:36 final size:37
Alignment explanation
Indices: 1136241--1136313 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
1136231 TTGTATCTCA
*
1136241 GAGAAAAAATGTCTCAAGCGAAAC-GAAATTTGTTTT
1 GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT
* * *
1136277 GAGAAAAATTTTCTCAAGCGAGACAAAAATTTGTTTT
1 GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT
1136314 AAAATTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (37 bp):
GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT
Found at i:1143639 original size:3 final size:3
Alignment explanation
Indices: 1143631--1143661 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1143621 AATTGTAAAT
*
1143631 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1143662 ATATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1143667 original size:15 final size:15
Alignment explanation
Indices: 1143626--1143685 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
1143616 GTGTAAATTG
*
1143626 TAAATATAATAATAA
1 TAAATATAACAATAA
1143641 TAATAATAATAACAATAA
1 T-A-AAT-ATAACAATAA
1143659 TAAATATAA-AATAAA
1 TAAATATAACAAT-AA
*
1143674 TAAATAAAACAA
1 TAAATATAACAA
1143686 AAAAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.08
15 15 0.39
16 6 0.16
17 4 0.11
18 10 0.26
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATATAACAATAA
Found at i:1147770 original size:28 final size:28
Alignment explanation
Indices: 1147712--1147802 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
1147702 TGAATAAAAT
* * *
1147712 TTTATAGGGTTTTTGAGATTATGATATAA
1 TTTATAGGG-TTTAGAGTTTATGATGTAA
1147741 TTTATAGGGTTTAGAGTTTATGATGTAA
1 TTTATAGGGTTTAGAGTTTATGATGTAA
* * * *
1147769 TTTATAGGATTTGGAATTTATGACGTAA
1 TTTATAGGGTTTAGAGTTTATGATGTAA
1147797 TTTATA
1 TTTATA
1147803 TGATTTGGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 46 0.84
29 9 0.16
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (28 bp):
TTTATAGGGTTTAGAGTTTATGATGTAA
Found at i:1147807 original size:28 final size:28
Alignment explanation
Indices: 1147738--1147811 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
1147728 GATTATGATA
* * * *
1147738 TAATTTATAGGGTTTAGAGTTTATGATG
1 TAATTTATAGGATTTGGAATTTATGACG
1147766 TAATTTATAGGATTTGGAATTTATGACG
1 TAATTTATAGGATTTGGAATTTATGACG
*
1147794 TAATTTATATGATTTGGA
1 TAATTTATAGGATTTGGA
1147812 CTAATTTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (28 bp):
TAATTTATAGGATTTGGAATTTATGACG
Found at i:1148044 original size:3 final size:3
Alignment explanation
Indices: 1148036--1148099 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
1148026 ACCATTATAT
** *
1148036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA AAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1148084 TTA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA
1148100 CAAACCCAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1148156 original size:18 final size:18
Alignment explanation
Indices: 1148119--1148158 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1148109 TACCTAACAT
* *
1148119 CCAAACCCAAACCCTGGC
1 CCAAACCAAAACCCTAGC
*
1148137 CCAAACCAAAACCTTAGC
1 CCAAACCAAAACCCTAGC
1148155 CCAA
1 CCAA
1148159 CACCTAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.45, G:0.07, T:0.07
Consensus pattern (18 bp):
CCAAACCAAAACCCTAGC
Found at i:1148883 original size:19 final size:19
Alignment explanation
Indices: 1148856--1148892 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1148846 TCAGCCGAGC
*
1148856 AGAGGAAAAGAGAGAGTTG
1 AGAGAAAAAGAGAGAGTTG
*
1148875 AGAGAAAAAGGGAGAGTT
1 AGAGAAAAAGAGAGAGTT
1148893 TTTTTGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.11
Consensus pattern (19 bp):
AGAGAAAAAGAGAGAGTTG
Found at i:1162296 original size:79 final size:79
Alignment explanation
Indices: 1162201--1162371 Score: 256
Period size: 79 Copynumber: 2.2 Consensus size: 79
1162191 AGAAGTTCAA
* *
1162201 AATGAGAAGAACTTATTTAACCTTAGCTAGATTCCATCATAG-AATGAGGTTG-ATCAACATTTC
1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAAT-AGG-TGAATCAACATTTC
1162264 CAATGGAAGGGTTCGT
64 CAATGGAAGGGTTCGT
* * *
1162280 AATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAATATGTGAATCAATATTTCCA
1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA
1162345 ATGGAAGGGTTCGT
66 ATGGAAGGGTTCGT
*
1162359 AATAAGAAGAACT
1 AATGAGAAGAACT
1162372 CGTCCTATGA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
78 2 0.02
79 79 0.94
80 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (79 bp):
AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA
ATGGAAGGGTTCGT
Found at i:1162678 original size:115 final size:118
Alignment explanation
Indices: 1162274--1162689 Score: 577
Period size: 118 Copynumber: 3.6 Consensus size: 118
1162264 CAATGGAAGG
* * ** * * *
1162274 GTTCGTAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAATATGTGAATCAATA
1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA
* * *
1162339 TTTCCAATGGAAGGGTTCGTAATAAGAAGAACTCGTCCTATGAGGGAGAAGAA
66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
* * * * *
1162392 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCATAGAATGAGGAGGGTTAACA
1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA
*
1162457 TTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
* *
1162510 GTTCACAATGAGAAGAACTTATTCAACCTTATCTCAATTCCATCACAGAAGGAGGTGGATCAACA
1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA
* *
1162575 TTTCTAATAGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAG-A-AA
66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
* * * * * *
1162626 -TTCGTAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCATATAAGGAGTTGGAACAACA
1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA
1162690 CAATCTTGGC
Statistics
Matches: 265, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
115 56 0.21
116 2 0.01
117 1 0.00
118 206 0.78
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (118 bp):
GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA
TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA
Found at i:1163061 original size:23 final size:23
Alignment explanation
Indices: 1163035--1163079 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1163025 TATTTTATTT
*
1163035 TATTATTATTATTTATTACAAAA
1 TATTATTATTATTTATGACAAAA
1163058 TATTATTATTATTTATGACAAA
1 TATTATTATTATTTATGACAAA
1163080 CCCAATACCC
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:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTATTATTATTTATGACAAAA
Found at i:1163070 original size:3 final size:3
Alignment explanation
Indices: 1162974--1163052 Score: 83
Period size: 3 Copynumber: 26.3 Consensus size: 3
1162964 TTTTTCAACC
* *
1162974 ATT A-T ATT ATT ATT ATT ATAA AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
*
1163019 ATAA ATT ATT -TT ATT -TT ATT ATT ATT ATTT ATT A
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
1163053 CAAAATATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 6 0.09
3 52 0.81
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1163846 original size:19 final size:19
Alignment explanation
Indices: 1163819--1163855 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1163809 TCGATTGAGC
*
1163819 AGAGGAAAAGAGAGAGTTG
1 AGAGAAAAAGAGAGAGTTG
*
1163838 AGAGAAAAAGGGAGAGTT
1 AGAGAAAAAGAGAGAGTT
1163856 TTTTTAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.11
Consensus pattern (19 bp):
AGAGAAAAAGAGAGAGTTG
Found at i:1169181 original size:51 final size:51
Alignment explanation
Indices: 1169126--1169252 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 51
1169116 ACGCATGGTA
* * * * *
1169126 AGGCGCGATGCATGGG-CTGCTCCTTACTGTCGTGTGACACACGCACCAAAT
1 AGGCGCGGTGCATGGGCCT-CGCCTTACTGTCATCTGACACAAGCACCAAAT
* * *
1169177 AGGCGCGGTGCATGGGCCTCGCCTTGCTGTCATCTGACACAAGCGCCAGAT
1 AGGCGCGGTGCATGGGCCTCGCCTTACTGTCATCTGACACAAGCACCAAAT
* * *
1169228 AGGCACGGTGCATGGGTCACGCCTT
1 AGGCGCGGTGCATGGGCCTCGCCTT
1169253 GTATAATTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 62 0.97
52 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20
Consensus pattern (51 bp):
AGGCGCGGTGCATGGGCCTCGCCTTACTGTCATCTGACACAAGCACCAAAT
Found at i:1169360 original size:29 final size:29
Alignment explanation
Indices: 1169309--1169375 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1169299 TATAAATATG
* * *
1169309 CTCTCAACCCGTAAACATTCACAACAATC
1 CTCTCAACCCGTAAAAATACACAACAAAC
1169338 CTCTCAACCCG-AAAAATCACACAACAAAC
1 CTCTCAACCCGTAAAAAT-ACACAACAAAC
*
1169367 CTTTCAACC
1 CTCTCAACC
1169376 GCTAAATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.40, C:0.39, G:0.03, T:0.18
Consensus pattern (29 bp):
CTCTCAACCCGTAAAAATACACAACAAAC
Found at i:1169465 original size:18 final size:21
Alignment explanation
Indices: 1169444--1169484 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1169434 TGTAAGGTAA
1169444 TTTTT-TAA-TATAT-AATAT
1 TTTTTATAATTATATGAATAT
1169462 TTTTTATAATTATATGAATAT
1 TTTTTATAATTATATGAATAT
1169483 TT
1 TT
1169485 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 5 0.25
21 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTATAATTATATGAATAT
Found at i:1174207 original size:23 final size:23
Alignment explanation
Indices: 1174181--1174231 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1174171 TAATTTTTAT
*
1174181 TATACACTAGATAAAATGATTAG
1 TATACACTAGATAAAATGATTAA
1174204 TATACACTAGATAAAATGATTAA
1 TATACACTAGATAAAATGATTAA
1174227 TATAC
1 TATAC
1174232 CAAATCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (23 bp):
TATACACTAGATAAAATGATTAA
Found at i:1175158 original size:13 final size:13
Alignment explanation
Indices: 1175142--1175193 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1175132 TAACTGCAAA
1175142 AAATAAAATAATT
1 AAATAAAATAATT
**
1175155 AAATAAAATACTAAA
1 AAATAAAATA--ATT
*
1175170 AAATTTAAATAATT
1 AAA-TAAAATAATT
1175184 AAATAAAATA
1 AAATAAAATA
1175194 CTAACAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 16 0.53
14 4 0.13
15 4 0.13
16 6 0.20
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1175179 original size:29 final size:29
Alignment explanation
Indices: 1175139--1175211 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
1175129 TTATAACTGC
*
1175139 AAAAAA-TAAAATAATTAAATAAAATACT
1 AAAAAATTTAAATAATTAAATAAAATACT
1175167 AAAAAATTTAAATAATTAAATAAAATACT
1 AAAAAATTTAAATAATTAAATAAAATACT
1175196 AACAAAATATTAAATA
1 AA-AAAAT-TTAAATA
1175212 GAATAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 6 0.15
29 23 0.56
30 5 0.12
31 7 0.17
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAAATTTAAATAATTAAATAAAATACT
Found at i:1175190 original size:21 final size:19
Alignment explanation
Indices: 1175140--1175193 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
1175130 TATAACTGCA
1175140 AAAAATAAAATAATTAAAT
1 AAAAATAAAATAATTAAAT
1175159 AAAATACTAAAA-AATTTAAAT
1 AAAA-A-TAAAATAA-TTAAAT
1175180 AATTAAATAAAATA
1 AA--AAATAAAATA
1175194 CTAACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 18 0.62
22 2 0.07
23 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATAAAATAATTAAAT
Found at i:1175491 original size:40 final size:41
Alignment explanation
Indices: 1175407--1175484 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
1175397 GTGTGTCAGT
* *
1175407 TGGCAGAAAGGCGTGGCCCATGCACCGTGCCTTACCCTACG
1 TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCTACG
* *
1175448 TGGCA-AAAGGCATGTCCCATGCATCGCGCCTTACCCT
1 TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCT
1175485 GTGTGGCGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.19
Consensus pattern (41 bp):
TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCTACG
Found at i:1182879 original size:78 final size:79
Alignment explanation
Indices: 1182685--1182873 Score: 326
Period size: 78 Copynumber: 2.4 Consensus size: 79
1182675 GCGAAACATT
* * *
1182685 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTTGACAATGTACCCATATACATT
1 CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT
1182750 TCAGCTATGGCATC
66 TCAGCTATGGCATC
* *
1182764 ATTTCATGCCAATAATGC-ACCATATGAATTATTCCTTTATGCTGACAATGTACCCATATACATT
1 CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT
1182828 TCAGCTATGGCATC
66 TCAGCTATGGCATC
1182842 CTTTCATGCCAATAATGCAACCATATGCATTA
1 CTTTCATGCCAATAATGCAACCATATGCATTA
1182874 CCCTTTTTCA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 73 0.72
79 29 0.28
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (79 bp):
CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT
TCAGCTATGGCATC
Found at i:1183313 original size:20 final size:22
Alignment explanation
Indices: 1183290--1183336 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1183280 TCAAAGTATC
*
1183290 GATACTACTACCCT-A-GTACT
1 GATACTACTACACTAAGGTACT
*
1183310 GATACTTCTACACTAAGGTACT
1 GATACTACTACACTAAGGTACT
1183332 GATAC
1 GATAC
1183337 CCCTTCCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 1 0.04
22 10 0.43
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (22 bp):
GATACTACTACACTAAGGTACT
Found at i:1183448 original size:19 final size:22
Alignment explanation
Indices: 1183399--1183450 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
1183389 CCCTCTATGT
*
1183399 GGTATCGATACTACCCTTCTAT
1 GGTATCGATACTACCCTTCTAC
*
1183421 GGTACCGATACT-CCC-T-TAC
1 GGTATCGATACTACCCTTCTAC
1183440 GGTATCGATAC
1 GGTATCGATAC
1183451 CGAAATTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 1 0.04
21 3 0.11
22 11 0.41
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTACCCTTCTAC
Found at i:1189671 original size:34 final size:34
Alignment explanation
Indices: 1189633--1189831 Score: 101
Period size: 34 Copynumber: 5.2 Consensus size: 34
1189623 TCAGCGAGGC
1189633 ATTCTTTCATGCCAATAATGCACCCATATGCATT
1 ATTCTTTCATGCCAATAATGCACCCATATGCATT
* ** * * *
1189667 ATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCT
1 ATTCTTTCATGCCAATAATGCACCCATATGCA--T----T
1189707 ATGTCATCATTTCATGCCAATAATGCACCCATATGCATT
1 A--T--TC-TTTCATGCCAATAATGCACCCATATGCATT
* ** * *
1189746 ATTCTTTTATGCTGACAATGCACCCATATACATTTCAACT
1 ATTCTTTCATGCCAATAATGCACCCATATGCA--T----T
1189786 ATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
1 AT----T-CTTTCATGCCAATAATGCACCCATATGCATT
1189825 ATTCTTT
1 ATTCTTT
1189832 TATGTTGAAA
Statistics
Matches: 121, Mismatches: 22, Indels: 44
0.65 0.12 0.24
Matches are distributed among these distances:
34 53 0.44
35 3 0.02
36 2 0.02
37 1 0.01
39 5 0.04
40 5 0.04
42 1 0.01
43 2 0.02
44 3 0.02
45 46 0.38
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (34 bp):
ATTCTTTCATGCCAATAATGCACCCATATGCATT
Found at i:1189889 original size:157 final size:158
Alignment explanation
Indices: 1189585--1189910 Score: 503
Period size: 157 Copynumber: 2.1 Consensus size: 158
1189575 TTCCATTTAA
* * * * * * *
1189585 ATTATACTTTTATTTCTGATAATGCACCCCTACGCATTTCAGCGAGGCATTCTTTCATGCCAATA
1 ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGAGGCATCCTTTCATGCCAATA
*
1189650 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGTCATC
66 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATC
1189715 ATTTCATGCCAATAATGCACCCATATGC
131 ATTTCATGCCAATAATGCACCCATATGC
* *
1189743 ATTATTCTTTTA-TGCTGACAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAAT
1 ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGA-GGCATCCTTTCATGCCAAT
*
1189807 AATGCACCCATATGCATTATTCTTTTATGTTGA-AATGTACCCATATACATTTCAGCTATGGCAT
65 AATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCAT
* *
1189871 CCTTTCATTCCAATAATGCACCCATATGC
130 CATTTCATGCCAATAATGCACCCATATGC
*
1189900 ATTACTCTTTT
1 ATTATTCTTTT
1189911 TCATTCATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
157 92 0.60
158 61 0.40
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (158 bp):
ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGAGGCATCCTTTCATGCCAATA
ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATC
ATTTCATGCCAATAATGCACCCATATGC
Found at i:1189930 original size:78 final size:79
Alignment explanation
Indices: 1189619--1189910 Score: 489
Period size: 79 Copynumber: 3.7 Consensus size: 79
1189609 CACCCCTACG
* *
1189619 CATTTCAGCGA-GGCATTCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
1189683 AATGTACCCATATA
66 AATGTACCCATATA
* *
1189697 CATTTCAGCTATGTCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
*
1189762 AATGCACCCATATA
66 AATGTACCCATATA
* *
1189776 CATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTTGA-
1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
1189840 AATGTACCCATATA
66 AATGTACCCATATA
* *
1189854 CATTTCAGCTATGGCATCCTTTCATTCCAATAATGCACCCATATGCATTACTCTTTT
1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
1189911 TCATTCATTT
Statistics
Matches: 200, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 77 0.38
79 123 0.62
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (79 bp):
CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC
AATGTACCCATATA
Found at i:1190551 original size:94 final size:94
Alignment explanation
Indices: 1190379--1190556 Score: 209
Period size: 94 Copynumber: 1.9 Consensus size: 94
1190369 CCTTCCTGGC
* * * *
1190379 ATCGATACCAAAATTAGGTTGATGTTTCATGGTATCGATACCCTCTACGTGGTATTGATACTACC
1 ATCGATACCAAAATTAGATTGATGTTTCATGGTATCGATACCCTCTACATAGTATCGATACTACC
* ***
1190444 CTTCTATGGTATCGATACTCCCTTAAGGT
66 CTTCAACAATATCGATACTCCCTTAAGGT
* * *
1190473 ATCGATACCGAAATTAGATTCGATGTTTGCTTGGTATCGATACCCTTTTA-ATAGTATCGATACT
1 ATCGATACCAAAATTAGATT-GATGTTT-CATGGTATCGATACCC-TCTACATAGTATCGATACT
1190537 A-CC-TCAACAATATCGATACT
63 ACCCTTCAACAATATCGATACT
1190557 GATTGAAACA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
94 31 0.44
95 9 0.13
96 27 0.39
97 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (94 bp):
ATCGATACCAAAATTAGATTGATGTTTCATGGTATCGATACCCTCTACATAGTATCGATACTACC
CTTCAACAATATCGATACTCCCTTAAGGT
Found at i:1193813 original size:2 final size:2
Alignment explanation
Indices: 1193806--1193841 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1193796 TGTGTAATTA
1193806 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
1193842 TTACACATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1194727 original size:21 final size:21
Alignment explanation
Indices: 1194701--1194800 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 21
1194691 GTATCGAATA
**
1194701 AGTTGGTATTGATACCAGATG
1 AGTTGGTATCAATACCAGATG
*
1194722 AGTTGGTATCAATACCAGATA
1 AGTTGGTATCAATACCAGATG
* * * * *
1194743 AATTGATGTCCATACCATATG
1 AGTTGGTATCAATACCAGATG
* * * *
1194764 AATTAGTATCCATAACAGATG
1 AGTTGGTATCAATACCAGATG
*
1194785 AGTTGGTATCCATACC
1 AGTTGGTATCAATACC
1194801 GTGTCGAAAT
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTTGGTATCAATACCAGATG
Found at i:1194797 original size:42 final size:42
Alignment explanation
Indices: 1194698--1194800 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 42
1194688 GATGTATCGA
** * * *
1194698 ATAAGTTGGTATTGATACCAGATGAGTTGGTATCAATACCAG
1 ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG
* * * * *
1194740 ATAAATTGATGTCCATACCATATGAATTAGTATCCATAACAG
1 ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG
*
1194782 ATGAGTTGGTATCCATACC
1 ATAAGTTGGTATCCATACC
1194801 GTGTCGAAAT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (42 bp):
ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG
Found at i:1202795 original size:74 final size:74
Alignment explanation
Indices: 1202595--1203170 Score: 487
Period size: 74 Copynumber: 8.0 Consensus size: 74
1202585 GGTAGTAAAA
* ** * * *
1202595 TGTCTCGACTGAGATGAAAGTTGTTTTAAGGCAAACTATCTCAAGTGACATAAAATTTTTGTTTC
1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC
*
1202660 AGGAGAAAC
66 AAGAGAAAC
** * * * * * * *
1202669 AATCTTGATTGAGACAAAATTTGTTTTAAAGG-AAATTTTCTTAAGAGAGATAAAATTTTTGTTT
1 TGTCTCGAGTGAGACAAAACTTGTTTT-AAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT
*
1202733 CGAGAGAAAC
65 CAAGAGAAAC
* **
1202743 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAAATATCTCAAGTTTGATAAAATTTTTGTTTC
1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC
* * **
1202808 GAG-GTGAGT
66 AAGAG-AAAC
*
1202817 TGTCTCGAGTGAGA-AGAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAGAATTTTTGTTT
1 TGTCTCGAGTGAGACA-AAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT
1202881 CAA-ATGAAAC
65 CAAGA-GAAAC
* * *
1202891 TGTCTC----GAGACACAACTTGTTTTAAGG-----GA----AAGTGAGACAAAATTTTTGTTTC
1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC
* ** *
1202943 TATTGAAAA
66 AAGAGAAAC
* *
1202952 TGTCTCGAGTGAGACGAAA-TTGATTTTAAGGAAAATTATCTCAAGTGAGATAAAATTTTTGTTT
1 TGTCTCGAGTGAGACAAAACTTG-TTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT
*
1203016 CAAAAGAAAC
65 CAAGAGAAAC
* * * * * *
1203026 TGTCTTGAGTTAGA-AGAAATTTGTTTTAAAGAAAACTATGTGAAGTGAGATAAAATTTTTGTTT
1 TGTCTCGAGTGAGACA-AAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT
*
1203090 TAAGA-AAAC
65 CAAGAGAAAC
* * * * *
1203099 TATCTCGAG-GAGACGAAATTTG-TTTAATGAAAA-TCATCTTAAGTGAGATAAAAATATTTTGT
1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACT-ATCTCAAGTGAGAT-AAAAT-TTTTGT
1203161 TTCAAGAGAA
63 TTCAAGAGAA
1203171 TCTATCTCAA
Statistics
Matches: 405, Mismatches: 68, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
61 32 0.08
64 3 0.01
65 16 0.04
70 20 0.05
71 23 0.06
72 15 0.04
73 29 0.07
74 259 0.64
75 8 0.02
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (74 bp):
TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC
AAGAGAAAC
Found at i:1203188 original size:40 final size:37
Alignment explanation
Indices: 1203071--1203210 Score: 101
Period size: 40 Copynumber: 3.7 Consensus size: 37
1203061 CTATGTGAAG
* * *
1203071 TGAGATAAAATTTTTGTTTTAAGA-AAACTATCTC-GA
1 TGAGATAAAATTTTTGTTTCAAGAGAATC-ATCTCAAA
* ** * * *
1203107 GGAGACGAAA--TTTGTTT-AATGAAAATCATCTTAAG
1 TGAGATAAAATTTTTGTTTCAA-GAGAATCATCTCAAA
1203142 TGAGATAAAAATATTTTGTTTCAAGAGAATCTATCTCAAA
1 TGAGAT-AAAAT-TTTTGTTTCAAGAGAATC-ATCTCAAA
1203182 TGAGATAAAATTTTTGTTTCTGAAGAGAA
1 TGAGATAAAATTTTTGTTTC--AAGAGAA
1203211 CCTCTTAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
33 2 0.03
34 13 0.16
35 7 0.09
36 10 0.12
38 9 0.11
39 18 0.22
40 21 0.26
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (37 bp):
TGAGATAAAATTTTTGTTTCAAGAGAATCATCTCAAA
Found at i:1203192 original size:39 final size:38
Alignment explanation
Indices: 1203117--1203210 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 38
1203107 GGAGACGAAA
* * *
1203117 TTTGTTT-AATGAAAATCATCTTAAGTGAGATAAAAATAT
1 TTTGTTTCAA-GAGAATCATCTCAAATGAGATAAAAAT-T
1203156 TTTGTTTCAAGAGAATCTATCTCAAATGAGAT-AAAATT
1 TTTGTTTCAAGAGAATC-ATCTCAAATGAGATAAAAATT
1203194 TTTGTTTCTGAAGAGAA
1 TTTGTTTC--AAGAGAA
1203211 CCTCTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 9 0.19
39 18 0.38
40 21 0.44
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (38 bp):
TTTGTTTCAAGAGAATCATCTCAAATGAGATAAAAATT
Found at i:1204185 original size:15 final size:16
Alignment explanation
Indices: 1204150--1204185 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1204140 AAAAAGTAGT
1204150 GCAAAAAGTGTTTCCC
1 GCAAAAAGTGTTTCCC
1204166 GCAAAAAGTGTTTCCC
1 GCAAAAAGTGTTTCCC
1204182 -CAAA
1 GCAAA
1204186 GATGAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (16 bp):
GCAAAAAGTGTTTCCC
Found at i:1205580 original size:21 final size:21
Alignment explanation
Indices: 1205556--1205603 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1205546 TTAAATGTCC
*
1205556 TGCAAAATACAAAGATGTAAA
1 TGCAAAATACAAAGATGCAAA
* *
1205577 TGCAGAATACAAAGATGCAAG
1 TGCAAAATACAAAGATGCAAA
1205598 TGCAAA
1 TGCAAA
1205604 TGTAAATGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (21 bp):
TGCAAAATACAAAGATGCAAA
Found at i:1208028 original size:16 final size:14
Alignment explanation
Indices: 1208007--1208048 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1207997 TAAAAACGAA
1208007 GAAAATAATAAATAG
1 GAAAAT-ATAAATAG
1208022 TGAAAATATAAA-AG
1 -GAAAATATAAATAG
1208036 GAAAATGATAAAT
1 GAAAAT-ATAAAT
1208049 GAAAAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.25
14 7 0.29
15 5 0.21
16 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
GAAAATATAAATAG
Found at i:1208116 original size:26 final size:24
Alignment explanation
Indices: 1208087--1208148 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
1208077 AAAATATGTA
*
1208087 AATATATATAATATAATATGATACAT
1 AATATATATAATATAATAT-A-AAAT
*
1208113 AATA-A-ATATTATAATATAAAAT
1 AATATATATAATATAATATAAAAT
1208135 -ATATATATAATATA
1 AATATATATAATATA
1208149 GAAAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 3 0.10
22 4 0.13
23 8 0.26
24 11 0.35
25 1 0.03
26 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATATATAATATAATATAAAAT
Found at i:1212670 original size:31 final size:31
Alignment explanation
Indices: 1212571--1212674 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
1212561 GTCGGTGCTA
* **
1212571 AACCTATACAAGGAATTACCAACAACGACTG
1 AACCTATACAATGAATTACCAACAGGGACTG
* *
1212602 AACCTGCTAGAGATAAGGAATTACCAATC-GGTG-CTG
1 AACCT-ATACA-AT---GAATTACCAA-CAGG-GACTG
1212638 AACCTATACAATGAATTACCAACAGGGACTG
1 AACCTATACAATGAATTACCAACAGGGACTG
1212669 AACCTA
1 AACCTA
1212675 CAAAGTCTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
30 2 0.04
31 26 0.46
32 3 0.05
33 1 0.02
34 2 0.04
35 3 0.05
36 18 0.32
37 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (31 bp):
AACCTATACAATGAATTACCAACAGGGACTG
Found at i:1219666 original size:27 final size:27
Alignment explanation
Indices: 1219621--1219672 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1219611 TCCTAACAAG
*
1219621 TTTGACCAATTGAATAAGTTTGATAAA
1 TTTGACCAATTGAACAAGTTTGATAAA
1219648 TTTGACCAATTTG-ACAAGTTTGATA
1 TTTGACCAA-TTGAACAAGTTTGATA
1219673 TGCAAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (27 bp):
TTTGACCAATTGAACAAGTTTGATAAA
Found at i:1221965 original size:23 final size:23
Alignment explanation
Indices: 1221939--1222002 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
1221929 ATGTTGTGAG
*
1221939 TTCTAGAATAGTTTGTTAGTTAA
1 TTCTAGAATAGTTTGTTAGCTAA
1221962 TTCTAGAATAGTTTGTTAGCTAA
1 TTCTAGAATAGTTTGTTAGCTAA
1221985 TTCTAGAATAGTTTGTTA
1 TTCTAGAATAGTTTGTTA
1222003 TCTTGTAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (23 bp):
TTCTAGAATAGTTTGTTAGCTAA
Found at i:1226396 original size:23 final size:23
Alignment explanation
Indices: 1226368--1226422 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1226358 CCTGGTTTTG
1226368 TGCAAGCTGGTGATGGTTTAGTT
1 TGCAAGCTGGTGATGGTTTAGTT
1226391 TGCAAGCTGGTGATGGTTTAGTT
1 TGCAAGCTGGTGATGGTTTAGTT
1226414 TGCAAGCTG
1 TGCAAGCTG
1226423 CATAAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.11, G:0.35, T:0.36
Consensus pattern (23 bp):
TGCAAGCTGGTGATGGTTTAGTT
Found at i:1233936 original size:22 final size:22
Alignment explanation
Indices: 1233901--1233954 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1233891 ACTTATGATG
*
1233901 GTATCGATACCGTAGTTCAGAA
1 GTATCGGTACCGTAGTTCAGAA
*
1233923 GTATCGGTATCGTAGTTCAGAA
1 GTATCGGTACCGTAGTTCAGAA
1233945 GTATCGGTAC
1 GTATCGGTAC
1233955 TTTAGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (22 bp):
GTATCGGTACCGTAGTTCAGAA
Found at i:1235751 original size:14 final size:14
Alignment explanation
Indices: 1235732--1235763 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1235722 GTATGAGCAG
*
1235732 GAGTTCATTTGAAT
1 GAGTTCATTCGAAT
1235746 GAGTTCATTCGAAT
1 GAGTTCATTCGAAT
1235760 GAGT
1 GAGT
1235764 AGATACACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (14 bp):
GAGTTCATTCGAAT
Found at i:1237742 original size:17 final size:17
Alignment explanation
Indices: 1237717--1237758 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1237707 TCCATGATAG
*
1237717 CTACCTCAATGACTAAA
1 CTACTTCAATGACTAAA
1237734 CTACTTCAATGACTAAA
1 CTACTTCAATGACTAAA
1237751 CTACTTCA
1 CTACTTCA
1237759 GAAGGGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.29
Consensus pattern (17 bp):
CTACTTCAATGACTAAA
Found at i:1249560 original size:22 final size:22
Alignment explanation
Indices: 1249532--1249583 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1249522 ACTCTCTTTC
1249532 TATATATACATACATACATACA
1 TATATATACATACATACATACA
* *
1249554 TATATATACATATATATATACA
1 TATATATACATACATACATACA
1249576 TATATATA
1 TATATATA
1249584 TATATAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATATACATACATACATACA
Found at i:1249582 original size:4 final size:4
Alignment explanation
Indices: 1249532--1249616 Score: 107
Period size: 4 Copynumber: 21.2 Consensus size: 4
1249522 ACTCTCTTTC
* * * * * *
1249532 TATA TATA CATA CATA CATA CATA TATA TACA TATA TATA TACA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
1249580 TATA TATA TAGA TATA TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA T
1249617 CACTGTTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:1254380 original size:2 final size:2
Alignment explanation
Indices: 1254373--1254399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1254363 AGGGATTCAC
1254373 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1254400 TAATCACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1266248 original size:20 final size:20
Alignment explanation
Indices: 1266220--1266261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1266210 AGGTGTTATG
1266220 ATGAATTTTTA-AAGTTTTTA
1 ATGAATTTTTATAA-TTTTTA
*
1266240 ATGATTTTTTATAATTTTTA
1 ATGAATTTTTATAATTTTTA
1266260 AT
1 AT
1266262 TCATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
ATGAATTTTTATAATTTTTA
Found at i:1266865 original size:87 final size:87
Alignment explanation
Indices: 1266768--1266941 Score: 287
Period size: 87 Copynumber: 2.0 Consensus size: 87
1266758 AAGAGGGAGT
* * *
1266768 TGAACATTTTCATACTTTTTTCGACAATTGGTATCTTTTTCATTAAATATTTTAATAAGGG-GAG
1 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTT-ATTAAATAATTTAATAAGGGAGAG
1266832 TTTTGCCAAAAACAATTTTTCAA
65 TTTTGCCAAAAACAATTTTTCAA
*
1266855 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTATTAAGGGAGAGT
1 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTAATAAGGGAGAGT
*
1266920 TTTGCCAAAAATAATTTTTCAA
66 TTTGCCAAAAACAATTTTTCAA
1266942 ATGTTTTGTT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 18 0.22
87 63 0.78
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (87 bp):
TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTAATAAGGGAGAGT
TTTGCCAAAAACAATTTTTCAA
Found at i:1271146 original size:32 final size:31
Alignment explanation
Indices: 1271071--1271219 Score: 131
Period size: 31 Copynumber: 4.7 Consensus size: 31
1271061 TCAACCTAAG
* * * *
1271071 GGAATGCCTTGGGGTCTTAGAGCATACCC-AA
1 GGAATACCTTGGGGCCTGAGAGC-GACCCAAA
* * * *
1271102 GAAATATCTTGGGGCCTCAGAGTCGACCCAAT
1 GGAATACCTTGGGGCCTGAGAG-CGACCCAAA
* *
1271134 GGAGTACCTTGGGGCCTGAGAGCCTA-CCAAA
1 GGAATACCTTGGGGCCTGAGAG-CGACCCAAA
1271165 GGAATACCTTGGGGCCTGAGAGCTGACCCAAA
1 GGAATACCTTGGGGCCTGAGAGC-GACCCAAA
* * *
1271197 GGAATATCTCGGGGCCTAAGAGC
1 GGAATACCTTGGGGCCTGAGAGC
1271220 CTACCTAAGA
Statistics
Matches: 95, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 47 0.49
32 47 0.49
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (31 bp):
GGAATACCTTGGGGCCTGAGAGCGACCCAAA
Found at i:1271176 original size:63 final size:63
Alignment explanation
Indices: 1271071--1271229 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 63
1271061 TCAACCTAAG
* * * * * * *
1271071 GGAATGCCTTGGGGTCTTAGAGCATACCCAAGAAATATCTTGGGGCCTCAGAG-TCGACCCAAT
1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCT-GACCCAAA
* * * *
1271134 GGAGTACCTTGGGGCCTGAGAGCCTACCAAAGGAATACCTTGGGGCCTGAGAGCTGACCCAAA
1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCTGACCCAAA
* * *
1271197 GGAATATCTCGGGGCCTAAGAGCCTACCTAAGA
1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGA
1271230 GTCACCTTAG
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
63 78 0.99
64 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.19
Consensus pattern (63 bp):
GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCTGACCCAAA
Found at i:1277079 original size:20 final size:20
Alignment explanation
Indices: 1277032--1277403 Score: 304
Period size: 20 Copynumber: 18.2 Consensus size: 20
1277022 AATGACCAAC
* *
1277032 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
1277051 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
1277071 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* * **
1277091 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
1277112 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
**
1277133 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1277154 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
1277175 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
*
1277195 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
1277215 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1277236 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
1277257 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* **
1277277 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1277298 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
1277319 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
1277339 AGAATCGCAACGCGATCTT-C
1 AAAATCGCAACGCGAT-TTAG
* *
1277359 CAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
*
1277379 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
1277399 AAAAT
1 AAAAT
1277404 GAGTAAATTC
Statistics
Matches: 286, Mismatches: 50, Indels: 33
0.78 0.14 0.09
Matches are distributed among these distances:
19 19 0.07
20 187 0.65
21 27 0.09
22 53 0.19
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1277142 original size:62 final size:61
Alignment explanation
Indices: 1277035--1277400 Score: 388
Period size: 62 Copynumber: 6.0 Consensus size: 61
1277025 GACCAACAAA
* * * * * *
1277035 ATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATAAGAAG
* * * * ***
1277094 ATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TAAGAAG
* * * *
1277157 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA
1 -ATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAGAAG
***
1277218 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG
***
1277279 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 -ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG
1277341 AATCGCAACGCGATCTTCC-A-AATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAGAA
1 -ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAGAA
1277401 AATGAGTAAA
Statistics
Matches: 265, Mismatches: 30, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
59 12 0.05
60 46 0.17
61 17 0.06
62 174 0.66
63 5 0.02
64 11 0.04
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (61 bp):
ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG
Found at i:1277201 original size:82 final size:81
Alignment explanation
Indices: 1277115--1277394 Score: 354
Period size: 82 Copynumber: 3.4 Consensus size: 81
1277105 ATCTTCCAAG
* *
1277115 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
1277180 CGCAACGCGATTCAGAA
66 CGCAACGCGATTCA-AA
*
1277197 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
*
1277262 CGCAACGCGATTCCAAG
66 CGCAACGCGATT-CAAA
* ***
1277279 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCCA-A
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CAGA
* *
1277340 GAATCGCAACGCGATCTTC-CA
62 AAATCGCAACGCGA--TTCAAA
*
1277361 AATCGCAACGCGATTAAGAAAATCGCAACGCGAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGAT
1277395 TAAGAAAATG
Statistics
Matches: 176, Mismatches: 14, Indels: 18
0.85 0.07 0.09
Matches are distributed among these distances:
79 1 0.01
80 17 0.10
82 130 0.74
83 7 0.04
84 19 0.11
85 2 0.01
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (81 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
CGCAACGCGATTCAAA
Found at i:1277491 original size:20 final size:19
Alignment explanation
Indices: 1277468--1277519 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1277458 TTCTTTTCAA
* *
1277468 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
* *
1277488 CGTTGCGGTTTTGATATCG
1 CGTTGCGATTTTGAAATCG
1277507 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1277520 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:1283947 original size:55 final size:54
Alignment explanation
Indices: 1283888--1284191 Score: 279
Period size: 54 Copynumber: 5.5 Consensus size: 54
1283878 TAGAATTAAC
1283888 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAA-T
* ***
1283943 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-T---AGCCAAAAT
* ** * * * *
1284004 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
* * *
1284058 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTTTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAT
* * * * * ****
1284113 GATTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGTAGCCAAAAT
*
1284167 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
1284192 TAAAATCAAG
Statistics
Matches: 204, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
53 1 0.00
54 72 0.35
55 70 0.34
56 14 0.07
57 1 0.00
58 2 0.01
59 1 0.00
61 38 0.19
62 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
Found at i:1283986 original size:27 final size:27
Alignment explanation
Indices: 1283895--1283987 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
1283885 AACGATTGAG
*
1283895 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
* ** * *
1283922 CACCTCTGTG-TAGCCAAAAGTG-ATTGA
1 CACCTCTGTGCT--TCAATCGAGAACTGA
1283949 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
1283977 CACCTCTGTGC
1 CACCTCTGTGC
1283988 AGTTAAAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
26 1 0.02
27 29 0.58
28 19 0.38
29 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:1284095 original size:27 final size:28
Alignment explanation
Indices: 1284061--1284137 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
1284051 CTAAGATGAT
1284061 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAC
* ** * * *
1284089 TGA-CACCTTTGTGCAGCCAA-CTATGAT
1 TGAGCACCTCTGTGC-TTCAATCGAGGAC
1284116 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
1284138 TAAATTCTGG
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGGAC
Found at i:1284095 original size:54 final size:55
Alignment explanation
Indices: 1283888--1284137 Score: 236
Period size: 55 Copynumber: 4.5 Consensus size: 55
1283878 TAGAATTAAC
* * * *
1283888 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAA-AAGT
1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGA-T
* * * ** **
1283943 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAG------CCAACGAT
* ** * *
1284004 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAA-GAT
1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGAT
* * *
1284058 GATTGAGCACCTCTGTGCTTCAATCGAGGA-CTGACACCTTTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCG-GGAGCTAACACCTCTGTGCAGCCAACGAT
1284113 GATTGAGCACCTCTGTGCTTCAATC
1 GATTGAGCACCTCTGTGCTTCAATC
1284138 TAAATTCTGG
Statistics
Matches: 164, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
54 42 0.26
55 77 0.47
61 43 0.26
62 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGAT
Found at i:1284096 original size:115 final size:116
Alignment explanation
Indices: 1283891--1284104 Score: 349
Period size: 115 Copynumber: 1.9 Consensus size: 116
1283881 AATTAACGAT
* *
1283891 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1283956 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC
* * * *
1284007 TGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
* *
1284071 TGTGCTTCAATCGAGGACTGACACCTTTGTGCAG
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG
1284105 CCAACTATGA
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
115 46 0.51
116 44 0.49
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (116 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC
Found at i:1285046 original size:37 final size:36
Alignment explanation
Indices: 1285000--1285078 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
1284990 ATATATATAT
* * *
1285000 ATATATATAATAATTATTAAATTTACTCTCTCAAAAA
1 ATATATATAAAAACTATTAAATTTAAT-TCTCAAAAA
*
1285037 ATATGTATAAAAACTATTAAATTTAATTCTCAAAAA
1 ATATATATAAAAACTATTAAATTTAATTCTCAAAAA
1285073 AT-TATA
1 ATATATA
1285079 CTATTTTAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.08
36 11 0.30
37 23 0.62
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (36 bp):
ATATATATAAAAACTATTAAATTTAATTCTCAAAAA
Found at i:1285227 original size:17 final size:18
Alignment explanation
Indices: 1285205--1285253 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1285195 TTCTTTGTTT
*
1285205 AGTTGTTCATCTT-TTTG
1 AGTTGTTCATCTTCATTG
*
1285222 AGTTGTTTATCTTCATTG
1 AGTTGTTCATCTTCATTG
*
1285240 AGTTGATCAT-TTCA
1 AGTTGTTCATCTTCA
1285254 ATCAAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.53
Consensus pattern (18 bp):
AGTTGTTCATCTTCATTG
Found at i:1286230 original size:24 final size:24
Alignment explanation
Indices: 1286201--1286248 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1286191 TCGATAATCC
*
1286201 GTTTGTTTATATTCATTCGTTTAT
1 GTTTGTTTATATTCATTCATTTAT
* *
1286225 GTTTGTTTATGTTCGTTCATTTAT
1 GTTTGTTTATATTCATTCATTTAT
1286249 ATTTAGCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (24 bp):
GTTTGTTTATATTCATTCATTTAT
Found at i:1287650 original size:22 final size:23
Alignment explanation
Indices: 1287625--1287671 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1287615 AAGATAAATG
*
1287625 AACATGCCA-AAAAGCAGAAGAA
1 AACATGCCATAAAAACAGAAGAA
* *
1287647 AACATGTCATAAAAACAGATGAA
1 AACATGCCATAAAAACAGAAGAA
1287670 AA
1 AA
1287672 TGTGCAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.11
Consensus pattern (23 bp):
AACATGCCATAAAAACAGAAGAA
Found at i:1291840 original size:21 final size:20
Alignment explanation
Indices: 1291802--1291840 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1291792 TAATGGATGG
*
1291802 TTGTTTTTATATGTTGTTAT
1 TTGTTTTTATATGATGTTAT
*
1291822 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TATATGATGTT
1291841 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.13, C:0.00, G:0.18, T:0.69
Consensus pattern (20 bp):
TTGTTTTTATATGATGTTAT
Found at i:1292442 original size:19 final size:21
Alignment explanation
Indices: 1292399--1292443 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1292389 CTAAATTTAC
1292399 TTTTGCCAAGACATTTCTATCCA
1 TTTTGCCAAGACA-TTC-ATCCA
1292422 TTTTGCCAAGACA-TC-TCCA
1 TTTTGCCAAGACATTCATCCA
1292441 TTT
1 TTT
1292444 GCTGCCGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
21 2 0.09
23 13 0.59
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGCCAAGACATTCATCCA
Found at i:1294020 original size:20 final size:20
Alignment explanation
Indices: 1293995--1294033 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1293985 TAGGATTCTT
*
1293995 GATTTT-AATATATAGGATGG
1 GATTTTGAAGATA-AGGATGG
1294015 GATTTTGAAGATAAGGATG
1 GATTTTGAAGATAAGGATG
1294034 TGTTAGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (20 bp):
GATTTTGAAGATAAGGATGG
Done.