Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 20
Found at i:1661303 original size:22 final size:22
Alignment explanation
Indices: 1661278--1661322 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1661268 AATATGGGAA
1661278 ACTTATAAGTATGATATATTCT
1 ACTTATAAGTATGATATATTCT
**
1661300 ACTTATTTGTATGATATATTCT
1 ACTTATAAGTATGATATATTCT
1661322 A
1 A
1661323 TGGGAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
ACTTATAAGTATGATATATTCT
Found at i:1661549 original size:19 final size:19
Alignment explanation
Indices: 1661525--1661570 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1661515 ATTTATATTT
*
1661525 ATAAATTTCATAAAATATA
1 ATAAATTACATAAAATATA
1661544 ATAAATTACATAAAATATA
1 ATAAATTACATAAAATATA
1661563 ATAAATTA
1 ATAAATTA
1661571 TATGTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATTACATAAAATATA
Found at i:1665388 original size:21 final size:21
Alignment explanation
Indices: 1665353--1665394 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1665343 AAAATATATA
1665353 ATATATATAGTTTTTGAAAAT
1 ATATATATAGTTTTTGAAAAT
1665374 ATATAGTATAGTTTTTGAAAA
1 ATATA-TATAGTTTTTGAAAA
1665395 CACAGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTTTGAAAAT
Found at i:1665426 original size:38 final size:37
Alignment explanation
Indices: 1665359--1665586 Score: 164
Period size: 38 Copynumber: 6.0 Consensus size: 37
1665349 TATAATATAT
1665359 ATAGTTTTTG-AAA-ATAT-ATAGTATAGTTTTTGAAAA
1 ATAG-TTTTGAAAACATATAATA-TATAGTTTTTGAAAA
* * *
1665395 CACAGTTTTGAAAACAAATAATATATAGTTTTCTTAAAA
1 -ATAGTTTTGAAAACATATAATATATAGTTTT-TGAAAA
* ** * *
1665434 ATTGTTTTTTAAACATTTTTTATATAATATAGTCTTTGAAAA
1 ATAGTTTTGAAAACA---TATA-AT-ATATAGTTTTTGAAAA
* *
1665476 CTATTTTTGAAAACATATAATATATAGTTTTT--AAA
1 ATAGTTTTGAAAACATATAATATATAGTTTTTGAAAA
* * *
1665511 ATGGTTTTTGAAAACATGTAATGTATAGTTTTT-AAAA
1 ATAG-TTTTGAAAACATATAATATATAGTTTTTGAAAA
*
1665548 ACTGGTTTTGGAAAACATAT-ATAATATAGTTTTTGAAAA
1 A-TAGTTTT-GAAAACATATAAT-ATATAGTTTTTGAAAA
1665587 TATATAGTAT
Statistics
Matches: 151, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
35 4 0.03
36 31 0.21
37 26 0.17
38 47 0.31
39 15 0.10
41 2 0.01
42 17 0.11
43 9 0.06
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (37 bp):
ATAGTTTTGAAAACATATAATATATAGTTTTTGAAAA
Found at i:1665585 original size:24 final size:24
Alignment explanation
Indices: 1665552--1665724 Score: 105
Period size: 22 Copynumber: 7.2 Consensus size: 24
1665542 TTAAAAACTG
*
1665552 GTTTTGGAAAACATATATAATATA
1 GTTTTTGAAAACATATATAATATA
*
1665576 GTTTTTG-AAA-ATATATAGTATA
1 GTTTTTGAAAACATATATAATATA
1665598 GTTTTTGAAAACATAT-T-ATATA
1 GTTTTTGAAAACATATATAATATA
**
1665620 GATTTTAAAAAAAACATATA-ATATATA
1 G-TTTT--TGAAAACATATATA-ATATA
* **
1665647 GTTTTT-AAAATCATATTGTTGTATA
1 GTTTTTGAAAA-CATA-TATAATATA
*
1665672 -ATTTTGAAAACATAT-T-ATAT-
1 GTTTTTGAAAACATATATAATATA
* *
1665692 GATTTTGAAAATATAATATATTATATA
1 GTTTTTGAAAACAT-ATATA--ATATA
1665719 GTTTTT
1 GTTTTT
1665725 TCTTTTAAAG
Statistics
Matches: 117, Mismatches: 13, Indels: 35
0.71 0.08 0.21
Matches are distributed among these distances:
21 15 0.13
22 26 0.22
23 17 0.15
24 22 0.19
25 18 0.15
26 8 0.07
27 11 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (24 bp):
GTTTTTGAAAACATATATAATATA
Found at i:1665633 original size:25 final size:26
Alignment explanation
Indices: 1665605--1665656 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
1665595 ATAGTTTTTG
1665605 AAAACATAT-TATATAGATTTTAAAA
1 AAAACATATATATATAGATTTTAAAA
*
1665630 AAAACATATAATATATAGTTTTTAAAA
1 AAAACATAT-ATATATAGATTTTAAAA
1665657 TCATATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAACATATATATATAGATTTTAAAA
Found at i:1666983 original size:18 final size:18
Alignment explanation
Indices: 1666959--1666998 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1666949 TTTTAATTTG
1666959 ATTTTTTTAAT-TCTTTT
1 ATTTTTTTAATATCTTTT
*
1666976 ATTTTTTTAATATTTTTT
1 ATTTTTTTAATATCTTTT
1666994 ATTTT
1 ATTTT
1666999 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTTTTAATATCTTTT
Found at i:1667006 original size:17 final size:16
Alignment explanation
Indices: 1666959--1667008 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1666949 TTTTAATTTG
*
1666959 ATTTTTTTAATTCTTTT
1 ATTTTTTTTATT-TTTT
1666976 ATTTTTTTAATATTTTTT
1 ATTTTTTT--TATTTTTT
1666994 ATTTTATTTTATTTT
1 ATTTT-TTTTATTTT
1667009 ATTGTTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 14 0.48
18 9 0.31
19 6 0.21
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTTTTTATTTTTT
Found at i:1667011 original size:10 final size:9
Alignment explanation
Indices: 1666960--1667008 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1666950 TTTAATTTGA
*
1666960 TTTTTTTAA
1 TTTTTTTAT
*
1666969 TTCTTTTAT
1 TTTTTTTAT
*
1666978 TTTTTTAAT
1 TTTTTTTAT
*
1666987 ATTTTTTAT
1 TTTTTTTAT
1666996 TTTATTTTAT
1 TTT-TTTTAT
1667006 TTT
1 TTT
1667009 ATTGTTTAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:1670772 original size:24 final size:24
Alignment explanation
Indices: 1670752--1670801 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1670742 TGAAAAAGTG
1670752 CAAGCTTCATCTGCTGCAAAAGCA
1 CAAGCTTCATCTGCTGCAAAAGCA
* *
1670776 CATGTTTCATCTGCTGCAAAAGCA
1 CAAGCTTCATCTGCTGCAAAAGCA
1670800 CA
1 CA
1670802 GGCCTCTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (24 bp):
CAAGCTTCATCTGCTGCAAAAGCA
Found at i:1679134 original size:24 final size:22
Alignment explanation
Indices: 1679107--1679153 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1679097 TTTCAAATAT
1679107 ATATAAGATATATAGTTTTTAAAA
1 ATAT-AGA-ATATAGTTTTTAAAA
* *
1679131 ATATATAATATAGTTTTTGAAA
1 ATATAGAATATAGTTTTTAAAA
1679153 A
1 A
1679154 CACAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 2 0.10
24 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (22 bp):
ATATAGAATATAGTTTTTAAAA
Found at i:1679180 original size:38 final size:37
Alignment explanation
Indices: 1679122--1679345 Score: 163
Period size: 37 Copynumber: 5.9 Consensus size: 37
1679112 AGATATATAG
*
1679122 TTTTTAAAA-ATAT-ATAATATAGTTTTTGAAAACACAA
1 TTTTGAAAACATATAAT-ATATAGTTTTTGAAAACA-AA
* *
1679159 TTTTGAAAACATATAATATATAATTTTCTTAAAA-AAA
1 TTTTGAAAACATATAATATATAGTTTT-TGAAAACAAA
* * * * *
1679196 -ATTGAAAACATATATAAAATATAGTCTTTGAAAACGTAT
1 TTTTGAAAAC--ATATAATATATAGTTTTTGAAAAC-AAA
* * ***
1679235 TTTTGAAAACATATAATATATAATTTTTTAAAACTGT
1 TTTTGAAAACATATAATATATAGTTTTTGAAAACAAA
* *
1679272 TTTTGAAAACATAAAATATATAGTTTTTTAAAA-AAA
1 TTTTGAAAACATATAATATATAGTTTTTGAAAACAAA
1679308 TGGTTTTTGGAAAACATAT-ATAATATAGTTTTTGAAAA
1 ----TTTT-GAAAACATATAAT-ATATAGTTTTTGAAAA
1679346 TATATAGTAT
Statistics
Matches: 150, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
36 8 0.05
37 48 0.32
38 48 0.32
39 8 0.05
40 14 0.09
41 24 0.16
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (37 bp):
TTTTGAAAACATATAATATATAGTTTTTGAAAACAAA
Found at i:1679346 original size:38 final size:37
Alignment explanation
Indices: 1679121--1679346 Score: 144
Period size: 38 Copynumber: 6.0 Consensus size: 37
1679111 AAGATATATA
*
1679121 GTTTTT-AAAA-ATATATA-ATATAGTTTTTGAAAACAC
1 GTTTTTGAAAACATATATATATATAGTTTTTG-AAA-AT
** * *
1679157 AATTTTGAAAACATATA-ATATATAATTTTCTTAAAA-
1 GTTTTTGAAAACATATATATATATAGTTTT-TGAAAAT
**** * *
1679193 AAAATTGAAAACATATATAAAATATAGTCTTTGAAAACGT
1 GTTTTTGAAAACATATAT-ATATATAGTTTTTGAAAA--T
* * *
1679233 ATTTTTGAAAACATATA-ATATATAATTTTTTAAAACT
1 GTTTTTGAAAACATATATATATATAGTTTTTGAAAA-T
* *
1679270 GTTTTTGAAAACATA-AAATATATAGTTTTTTAAAAAAAT
1 GTTTTTGAAAACATATATATATATAG-TTTTT--GAAAAT
1679309 GGTTTTTGGAAAACATATATA-ATATAGTTTTTGAAAAT
1 -GTTTTT-GAAAACATATATATATATAGTTTTTGAAAAT
1679347 ATATAGTATA
Statistics
Matches: 151, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
36 20 0.13
37 33 0.22
38 50 0.33
39 2 0.01
40 29 0.19
41 15 0.10
42 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (37 bp):
GTTTTTGAAAACATATATATATATAGTTTTTGAAAAT
Found at i:1679351 original size:22 final size:22
Alignment explanation
Indices: 1679323--1679418 Score: 102
Period size: 22 Copynumber: 4.2 Consensus size: 22
1679313 TTTGGAAAAC
1679323 ATATATAATATAGTTTTTGAAA
1 ATATATAATATAGTTTTTGAAA
*
1679345 ATATATAGTATAGTTTTTGAAA
1 ATATATAATATAGTTTTTGAAA
* * * *
1679367 ACATATTATATAATTTTTAAAAA
1 ATATATAATATAGTTTTT-GAAA
* *
1679390 ACATATAATATATATTTTTTGAAA
1 ATATAT-A-ATATAGTTTTTGAAA
1679414 ATATA
1 ATATA
1679419 ATCTATTATA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
22 35 0.57
23 9 0.15
24 7 0.11
25 10 0.16
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (22 bp):
ATATATAATATAGTTTTTGAAA
Found at i:1679396 original size:47 final size:46
Alignment explanation
Indices: 1679310--1679414 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 46
1679300 TAAAAAAATG
* *
1679310 GTTTTTGGAAAACATATATAATATAGTTTTTGAAAATAT-ATAGTATA
1 GTTTTT-GAAAACATATATAATATAATTTTTAAAAATATAATA-TATA
1679357 GTTTTTGAAAACATAT-T-ATATAATTTTTAAAAAACATATAATATATA
1 GTTTTTGAAAACATATATAATATAATTTTT--AAAA-ATATAATATATA
*
1679404 TTTTTTGAAAA
1 GTTTTTGAAAA
1679415 TATAATCTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
44 10 0.20
45 1 0.02
46 13 0.25
47 24 0.47
48 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (46 bp):
GTTTTTGAAAACATATATAATATAATTTTTAAAAATATAATATATA
Found at i:1679409 original size:25 final size:23
Alignment explanation
Indices: 1679364--1679408 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1679354 ATAGTTTTTG
1679364 AAAACATATTATATAATTTTTAA
1 AAAACATATTATATAATTTTTAA
*
1679387 AAAACATATAATATATATTTTT
1 AAAACATATTATATA-ATTTTT
1679409 TGAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAACATATTATATAATTTTTAA
Found at i:1679420 original size:22 final size:22
Alignment explanation
Indices: 1679311--1679420 Score: 87
Period size: 22 Copynumber: 4.8 Consensus size: 22
1679301 AAAAAAATGG
* *
1679311 TTTTTGGAAAACATATATAATATA
1 TTTTTTGAAAATATA-AT-ATATA
*
1679335 GTTTTTGAAAATAT-ATAGTATA
1 TTTTTTGAAAATATAATA-TATA
* * *
1679357 GTTTTTGAAAACATATTATATAA
1 TTTTTTGAAAATATAATATAT-A
**
1679380 TTTTTAAAAAACATATAATATATA
1 TTTTT-TGAAA-ATATAATATATA
1679404 TTTTTTGAAAATATAAT
1 TTTTTTGAAAATATAAT
1679421 CTATTATATA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.01
22 29 0.42
23 10 0.14
24 20 0.29
25 9 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTTTGAAAATATAATATATA
Found at i:1679472 original size:3 final size:3
Alignment explanation
Indices: 1679464--1679501 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1679454 ATATTATAGT
1679464 TTA TTA TTA TTA TTA TT- TTA TATA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1679502 ATTTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1680378 original size:12 final size:12
Alignment explanation
Indices: 1680361--1680393 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1680351 CACCAGGGGA
1680361 GGTGGTCGGAGT
1 GGTGGTCGGAGT
1680373 GGTGGTCGGAGT
1 GGTGGTCGGAGT
1680385 GGTGGTCGG
1 GGTGGTCGG
1680394 CGGCGGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.09, G:0.61, T:0.24
Consensus pattern (12 bp):
GGTGGTCGGAGT
Found at i:1680764 original size:15 final size:15
Alignment explanation
Indices: 1680744--1680792 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1680734 ATCATTGACT
1680744 TTTAATTCTTTTTAA
1 TTTAATTCTTTTTAA
* *
1680759 TTTAATCCCTTTTAA
1 TTTAATTCTTTTTAA
*
1680774 TTTGAATTTTCTTTTAA
1 TTT-AATTCT-TTTTAA
1680791 TT
1 TT
1680793 CTTTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.59
16 3 0.11
17 8 0.30
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTAATTCTTTTTAA
Found at i:1680921 original size:19 final size:19
Alignment explanation
Indices: 1680899--1680949 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1680889 ATTTGAATCG
1680899 AACTTTTAAATTTTAATTT
1 AACTTTTAAATTTTAATTT
1680918 AACTTTTAAATTTTAATTT
1 AACTTTTAAATTTTAATTT
1680937 AACTTTT-AATTTT
1 AACTTTTAAATTTT
1680950 CACAATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.19
19 26 0.81
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
AACTTTTAAATTTTAATTT
Found at i:1682056 original size:12 final size:13
Alignment explanation
Indices: 1682029--1682061 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1682019 TTTGTCAGGG
1682029 TTATTATTTAATA
1 TTATTATTTAATA
1682042 TTATTATTT-ATA
1 TTATTATTTAATA
1682054 TTATTATT
1 TTATTATT
1682062 ATTAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATTTAATA
Found at i:1682075 original size:25 final size:25
Alignment explanation
Indices: 1682029--1682089 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 25
1682019 TTTGTCAGGG
*
1682029 TTATTATTTAATATTATTATTTATATT
1 TTATTA-TTAATA-TATAATTTATATT
*
1682056 ATTATTATTAATA-ATAATTTTTATT
1 -TTATTATTAATATATAATTTATATT
1682081 TTCATTATT
1 TT-ATTATT
1682090 TTTAAAGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 16 0.53
27 6 0.20
28 6 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTATTAATATATAATTTATATT
Found at i:1683510 original size:12 final size:12
Alignment explanation
Indices: 1683493--1683517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1683483 TATTCACTGG
1683493 TTTTTATTCTAT
1 TTTTTATTCTAT
1683505 TTTTTATTCTAT
1 TTTTTATTCTAT
1683517 T
1 T
1683518 ATAATTTAGA
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTCTAT
Found at i:1684301 original size:15 final size:15
Alignment explanation
Indices: 1684281--1684310 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1684271 CATTTTTATC
1684281 TCTTAAAATTATTTT
1 TCTTAAAATTATTTT
1684296 TCTTAAAATTATTTT
1 TCTTAAAATTATTTT
1684311 AAAAGGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTAAAATTATTTT
Found at i:1692008 original size:20 final size:20
Alignment explanation
Indices: 1691979--1692023 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1691969 CCCAAATTGC
* * *
1691979 TAAGTCTTTCGTGCCATCAG
1 TAAGTATTTCGGGCCAACAG
1691999 TAAGTATTTCGGGCCAACAG
1 TAAGTATTTCGGGCCAACAG
1692019 TAAGT
1 TAAGT
1692024 CTTTAGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TAAGTATTTCGGGCCAACAG
Found at i:1692066 original size:42 final size:41
Alignment explanation
Indices: 1692006--1692099 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 41
1691996 CAGTAAGTAT
* * * *
1692006 TTCGGGCCAACAGTAAGTCTTTAGAGCATGATGATTAAATCC
1 TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGA-TAAATCC
* * *
1692048 TTCGGGTCATCTGCAAGTCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGATAAATCC
1692089 TTCGGGCCATC
1 TTCGGGCCATC
1692100 CGTAAGACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGATAAATCC
Found at i:1692321 original size:42 final size:41
Alignment explanation
Indices: 1692259--1692363 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 41
1692249 AATTGGTAAG
** *
1692259 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGA-TAAA
* *
1692301 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAA
* *
1692342 TCCTTCGAGCCATTTGTAAGTC
1 TCCTTCGGGCCATCTGTAAGTC
1692364 CTTCAGGTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.40
42 33 0.60
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:1692341 original size:21 final size:21
Alignment explanation
Indices: 1692274--1692351 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
1692264 CGGGCCATCA
* *
1692274 ATAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGAGCAAGATG
* * **
1692295 ATTAAATCCTTCGGGTC-ATCTG
1 A-TAAGTCCTTCGAG-CAAGATG
*
1692317 -TAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGAGCAAGATG
1692337 ATAAGTCCTTCGAGC
1 ATAAGTCCTTCGAGC
1692352 CATTTGTAAG
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
19 1 0.02
20 13 0.32
21 14 0.34
22 12 0.29
23 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCAAGATG
Found at i:1692351 original size:277 final size:276
Alignment explanation
Indices: 1691729--1692424 Score: 752
Period size: 277 Copynumber: 2.6 Consensus size: 276
1691719 TGGTAAGTCC
* * * ** * ** *
1691729 TTCGAGCCATCAGTAAGTCTTTCTAGTATGATGATTAAATCCTTCG-GTTCATCTCTAAGTCTTT
1 TTCGAGCCAACAGTAAATCCTTAGAGCATGATGA-TAAATCCTTCGAG-TCAGATGTAAGTCTTT
* *
1691793 CGAGAAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCGGGTAAGATGCTTTCACATGAAT
64 CGAGCAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCAGGTAAGATGCTTTCACATGAAT
* * * * *
1691858 TTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTTTGAAAATGAAATTTTTG
129 TTCGAAAAATGAGAAAGCGAATTCCAAAGTTTCTCATTTAATCTTTTCTCAAAATGAAATCTTTA
* * *
1691923 AAAAGTATGAAAGAGATTTCCAAAGTTTCTTACCTAGTAACTATTTCCCAAATTGCTAAGTCTTT
194 AAAAATAAGAAAGAGATTTCCAAAGTTTCTTACCTAGTAACTATTTCCCAAATTGCTAAGTCCTT
* *
1691988 CGTGCCATCAGTAAGTAT
259 CGGGCCATCAATAAGTAT
* * * * ** *
1692006 TTCGGGCCAACAGTAAGTCTTTAGAGCATGATGATTAAATCCTTCGGGTCATCTGCAAGTCTTTC
1 TTCGAGCCAACAGTAAATCCTTAGAGCATGATGA-TAAATCCTTCGAGTCAGATGTAAGTCTTTC
* * * * *
1692071 GAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAGGTAGGATGTTTTTACATGAATT
65 GAGCAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCAGGTAAGATGCTTTCACATGAATT
1692136 TCGAAAAATGAGAAAGCGAATTCCAAAGTTTCTCATTTAATCTTTTCTCAAAATGAAATCTTTAA
130 TCGAAAAATGAGAAAGCGAATTCCAAAGTTTCTCATTTAATCTTTTCTCAAAATGAAATCTTTAA
* *
1692201 AAAATAAGAAAGTGATTTCCAAAGTTTCTTA-C-AGTAAACTATTTCCCAAATTGGTAAGTCCTT
195 AAAATAAGAAAGAGATTTCCAAAGTTTCTTACCTAGT-AACTATTTCCCAAATTGCTAAGTCCTT
*
1692264 CGGGCCATCAATAAGTCT
259 CGGGCCATCAATAAGTAT
* **
1692282 TTCGAG----C-----A----T---G-ATGAT--TAAATCCTTCGGGTCATCTGTAAGTCTTTCG
1 TTCGAGCCAACAGTAAATCCTTAGAGCATGATGATAAATCCTTCGAGTCAGATGTAAGTCTTTCG
* * *** * * *
1692328 AGCAAGATGATAAGTCCTTCGAGCCATTTGTAAGTCCTTCAGGTAGGATGTTTTCACATGAATTT
66 AGCAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCAGGTAAGATGCTTTCACATGAATTT
* * *
1692393 TGAAAAATGAGAAAGAGATTTCCAAAGTTTCT
131 CGAAAAATGAGAAAGCGAATTCCAAAGTTTCT
1692425 TACCCAGTAA
Statistics
Matches: 379, Mismatches: 38, Indels: 25
0.86 0.09 0.06
Matches are distributed among these distances:
256 119 0.31
259 5 0.01
260 1 0.00
263 1 0.00
272 1 0.00
275 3 0.01
276 46 0.12
277 202 0.53
278 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (276 bp):
TTCGAGCCAACAGTAAATCCTTAGAGCATGATGATAAATCCTTCGAGTCAGATGTAAGTCTTTCG
AGCAAGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCAGGTAAGATGCTTTCACATGAATTT
CGAAAAATGAGAAAGCGAATTCCAAAGTTTCTCATTTAATCTTTTCTCAAAATGAAATCTTTAAA
AAATAAGAAAGAGATTTCCAAAGTTTCTTACCTAGTAACTATTTCCCAAATTGCTAAGTCCTTCG
GGCCATCAATAAGTAT
Found at i:1692363 original size:20 final size:20
Alignment explanation
Indices: 1692254--1692367 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
1692244 TCCCAAATTG
*
1692254 GTAAGTCCTTCGGGCCATCA-
1 GTAAGTCCTTCGAGCCAT-AT
* *
1692274 ATAAGTCTTTCGAG-CATGAT
1 GTAAGTCCTTCGAGCCAT-AT
* * * *
1692294 GATTAAATCCTTCGGGTCATCT
1 G--TAAGTCCTTCGAGCCATAT
* * *
1692316 GTAAGTCTTTCGAGCAAGAT
1 GTAAGTCCTTCGAGCCATAT
*
1692336 GATAAGTCCTTCGAGCCATTT
1 G-TAAGTCCTTCGAGCCATAT
1692357 GTAAGTCCTTC
1 GTAAGTCCTTC
1692368 AGGTAGGATG
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
19 4 0.06
20 34 0.49
21 16 0.23
22 12 0.17
23 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (20 bp):
GTAAGTCCTTCGAGCCATAT
Found at i:1700197 original size:5 final size:5
Alignment explanation
Indices: 1700187--1700220 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1700177 TAGTAGCATA
1700187 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1700221 GGTCAGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1702808 original size:18 final size:18
Alignment explanation
Indices: 1702782--1702822 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1702772 ATTGTTCGGA
* *
1702782 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
1702800 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
1702818 AAGAT
1 AAGAT
1702823 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:1708478 original size:2 final size:2
Alignment explanation
Indices: 1708473--1708686 Score: 62
Period size: 2 Copynumber: 108.0 Consensus size: 2
1708463 TCAAAAAATA
*
1708473 AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
1708512 AT AT AT AT ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
1708552 AGT -T AT AT AT AA AT -T AT GGT CAT AT GAA AT AT AT AT AA ACT AT
1 A-T AT AT AT AT AT AT AT AT -AT -AT AT -AT AT AT AT AT AT A-T AT
** * * * *
1708595 AT AT GC AA ACT AT AT AT GT AT AA ACT AT A- AA AGT AT AT -T AT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT
* * *
1708636 TT AT AA ACT AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1708677 AT AT AT AT AT
1 AT AT AT AT AT
1708687 TTAAAGTGAG
Statistics
Matches: 154, Mismatches: 31, Indels: 54
0.64 0.13 0.23
Matches are distributed among these distances:
1 15 0.10
2 126 0.82
3 13 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1708516 original size:31 final size:31
Alignment explanation
Indices: 1708478--1708568 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
1708468 AAATAATATA
1708478 TATATATATATAATATAAGTTTATATATAAT
1 TATATATATATAATATAAGTTTATATATAAT
*
1708509 TATATATATATACTAT-A-TTTATAT-T-A-
1 TATATATATATAATATAAGTTTATATATAAT
1708535 TA-A-ACTATATAATTATAAG-TTATATATAAAT
1 TATATA-TATATAA-TATAAGTTTATATAT-AAT
1708566 TAT
1 TAT
1708569 GGTCATATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 5 0.10
27 8 0.16
28 2 0.04
29 7 0.14
30 2 0.04
31 17 0.35
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TATATATATATAATATAAGTTTATATATAAT
Found at i:1708587 original size:11 final size:12
Alignment explanation
Indices: 1708573--1708612 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
1708563 AATTATGGTC
1708573 ATATGAAA-TAT
1 ATATGAAACTAT
1708584 ATAT-AAACTAT
1 ATATGAAACTAT
1708595 ATATGCAAACTAT
1 ATATG-AAACTAT
1708608 ATATG
1 ATATG
1708613 TATAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.12
11 11 0.42
13 12 0.46
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (12 bp):
ATATGAAACTAT
Found at i:1708598 original size:13 final size:13
Alignment explanation
Indices: 1708580--1708623 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1708570 GTCATATGAA
1708580 ATATATATAAACT
1 ATATATATAAACT
**
1708593 ATATATGCAAACT
1 ATATATATAAACT
1708606 ATATATGTATAAACT
1 ATATA--TATAAACT
1708621 ATA
1 ATA
1708624 AAAGTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 16 0.64
15 9 0.36
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:1708805 original size:17 final size:17
Alignment explanation
Indices: 1708783--1708824 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1708773 TTGGAAAATT
1708783 TTGAGATTATAGA-GAAA
1 TTGAGATT-TAGAGGAAA
1708800 TTGAGAATTTAGAGGGAAA
1 TTGAG-ATTTAGA-GGAAA
1708819 TTGAGA
1 TTGAGA
1708825 ATTGAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
TTGAGATTTAGAGGAAA
Found at i:1709053 original size:8 final size:8
Alignment explanation
Indices: 1709041--1709255 Score: 159
Period size: 8 Copynumber: 26.6 Consensus size: 8
1709031 GCGCGCGCGC
1709041 GCGTGTGT
1 GCGTGTGT
*
1709049 ACGTGTGT
1 GCGTGTGT
* *
1709057 GTGCGTGT
1 GCGTGTGT
*
1709065 GTGTGTGT
1 GCGTGTGT
*
1709073 GCTTGTGT
1 GCGTGTGT
1709081 GCGTGTGT
1 GCGTGTGT
1709089 GCGTGTGT
1 GCGTGTGT
1709097 GCGTGTGTGT
1 GC--GTGTGT
*
1709107 GCGTGCGTGC
1 GCGT--GTGT
*
1709117 GCGTGCGT
1 GCGTGTGT
*
1709125 GCGTGCGCGT
1 GCGT--GTGT
1709135 GCGTGTG-
1 GCGTGTGT
1709142 G-GTGTGT
1 GCGTGTGT
1709149 GCGTGTGT
1 GCGTGTGT
1709157 GCGTGTGT
1 GCGTGTGT
*
1709165 GTGTGTGT
1 GCGTGTGT
*
1709173 ACGTGTGT
1 GCGTGTGT
* *
1709181 GTGCGTGT
1 GCGTGTGT
* *
1709189 GTGTGCGT
1 GCGTGTGT
* *
1709197 CCGTGCGT
1 GCGTGTGT
1709205 GC--GTGT
1 GCGTGTGT
*
1709211 GCGTGCGT
1 GCGTGTGT
1709219 GCGTGTGT
1 GCGTGTGT
* *
1709227 GTGTGTGC
1 GCGTGTGT
*
1709235 GTGTGTGT
1 GCGTGTGT
*
1709243 GCGTGCGT
1 GCGTGTGT
1709251 GCGTG
1 GCGTG
1709256 CGCGTGCGTG
Statistics
Matches: 166, Mismatches: 31, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
6 10 0.06
7 2 0.01
8 131 0.79
10 23 0.14
ACGTcount: A:0.01, C:0.15, G:0.49, T:0.35
Consensus pattern (8 bp):
GCGTGTGT
Found at i:1709056 original size:10 final size:10
Alignment explanation
Indices: 1709043--1709247 Score: 166
Period size: 10 Copynumber: 20.1 Consensus size: 10
1709033 GCGCGCGCGC
*
1709043 GTGTGTACGT
1 GTGTGTGCGT
1709053 GTGTGTGCGT
1 GTGTGTGCGT
*
1709063 GTGTGTGTGT
1 GTGTGTGCGT
1709073 GCTTGTGTGCGT
1 G--TGTGTGCGT
* *
1709085 GTGTGCGTGT
1 GTGTGTGCGT
* *
1709095 GTGCGTGTGT
1 GTGTGTGCGT
*
1709105 GTGCGTGCGT
1 GTGTGTGCGT
* *
1709115 GCGCGTGCGT
1 GTGTGTGCGT
* *
1709125 GCGTGCGCGT
1 GTGTGTGCGT
*
1709135 GCGTGTG-G-
1 GTGTGTGCGT
1709143 GTGTGTGCGT
1 GTGTGTGCGT
*
1709153 GTGTGCGTGTGT
1 GTGT--GTGCGT
1709165 GTGTGTGTACGT
1 GTGTGTG--CGT
1709177 GTGTGTGCGT
1 GTGTGTGCGT
1709187 GTGTGTGCGT
1 GTGTGTGCGT
*
1709197 CCGTGCGTGCGT
1 --GTGTGTGCGT
*
1709209 GTGCGTGCGT
1 GTGTGTGCGT
*
1709219 GCGTGT--GT
1 GTGTGTGCGT
1709227 GTGTGTGCGT
1 GTGTGTGCGT
1709237 GTGTGTGCGT
1 GTGTGTGCGT
1709247 G
1 G
1709248 CGTGCGTGCG
Statistics
Matches: 164, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
8 13 0.08
9 2 0.01
10 113 0.69
12 36 0.22
ACGTcount: A:0.01, C:0.14, G:0.49, T:0.36
Consensus pattern (10 bp):
GTGTGTGCGT
Found at i:1709058 original size:4 final size:4
Alignment explanation
Indices: 1709051--1709243 Score: 118
Period size: 4 Copynumber: 48.2 Consensus size: 4
1709041 GCGTGTGTAC
* * * *
1709051 GTGT GTGT GCGT GTGT GTGT GTGCT -TGT GTGC GTGT GTGC GTGT GTGC
1 GTGT GTGT GTGT GTGT GTGT GTG-T GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * * * * *
1709099 GTGT GTGT GCGT GCGT GCGC GTGC GTGC GTGC GCGT GCGT GTGG GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * ** * *
1709147 GTGC GTGT GTGC GTGT GTGT GTGT GTAC GTGT GTGT GCGT GTGT GTGC
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
** * * * * * *
1709195 GTCC GTGC GTGC GTGT GCGT GCGT GCGT GTGT GTGT GTGC GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
1709243 G
1 G
1709244 CGTGCGTGCG
Statistics
Matches: 153, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
3 1 0.01
4 151 0.99
5 1 0.01
ACGTcount: A:0.01, C:0.14, G:0.49, T:0.36
Consensus pattern (4 bp):
GTGT
Found at i:1709070 original size:14 final size:14
Alignment explanation
Indices: 1709051--1709266 Score: 157
Period size: 14 Copynumber: 15.0 Consensus size: 14
1709041 GCGTGTGTAC
1709051 GTGTGTGTGCGTGT
1 GTGTGTGTGCGTGT
1709065 GTGTGTGTGCTTGTGT
1 GTGTGTGTGC--GTGT
*
1709081 GCGTGTGTGCGTGTGT
1 GTGTGTGTGC--GTGT
*
1709097 GCGTGTGTGTGCGTGC
1 --GTGTGTGTGCGTGT
* * *
1709113 GTGCGCGTGCGTGC
1 GTGTGTGTGCGTGT
* *
1709127 GTGCGCGTGCGTGT
1 GTGTGTGTGCGTGT
*
1709141 GGGTGTGTGCGTGT
1 GTGTGTGTGCGTGT
* *
1709155 GTGCGTGTGTGTGT
1 GTGTGTGTGCGTGT
* *
1709169 GTGTACGTGTGTGTGC
1 GTGT--GTGTGCGTGT
1709185 GTGTGTGTGC--GT
1 GTGTGTGTGCGTGT
** *
1709197 CCGTGCGTGCGTGT
1 GTGTGTGTGCGTGT
* *
1709211 GCGTGCGTGCGTGT
1 GTGTGTGTGCGTGT
1709225 GTGTGTGTGCGTGT
1 GTGTGTGTGCGTGT
* *
1709239 GTGTGCGTGCGTGC
1 GTGTGTGTGCGTGT
* *
1709253 GTGCGCGTGCGTGT
1 GTGTGTGTGCGTGT
1709267 ATAAACTATA
Statistics
Matches: 167, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
12 8 0.05
14 116 0.69
16 34 0.20
18 9 0.05
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.35
Consensus pattern (14 bp):
GTGTGTGTGCGTGT
Found at i:1709359 original size:2 final size:2
Alignment explanation
Indices: 1709352--1709389 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1709342 ATAAGCAATC
1709352 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
1709390 GAAATTGTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1709482 original size:7 final size:7
Alignment explanation
Indices: 1709470--1709502 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1709460 CCCTAAATAT
1709470 TTAACCC
1 TTAACCC
1709477 TTAACCC
1 TTAACCC
1709484 TTAACCC
1 TTAACCC
1709491 -TAA-CC
1 TTAACCC
1709496 TTAACCC
1 TTAACCC
1709503 ATGAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.08
6 6 0.25
7 16 0.67
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.27
Consensus pattern (7 bp):
TTAACCC
Found at i:1709528 original size:4 final size:4
Alignment explanation
Indices: 1709521--1709546 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1709511 TATATATATA
1709521 TGCG TGCG TGCG TGCG TGCG TGCG TG
1 TGCG TGCG TGCG TGCG TGCG TGCG TG
1709547 TATAAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.27
Consensus pattern (4 bp):
TGCG
Found at i:1709636 original size:76 final size:76
Alignment explanation
Indices: 1709547--1709691 Score: 272
Period size: 76 Copynumber: 1.9 Consensus size: 76
1709537 TGCGTGCGTG
1709547 TATAAACTATATAAAATATATAGTTTATAAATTATAATTTATATTAATATAGTATATATATGTAT
1 TATAAACTATATAAAATATATAGTTTATAAATTATAATTTATATTAATATAGTATATATATGTAT
1709612 GTATGTATGTA
66 GTATGTATGTA
* *
1709623 TATAAACTATATAAACTATATAGTTTATAAATTGTAATTTATATTAATATAGTATATATATGTAT
1 TATAAACTATATAAAATATATAGTTTATAAATTATAATTTATATTAATATAGTATATATATGTAT
1709688 GTAT
66 GTAT
1709692 AACTAATATA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (76 bp):
TATAAACTATATAAAATATATAGTTTATAAATTATAATTTATATTAATATAGTATATATATGTAT
GTATGTATGTA
Found at i:1709723 original size:2 final size:2
Alignment explanation
Indices: 1709716--1709770 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1709706 ATCTATAGAT
1709716 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
1709758 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
1709771 GAAACATTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1709867 original size:7 final size:7
Alignment explanation
Indices: 1709855--1709887 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1709845 CCCTAAATAT
1709855 TTAACCC
1 TTAACCC
1709862 TTAACCC
1 TTAACCC
1709869 TTAACCC
1 TTAACCC
1709876 -TAA-CC
1 TTAACCC
1709881 TTAACCC
1 TTAACCC
1709888 ATGAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.08
6 6 0.25
7 16 0.67
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.27
Consensus pattern (7 bp):
TTAACCC
Found at i:1709929 original size:20 final size:19
Alignment explanation
Indices: 1709894--1709955 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
1709884 ACCCATGAAC
1709894 TATATATATATATAAACCA
1 TATATATATATATAAACCA
* * *
1709913 TGTATAGTATTTATAAACTA
1 TATATA-TATATATAAACCA
*
1709933 TATATATATATATAAACTA
1 TATATATATATATAAACCA
1709952 TATA
1 TATA
1709956 AAGTAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (19 bp):
TATATATATATATAAACCA
Found at i:1710068 original size:21 final size:21
Alignment explanation
Indices: 1710038--1710081 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1710028 AGTTTTATAG
1710038 AAATCCTAAACCCTAAACACT
1 AAATCCTAAACCCTAAACACT
* * *
1710059 AAATCTTAAACCTTAAACCCT
1 AAATCCTAAACCCTAAACACT
1710080 AA
1 AA
1710082 TATAAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCTAAACCCTAAACACT
Found at i:1710504 original size:2 final size:2
Alignment explanation
Indices: 1710449--1710495 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
1710439 ATAACCCATG
1710449 TA TA GTA 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
1710492 TA TA
1 TA TA
1710496 AACTATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1710601 original size:14 final size:14
Alignment explanation
Indices: 1710578--1710628 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1710568 AGTTTATACA
1710578 AAACTCTAAACCCT
1 AAACTCTAAACCCT
* * *
1710592 AAACTTTAAAGCAT
1 AAACTCTAAACCCT
1710606 AAA-TCCTAAACCCT
1 AAACT-CTAAACCCT
*
1710620 AAACCCTAA
1 AAACTCTAA
1710629 TATTAATGGA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
13 1 0.04
14 27 0.96
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACTCTAAACCCT
Found at i:1711004 original size:2 final size:2
Alignment explanation
Indices: 1710992--1711041 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
1710982 ATAAACCATG
*
1710992 TA TA GTA TA TA TA AA CTA 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
1711036 TA TA TA
1 TA TA TA
1711042 AACTATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1711004 original size:20 final size:19
Alignment explanation
Indices: 1710981--1711048 Score: 93
Period size: 18 Copynumber: 3.6 Consensus size: 19
1710971 AATATGTATG
* *
1710981 TATAAACCATGTATAGTATA
1 TATAAACTATATATA-TATA
1711001 TATAAACTATATATATATA
1 TATAAACTATATATATATA
*
1711020 TATATA-TATATATATATA
1 TATAAACTATATATATATA
1711038 TATAAACTATA
1 TATAAACTATA
1711049 AAAAGTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 17 0.40
19 13 0.30
20 13 0.30
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:1711148 original size:7 final size:7
Alignment explanation
Indices: 1711138--1711189 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1711128 TCCTAAATCA
1711138 TAAACCC
1 TAAACCC
1711145 TAAACCC
1 TAAACCC
***
1711152 TAAATTT
1 TAAACCC
**
1711159 TAAACTA
1 TAAACCC
*
1711166 TAAACAC
1 TAAACCC
1711173 TAAACCC
1 TAAACCC
1711180 TAAACCC
1 TAAACCC
1711187 TAA
1 TAA
1711190 TGTAAATAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:1711153 original size:21 final size:21
Alignment explanation
Indices: 1711129--1711189 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1711119 TTATAAAAAT
1711129 CCTAAATCATAAACCCTAAAC
1 CCTAAATCATAAACCCTAAAC
** **
1711150 CCTAAATTTTAAACTATAAAC
1 CCTAAATCATAAACCCTAAAC
* * *
1711171 ACTAAACCCTAAACCCTAA
1 CCTAAATCATAAACCCTAA
1711190 TGTAAATAAA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTAAATCATAAACCCTAAAC
Found at i:1711570 original size:2 final size:2
Alignment explanation
Indices: 1711558--1711607 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
1711548 ATAAATCATG
*
1711558 TA TA GTA TA TA TA AA CTA 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
1711602 TA TA TA
1 TA TA TA
1711608 AACTATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1711837 original size:565 final size:562
Alignment explanation
Indices: 1709896--1712144 Score: 3264
Period size: 565 Copynumber: 4.0 Consensus size: 562
1709886 CCATGAACTA
* * * * *
1709896 TATA-TATATATAAACCATGTATAGTATTTATAAACTATATATATATATATAAACTATATAAAGT
1 TATAGTATATATAAACTATATATA-TATATATATA-TATATATATATATATAAACTATAAAAAGT
* * * * *
1709960 AAATTACTTATATAGTTTATAGAAATACTTTTCATAAAATATATAAAGTAATAAAGTA-ATAAAT
64 AAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATAT-AGT
* * ** * * *
1710024 GTATAG---TTTTAT-AGAAATCCTAAACCCTAAA-CACTAAAT-CT------TAAACCTTAAAC
128 TTATAGAAACTAAATCATAAACCCTAAACTCTAAACCA-TAAATACTAAACCCTAAACC-TAAAC
** * * ** *
1710077 CCTAATATAAATAGACTAATACTAATGTATATATATTTATAATAAAATTGTGGGCTTATGTATTG
191 CCTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGT-GACTTATGTATTG
* *
1710142 GG-CTATGTAAACTAATATAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATT
255 GGCCTATGTAAACTAATGTAAATGGACTAACACTAATGCAAATGGACTTATTTTTTGGTTTTATT
* *
1710206 ATTACTTATTCATAACAACAAAATTAATGGGCTATTAATGTGAATTAATCTAACATGCAACTAAA
320 ATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAA
* * *
1710271 ATATTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAATCATATAATATGCAA
385 ATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAA
* *
1710336 TGTGACGTACTAATTATTTAACA-CATAATAAATCATGTTTTATATAATTTACATTTAAATAATT
450 TGTGACATACTAATTATTTAACACCA-AATTAATCATGTTTTATATAATTTACATTTAAATAATT
*
1710400 TTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAACCCATG
514 TTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
*
1710449 TATAGTATATAT--A-TATATATATATATATATATATATATATATATATAAACTATATAAAGTAA
1 TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
* * * *
1710511 ATTACTTATATAGTTTATAGAAACAATATGCATAAACTAAATAAAGAAATAAAG--CATAGTTTA
66 ATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTA
* * * * *
1710574 TA-CAA--AACTC-TAAACCCTAAACTTTAAAGCATAAATCCTAAA--C----CCTAAACCCTAA
131 TAGAAACTAAATCATAAACCCTAAACTCTAAACCATAAATACTAAACCCTAAACCTAAACCCTAA
* * *
1710629 TATTAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCCTATGTATTGGGCCT
196 TATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGA-CTTATGTATTGGGCCT
* * * * *
1710694 ATATAAACTAATGTAAATGTAC-AAGCACTATTGCAAATTGACTTATTTTTTTGTTTTATTATTA
260 ATGTAAACTAATGTAAATGGACTAA-CACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTA
*
1710758 TTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATAC
324 CTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATAC
*
1710823 TAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATTAACCATAT-ATAT---ATGTG
389 TAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTG
* *
1710884 ACATACTAATTATTTAA-ACCAAATTAACCATGTTTTATATAATTTACATTTGAATAATTTTATT
454 ACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATT
1710948 AATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
519 AATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
1710992 TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
1 TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
* * * *
1711057 ATTACTTATATAATTTATAGAAATACTATGCATTAACTATATAAAGTAATAAAGTATACAGTTTA
66 ATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTA
* * *** *
1711122 TAAAAATCCTAAATCATAAACCCTAAACCCTAAATTTTAAACTA-TAAACACTAAACCCTAAACC
131 TAGAAA--CTAAATCATAAACCCTAAACTCTAAACCATAAA-TACTAAACCCTAAA-CCTAAACC
* * * *
1711186 CTAATGTAAATAAACTAGCACTAATACATATATATTTGTAATAAAAGAGTGAACTTATGTATCGG
192 CTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTG-ACTTATGTATTGG
* * *
1711251 GCCTATGTAAACTAATGTAAATGAACTAACACTAATACAAATAGACTTATTTTTTGGTTTTATTA
256 GCCTATGTAAACTAATGTAAATGGACTAACACTAATGCAAATGGACTTATTTTTTGGTTTTATTA
1711316 TTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAA
321 TTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAA
1711381 TACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAAT
386 TACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAAT
* *
1711446 TTGACATACTAATTATTTAACACCAAATTAATCATGTGTTATATAATTTACATTTAAATAATTTT
451 GTGACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTT
* * *
1711511 ATCAATTTTATTAAATAATTTTATATAATATGCATGTATAAATCATG
516 ATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
1711558 TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
1 TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
1711623 ATTACTTATATAG-TTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTA
66 ATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTA
* * * *
1711687 TAGAAACCCTAAATCATTAACCCTTAACTTTAAACCATAAATACTAAACCCTAAACCATAAACCA
131 TAGAAA--CTAAATCATAAACCCTAAACTCTAAACCATAAATACTAAACCCTAAACC-TAAACCC
1711752 TAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGCACTTATGTATTGGG
193 TAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTG-ACTTATGTATTGGG
*
1711817 CCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTAT
257 CCTATGTAAACTAATGTAAATGGACTAACACTAATGCAAATGGACTTATTTTTTGGTTTTATTAT
* *
1711882 TACTTATTCATAACAACAAAATAAATGGGCTATTAATTTGAATTAATCTAACATGCAACTAAAAT
322 TACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAAT
*
1711947 ACTAATTATGCAAATGAAATTAATGTGGCATGTACTACTATTTATGAACCATATAATATGCAATG
387 ACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATG
*
1712012 TGACATACTAATTATTTAACACCAAATTAATCATGTTTTATGTAATTTACATTTAAATAATTTTA
452 TGACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTA
1712077 TTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
517 TTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
*
1712123 TATAGTATATATATA-TATATAT
1 TATAGTATATATAAACTATATAT
1712145 GAACTAAATT
Statistics
Matches: 1530, Mismatches: 122, Indels: 77
0.88 0.07 0.04
Matches are distributed among these distances:
543 96 0.06
544 23 0.02
545 1 0.00
546 97 0.06
547 91 0.06
548 184 0.12
549 80 0.05
550 8 0.01
551 6 0.00
552 1 0.00
553 8 0.01
554 31 0.02
555 1 0.00
556 1 0.00
561 238 0.16
562 7 0.00
564 11 0.01
565 484 0.32
566 162 0.11
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (562 bp):
TATAGTATATATAAACTATATATATATATATATATATATATATATATATAAACTATAAAAAGTAA
ATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTA
TAGAAACTAAATCATAAACCCTAAACTCTAAACCATAAATACTAAACCCTAAACCTAAACCCTAA
TATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGACTTATGTATTGGGCCTA
TGTAAACTAATGTAAATGGACTAACACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTACT
TATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTA
ATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGAC
ATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAA
TTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
Found at i:1712533 original size:25 final size:23
Alignment explanation
Indices: 1712497--1712554 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
1712487 ATTAATCATG
1712497 TTTTA-TATAATTTACATTTAAATAA
1 TTTTATTATAATTT--A-TTAAATAA
1712522 TTTTATTA-AATTTATTAAATAA
1 TTTTATTATAATTTATTAAATAA
1712544 TTTTA-TATAAT
1 TTTTATTATAAT
1712555 ATGTATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 1 0.03
25 10 0.32
26 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTATTATAATTTATTAAATAA
Found at i:1712566 original size:450 final size:451
Alignment explanation
Indices: 1711829--1712755 Score: 1637
Period size: 450 Copynumber: 2.1 Consensus size: 451
1711819 TATGTAAACT
*
1711829 AATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATA
1 AATGTAAATGGACTAGCACTAATGCAAATAGACTTATTTTTTGGTTTTATTATTACTTATTCATA
* *
1711894 ACAACAAAATAAATGGGCTATTAATTTGAATTAATCTAACATGCAACTAAAATACTAATTATGCA
66 ACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCA
*
1711959 AATGAAATTAATGTGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
131 AATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
* *
1712024 TATTTAACACCAAATTAATCATGTTTTATGTAATTTACATTTAAATAATTTTATTAATTTTATTA
196 TATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAAATTTATTA
1712089 AATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATATATATATATGA-ACTAA-
261 AATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATATATATATAT-ATA-TAAG
* *
1712152 ATTACTTAC-TATATAGTTTATAGAAATA-CTATGCATAAACTATATAAAGTAATAAAATATATA
324 ATAAATTACTTATATAGTTTATAGAAA-ACCTATGCATAAACTATATAAAGTAATAAAATATATA
* *
1712215 GTATATAAAAACCCTAAACCCTCAACTTTAAACCACAAGCACTAAGCCATAAACCATAAACTCA
388 GTATATAAAAACCCTAAACCCTAAACTTTAAACCACAAACACTAAGCCATAAACCATAAACTCA
*
1712279 AATGTAAATGGACTAGCACTATTGCAAATAGACTTATTTTTTGGTTTTATTATTACTTATTCATA
1 AATGTAAATGGACTAGCACTAATGCAAATAGACTTATTTTTTGGTTTTATTATTACTTATTCATA
1712344 ACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCA
66 ACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCA
* *
1712409 AATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGTAATGTGGCATACTAAT
131 AATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
1712474 TATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAAATTTATTA
196 TATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAAATTTATTA
*
1712539 AATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATATATATATATATATAAGGT
261 AATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATATATATATATATATAAGAT
* *
1712604 AAATTACTTATATAGTTTATAGAAAACCTATGCATAAACTATATAAAGTAATAAAGTATATAGTT
326 AAATTACTTATATAGTTTATAGAAAACCTATGCATAAACTATATAAAGTAATAAAATATATAGTA
* *
1712669 TATAAAAACCCTAAACCCTAAACTTTAAACTACAAACACTAAGCCATAAACCATAAACTCT
391 TATAAAAACCCTAAACCCTAAACTTTAAACCACAAACACTAAGCCATAAACCATAAACTCA
1712730 AATGTAAATGGACTAGCACTAATGCA
1 AATGTAAATGGACTAGCACTAATGCA
1712756 TATATATTTG
Statistics
Matches: 454, Mismatches: 19, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
449 4 0.01
450 315 0.69
451 135 0.30
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (451 bp):
AATGTAAATGGACTAGCACTAATGCAAATAGACTTATTTTTTGGTTTTATTATTACTTATTCATA
ACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCA
AATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
TATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAAATTTATTA
AATAATTTTATATAATATGTATGTATAAACCATGTATAGTATATATATATATATATATATAAGAT
AAATTACTTATATAGTTTATAGAAAACCTATGCATAAACTATATAAAGTAATAAAATATATAGTA
TATAAAAACCCTAAACCCTAAACTTTAAACCACAAACACTAAGCCATAAACCATAAACTCA
Found at i:1713112 original size:2 final size:2
Alignment explanation
Indices: 1713100--1713157 Score: 89
Period size: 2 Copynumber: 28.0 Consensus size: 2
1713090 ATAAACCATG
*
1713100 TA TA GTA TA TA TA AA CTA 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
1713144 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1713158 AACTATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 49 0.94
3 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1713283 original size:28 final size:29
Alignment explanation
Indices: 1713246--1713320 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 29
1713236 ATAGAAATAC
* **
1713246 TAAACCCTAAACCA-TAAACTTTAAATTA
1 TAAACACTAAACCACTAAACTTTAAACCA
1713274 TAAACACTAAA-CACTAAACTTTAAACCA
1 TAAACACTAAACCACTAAACTTTAAACCA
1713302 TAAACACTAAA-CACTAAAC
1 TAAACACTAAACCACTAAAC
1713321 CATAAACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (29 bp):
TAAACACTAAACCACTAAACTTTAAACCA
Found at i:1713307 original size:21 final size:21
Alignment explanation
Indices: 1713244--1713327 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
1713234 TTATAGAAAT
*
1713244 ACTAAACCCTAAACCATAAAC
1 ACTAAACTCTAAACCATAAAC
** * *
1713265 TTTAAATTATAAA-CACTAAAC
1 ACTAAACTCTAAACCA-TAAAC
*
1713286 ACTAAACTTTAAACCATAAAC
1 ACTAAACTCTAAACCATAAAC
*
1713307 ACTAAACACTAAACCATAAAC
1 ACTAAACTCTAAACCATAAAC
1713328 CCTCATGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.04
21 46 0.92
22 2 0.04
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (21 bp):
ACTAAACTCTAAACCATAAAC
Found at i:1713319 original size:14 final size:14
Alignment explanation
Indices: 1713274--1713320 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1713264 CTTTAAATTA
1713274 TAAACACTAAACAC
1 TAAACACTAAACAC
**
1713288 TAAACTTTAAAC-C
1 TAAACACTAAACAC
1713301 ATAAACACTAAACAC
1 -TAAACACTAAACAC
1713316 TAAAC
1 TAAAC
1713321 CATAAACCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACACTAAACAC
Found at i:1713326 original size:28 final size:28
Alignment explanation
Indices: 1713273--1713328 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1713263 ACTTTAAATT
**
1713273 ATAAACACTAAACACTAAACTTTAAACC
1 ATAAACACTAAACACTAAACCATAAACC
1713301 ATAAACACTAAACACTAAACCATAAACC
1 ATAAACACTAAACACTAAACCATAAACC
1713329 CTCATGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (28 bp):
ATAAACACTAAACACTAAACCATAAACC
Found at i:1713327 original size:14 final size:14
Alignment explanation
Indices: 1713246--1713313 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
1713236 ATAGAAATAC
*
1713246 TAAACCCTAAACCA
1 TAAACACTAAACCA
** **
1713260 TAAACTTTAAATTA
1 TAAACACTAAACCA
1713274 TAAACACTAAA-CA
1 TAAACACTAAACCA
**
1713287 CTAAACTTTAAACCA
1 -TAAACACTAAACCA
1713302 TAAACACTAAAC
1 TAAACACTAAAC
1713314 ACTAAACCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
13 1 0.02
14 38 0.93
15 2 0.05
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACACTAAACCA
Found at i:1713760 original size:2 final size:2
Alignment explanation
Indices: 1713701--1713742 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
1713691 ATAAACCATG
1713701 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
1713743 AAGTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1713840 original size:7 final size:7
Alignment explanation
Indices: 1713830--1713867 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1713820 CCCTAAACTT
1713830 TAAACCA
1 TAAACCA
*
1713837 TAAACAA
1 TAAACCA
1713844 T-AACCA
1 TAAACCA
1713850 CTAAACCA
1 -TAAACCA
1713858 TAAACCA
1 TAAACCA
1713865 TAA
1 TAA
1713868 TATAAATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 18 0.67
8 5 0.19
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCA
Found at i:1714120 original size:21 final size:21
Alignment explanation
Indices: 1714096--1714151 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1714086 TAATTTACAT
1714096 TTAAATAATTTTATTATTTTA
1 TTAAATAATTTTATTATTTTA
1714117 TTAAATAATTTTATTATTTTA
1 TTAAATAATTTTATTATTTTA
1714138 TTAAATAATTTTAT
1 TTAAATAATTTTAT
1714152 ATAATAGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATAATTTTATTATTTTA
Found at i:1714368 original size:16 final size:16
Alignment explanation
Indices: 1714347--1714385 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1714337 CGGATCATTT
*
1714347 ACAGGTCAGGTTGAAA
1 ACAGGTCAGATTGAAA
*
1714363 ACAGGTCATATTGAAA
1 ACAGGTCAGATTGAAA
1714379 ACAGGTC
1 ACAGGTC
1714386 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGATTGAAA
Found at i:1722401 original size:63 final size:64
Alignment explanation
Indices: 1722306--1722425 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 64
1722296 TGTATCAGTC
* *
1722306 TGTCTTTAATCCAAAGAACGTATATGATCAAAAGAAACACAAAATATTACTTACCTATGAATTG
1 TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTATGAATTG
* * * *
1722370 TGTCTTTAGTGCAAAGAA-GTGTATGACCAAAAGAAACCCAAAAAATTACTTACCTA
1 TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTA
1722426 GGAGTTGTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 34 0.68
64 16 0.32
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (64 bp):
TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTATGAATTG
Found at i:1724885 original size:21 final size:20
Alignment explanation
Indices: 1724860--1724899 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1724850 TATTTAAAAA
1724860 ATAATATTATAAATATATTTT
1 ATAATATTAT-AATATATTTT
* *
1724881 ATAATTTTATATTATATTT
1 ATAATATTATAATATATTT
1724900 ATTTATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATAATATTATAATATATTTT
Found at i:1725225 original size:20 final size:21
Alignment explanation
Indices: 1725197--1725268 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
1725187 ATTATGTTTT
*
1725197 GGATTGATCCCTTCA-AAAAA
1 GGATCGATCCCTTCACAAAAA
* **
1725217 GGATCGATCCCTTGAGGAAAA
1 GGATCGATCCCTTCACAAAAA
* *
1725238 GGATCGATCCTTTCACCAAAA
1 GGATCGATCCCTTCACAAAAA
1725259 GGATCGATCC
1 GGATCGATCC
1725269 ATCGATGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 13 0.30
21 31 0.70
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
GGATCGATCCCTTCACAAAAA
Found at i:1725239 original size:21 final size:21
Alignment explanation
Indices: 1725213--1725292 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
1725203 ATCCCTTCAA
*
1725213 AAAAGGATCGATCCCTTGAGG
1 AAAAGGATCGATCCCTTGACG
* * *
1725234 AAAAGGATCGATCCTTTCACC
1 AAAAGGATCGATCCCTTGACG
* * *
1725255 AAAAGGATCGATCCATCGATG
1 AAAAGGATCGATCCCTTGACG
*
1725276 AAAAGGATCAATCCCTT
1 AAAAGGATCGATCCCTT
1725293 TTCCTAAAGG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTGACG
Found at i:1725260 original size:42 final size:42
Alignment explanation
Indices: 1725213--1725313 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1725203 ATCCCTTCAA
*
1725213 AAAAGGATCGATCCCTTGAGGAAAAGGATCGAT-CCTTTCACC
1 AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTT-ACC
* * * *
1725255 AAAAGGATCGATCCATCGATGAAAAGGATCAATCCCTTTTCC
1 AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTTACC
* *
1725297 TAAAGGATCGATTCCTT
1 AAAAGGATCGATCCCTT
1725314 TATTGCAACA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 44 0.90
43 5 0.10
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTTACC
Found at i:1728098 original size:51 final size:51
Alignment explanation
Indices: 1728022--1728136 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
1728012 GTAACTACTG
* * * *
1728022 AATAAATTAATAGTAAACTAAAGATAATATTTTGA-T-TTTATCTCAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTGTAT-T-AATTCCT
1728073 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTGTATTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTGTATTAATTCCT
1728124 AATAAAATAATAA
1 AATAAAATAATAA
1728137 ATCTAATCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
51 52 0.90
52 2 0.03
53 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTGTATTAATTCCT
Found at i:1734918 original size:32 final size:32
Alignment explanation
Indices: 1734882--1734963 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
1734872 AACTGTTACA
*
1734882 CATTATCTAAATGTGACACTAACACTCA-TGTG
1 CATTATCTAAATGTAACACTAACACT-ATTGTG
* * *
1734914 CATTATATAAATGTAACGCTAACTCTATTGTG
1 CATTATCTAAATGTAACACTAACACTATTGTG
* * *
1734946 AATTATCTGAATGCAACA
1 CATTATCTAAATGTAACA
1734964 TTGCTAGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
CATTATCTAAATGTAACACTAACACTATTGTG
Found at i:1739214 original size:15 final size:14
Alignment explanation
Indices: 1739189--1739231 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1739179 AACAAAATAT
*
1739189 TAATATGAAGATAA
1 TAATATAAAGATAA
*
1739203 TGAATATTAAGATAA
1 T-AATATAAAGATAA
*
1739218 TAAGATAAAGATAA
1 TAATATAAAGATAA
1739232 GATGACTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (14 bp):
TAATATAAAGATAA
Found at i:1742247 original size:81 final size:81
Alignment explanation
Indices: 1741995--1742652 Score: 890
Period size: 81 Copynumber: 8.1 Consensus size: 81
1741985 TAAACATTTC
* * * * * * * *
1741995 ATCTTTTACCCAAAGGCATTTTAGCCTTTCATCTAATTTGTATGATTGACACATTTCTGCCAAAT
1 ATCTTTTACTCAAAGGTA-TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
* * **
1742060 GCACACCTAGGCCACAA
65 ACACAACTAGGCCATTA
* ** * * *
1742077 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-GACATAATTTCCACCTTTATGCAAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
*
1742141 CACAGCTAGGCCATTA
66 CACAACTAGGCCATTA
* * * *
1742157 ATCTTTTACTCAAAGGTATTTAACTTTTCATCTAACTGGCATAATTGACATCTTTATGCCGAATA
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
1742222 CACAACTAGGCCATTA
66 CACAACTAGGCCATTA
* * * * *
1742238 ATCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAAGTGACACCTTTATGCTAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
* *
1742303 CACAGCTAGACCATTA
66 CACAACTAGGCCATTA
1742319 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAA-A
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
1742383 GCACAACTAGGCCATTA
66 -CACAACTAGGCCATTA
* *
1742400 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTTACACCTTTCTACCAAATA
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
*
1742465 CACAACTAGGCAATTA
66 CACAACTAGGCCATTA
* * *
1742481 ATCTTTTACTCAAACGTATTTAACCTTGCATCTAACTGGCATAATTGACACCTTTCTTCCAAATA
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
1742546 CACAGA-TAGGCCATTA
66 CACA-ACTAGGCCATTA
* ** * *
1742562 ATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTAACATAATTGACACTTTTCTGCCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
*
1742627 CACATCTAGGCCATTA
66 CACAACTAGGCCATTA
1742643 ATCTTTTACT
1 ATCTTTTACT
1742653 TTAGAATAGT
Statistics
Matches: 513, Mismatches: 58, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
80 67 0.13
81 428 0.83
82 18 0.04
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.34
Consensus pattern (81 bp):
ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATA
CACAACTAGGCCATTA
Found at i:1748043 original size:81 final size:81
Alignment explanation
Indices: 1747890--1748524 Score: 947
Period size: 81 Copynumber: 7.9 Consensus size: 81
1747880 TTTAAGGCAT
* * * * * *
1747890 TTTAGCCTTTCATCTAACTTGCATGATTGACAGCTTTCT-ACAAATGCACAGCTAGGCCATAAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
*
1747954 ATTTTACTCAAAGGTA
66 CTTTTACTCAAAGGTA
*
1747970 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
*
1748035 CTTTTACTCAAAGCTA
66 CTTTTACTCAAAGGTA
* *
1748051 TTTGACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAACTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
1748115 CTTTTACTCAAAGGTA
66 CTTTTACTCAAAGGTA
* *
1748131 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGACAATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
1748196 CTTTTACTCAAAGGTA
66 CTTTTACTCAAAGGTA
* * * * * * *
1748212 TTTAACCTTTCACCTAACTGGCATAATTGAGACATTTATTCCAAATGTACATCTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
*
1748277 CTTTTACTCAATGGTA
66 CTTTTACTCAAAGGTA
* *
1748293 TTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTTCCAAATGCACAGCTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
*
1748358 CTTTTACTCAAACGTA
66 CTTTTACTCAAAGGTA
* * * *
1748374 ---AACCTTTCATCTAACTTGCATAATTGACACATTTCTGCGAAATGCACAGCGAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
1748436 CTTTTACTCAAAGGTA
66 CTTTTACTCAAAGGTA
* * * *
1748452 TTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCTACCAAATGTACATCTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
1748517 CTTTTACT
66 CTTTTACT
1748525 TTAGAACAAT
Statistics
Matches: 503, Mismatches: 47, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
78 73 0.15
80 111 0.22
81 319 0.63
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (81 bp):
TTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAT
CTTTTACTCAAAGGTA
Found at i:1748082 original size:161 final size:161
Alignment explanation
Indices: 1747890--1748524 Score: 940
Period size: 161 Copynumber: 4.0 Consensus size: 161
1747880 TTTAAGGCAT
* * * * *
1747890 TTTAGCCTTTCATCTAACTTGCATGATTGACAGC-TTTCTACAAATGCACAGCTAGGCCATAAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACA-CATTTCTCCAAATGCACAGCTAGGCCATTAAT
* *
1747954 ATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACA
65 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
1748019 CAGCTAGGCCATTAATCTTTTACTCAAAGCTA
130 CAGCTAGGCCATTAATCTTTTACTCAAAGCTA
* *
1748051 TTTGACCTTTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAACTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACATTTCT-CCAAATGCACAGCTAGGCCATTAAT
1748115 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
65 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
* * *
1748180 CAGCTAGACAATTAATCTTTTACTCAAAGGTA
130 CAGCTAGGCCATTAATCTTTTACTCAAAGCTA
* * * * *
1748212 TTTAACCTTTCACCTAACTGGCATAATTGAGACATTTATTCCAAATGTACATCTAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACATTT-CTCCAAATGCACAGCTAGGCCATTAAT
* * *
1748277 CTTTTACTCAATGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTTCCAAATGCA
65 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
1748342 CAGCTAGGCCATTAATCTTTTACTCAAA-CGTA
130 CAGCTAGGCCATTAATCTTTTACTCAAAGC-TA
* * *
1748374 ---AACCTTTCATCTAACTTGCATAATTGACACATTTCTGCGAAATGCACAGCGAGGCCATTAAT
1 TTTAACCTTTCATCTAACTGGCATAATTGACACATTTCT-CCAAATGCACAGCTAGGCCATTAAT
* * *
1748436 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCTACCAAATGTA
65 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
*
1748501 CATCTAGGCCATTAATCTTTTACT
130 CAGCTAGGCCATTAATCTTTTACT
1748525 TTAGAACAAT
Statistics
Matches: 431, Mismatches: 38, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
158 1 0.00
159 135 0.31
160 6 0.01
161 172 0.40
162 116 0.27
163 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (161 bp):
TTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTCCAAATGCACAGCTAGGCCATTAATC
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
AGCTAGGCCATTAATCTTTTACTCAAAGCTA
Found at i:1749279 original size:17 final size:19
Alignment explanation
Indices: 1749253--1749301 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1749243 TTTACCTTTT
*
1749253 AGTATTGATACC-C-CATC
1 AGTATCGATACCACTCATC
1749270 AGTATCGATACCACTTGCATC
1 AGTATCGATACCAC-T-CATC
1749291 AGTATCGATAC
1 AGTATCGATAC
1749302 TGTTCGTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
21 15 0.56
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (19 bp):
AGTATCGATACCACTCATC
Found at i:1751553 original size:21 final size:21
Alignment explanation
Indices: 1751492--1751585 Score: 86
Period size: 21 Copynumber: 4.5 Consensus size: 21
1751482 AGAAACTTTT
*
1751492 GGATCGATCTCTTCA-CAAAA
1 GGATCGATCCCTTCACCAAAA
* * **
1751512 GGATTGATCCC-ACGAGGAAAA
1 GGATCGATCCCTTC-ACCAAAA
1751533 GGATCGATCCCTTCACCAAAA
1 GGATCGATCCCTTCACCAAAA
**
1751554 CTATCGATCCCTTCACC-AAA
1 GGATCGATCCCTTCACCAAAA
1751574 GTGATCGATCCC
1 G-GATCGATCCC
1751586 GTGATGATAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 13 0.22
21 43 0.74
22 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (21 bp):
GGATCGATCCCTTCACCAAAA
Found at i:1767211 original size:969 final size:973
Alignment explanation
Indices: 1765170--1768104 Score: 5333
Period size: 990 Copynumber: 3.0 Consensus size: 973
1765160 TTCTAAAATG
* *
1765170 TTTTGTTATATCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAATT
1 TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
*
1765235 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAAATATTTGAATAT
66 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
1765300 -AAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
131 AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
* *
1765364 TATACTTAAAATAATTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATCGAGTCAAAATTG
196 TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
*
1765429 AGTTTTTAATAGAGAAGTATCGATACCTCTTTAACGAGTATCGATACCCCTAAAACATTGAATGC
261 AGTTTTTAAT--AG-AG--T-G---------T-AC-AGTATCGATACCCCTAAAACATCGAATGC
*
1765494 AAAAAAGGTAATGAAACCCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCC
309 AAAAAAGGTACTGAAACCCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCC
*
1765559 AAAGGTACCGATACCACTCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTACCG
374 AAAGGTACCGATACCACTCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCG
* * *
1765624 ATACCATGGCAGGTATCGATACCTCCTTACATAGTAGTATCGATACCCCCTTGAGAGGTACTGAT
439 ATACCATGGCAGGTATCGATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGAT
*
1765689 ACCATTGTTTCTGCAACAGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAA
504 ACCATTGTTTCTGCAACGGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAA
1765754 GGAGTACCGATACCCATACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTA
569 GGAGTACCGATACCCATACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTA
*
1765819 TTGACTCCACCAAGATCCCCAACATCTAGAATTGATCTGAGGTGTATTTAAACAAGTTCTTGGAG
634 TTGACTCCACCAAGATCCCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAG
1765884 -CATTGGTGATTAAGAGAAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAAT
699 CCATTGGTGATTAAGAGAAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAAT
1765948 TCAAGCCAAAATCCATTCAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTC
764 TCAAGCCAAAATCCATTCAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTC
1766013 ATCTTTGAGTGTTTTTTCTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGT
829 ATCTTTGAGTGTTTTTTCTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGT
1766078 AAGTTTGCAAAGTTTGTAATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATT
894 AAGTTTGCAAAGTTTGTAATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATT
1766143 CTTTGTTCTCAAGAC
959 CTTTGTTCTCAAGAC
1766158 TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
1 TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
1766223 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
66 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
1766288 AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
131 AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
1766353 TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
196 TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
1766418 AGTTTTTAATAG-G-G-A-AGTATCGATACCCCTAAAACATCGAATGCAAAAAAGGTACTGAAAC
261 AGTTTTTAATAGAGTGTACAGTATCGATACCCCTAAAACATCGAATGCAAAAAAGGTACTGAAAC
1766479 CCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCCAAAGGTACCGATACCAC
326 CCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCCAAAGGTACCGATACCAC
1766544 TCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCGATACCATGGCAGGTATC
391 TCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCGATACCATGGCAGGTATC
1766609 GATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGATACCATTGTTTCTGCAAC
456 GATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGATACCATTGTTTCTGCAAC
1766674 GGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAAGGAGTACCGATACCCAT
521 GGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAAGGAGTACCGATACCCAT
1766739 ACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTATTGACTCCACCAAGATC
586 ACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTATTGACTCCACCAAGATC
1766804 CCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAGCCATTGGTGATTAAGAG
651 CCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAGCCATTGGTGATTAAGAG
*
1766869 AAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGCTTGAGCAATTCAAGCCAAAATCCATT
716 AAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAATTCAAGCCAAAATCCATT
1766934 CAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTCATCTTTGAGTGTTTTTT
781 CAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTCATCTTTGAGTGTTTTTT
1766999 CTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGTAAGTTTGCAAAGTTTGT
846 CTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGTAAGTTTGCAAAGTTTGT
1767064 AATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATTCTTTGTTCTCAAGAC
911 AATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATTCTTTGTTCTCAAGAC
1767127 TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
1 TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
1767192 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
66 GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
1767257 AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
131 AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
1767322 TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
196 TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
1767387 AGTTTTTAATAGGGAAGTATCGATACCTCTTTAACGAGTATCGATACCCCTAAAACATCGAATGC
261 AGTTTTTAATA--G-AG--T-G---------T-AC-AGTATCGATACCCCTAAAACATCGAATGC
*
1767452 AAAAAAGGTACTGAAACCCTACAGGATATCAATACCCCTATATAAAGTAGTACCTATACCTAGCC
309 AAAAAAGGTACTGAAACCCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCC
1767517 AAAGGTACCGATACCACTCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCG
374 AAAGGTACCGATACCACTCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCG
1767582 ATACCATGGCAGGTATCGATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGAT
439 ATACCATGGCAGGTATCGATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGAT
1767647 ACCATTGTTTCTGCAACGGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAA
504 ACCATTGTTTCTGCAACGGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAA
* *
1767712 GGAGTACCGATACCCATACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACATCAGCTCTA
569 GGAGTACCGATACCCATACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTA
1767777 TTGACTCCACCAAGATCCCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAG
634 TTGACTCCACCAAGATCCCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAG
1767842 CCATTGGTGATTAAGAGAAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAAT
699 CCATTGGTGATTAAGAGAAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAAT
*
1767907 TCAAGCCAAAATCCATTCAATATTCATTTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTC
764 TCAAGCCAAAATCCATTCAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTC
* *
1767972 ATCTTTGAGTGTTTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAGGTTTTTCTGT
829 ATCTTTGAGTGTTTTTTCTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGT
*
1768037 AAGTTTGCAAAGTTTGTAATTTTCTCTTTGAGAATAGAGTGTTCTCAAGAATTTGGGGTATAATT
894 AAGTTTGCAAAGTTTGTAATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATT
1768102 CTT
959 CTT
1768105 GAGGGAGTTG
Statistics
Matches: 1902, Mismatches: 22, Indels: 44
0.97 0.01 0.02
Matches are distributed among these distances:
968 411 0.22
969 544 0.29
970 1 0.00
971 1 0.00
973 1 0.00
977 1 0.00
981 1 0.00
985 1 0.00
987 2 0.00
988 128 0.07
989 137 0.07
990 674 0.35
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (973 bp):
TTTTGTTATACCAAAAAGGGGGAGATTGTTGAGAAAACATTTTGATATTTCGATATAACAAAAGT
GTTAATGAATTTTAAGATTTTATATTCGATTCAAAATAATATATTCGATTCAATTATTTGAATAT
AAAAAATATTACTCCAAGTTTTCAAAGATCAATTTTTACTCCTTACTTAATGAAAAATTGTGATT
TATACTTAAAATATTTTTAAAACAATTTTTACAAAGTGTTTCGAACCATAATGGAGTCAAAATTG
AGTTTTTAATAGAGTGTACAGTATCGATACCCCTAAAACATCGAATGCAAAAAAGGTACTGAAAC
CCTACAGGATATCAATACCCCTATATAAAGTAGTACCCATACCTAGCCAAAGGTACCGATACCAC
TCCTTTGATTTTGACTCCGAAAAATAACAGAATGCAAAATGGGTTCCGATACCATGGCAGGTATC
GATACCTCTTTACATAGTAGTATCGATACCCACTTGAGAGGTACCGATACCATTGTTTCTGCAAC
GGTCAAAATATTTGAATTTTATACACGTAGTATCGATACCCCTATGAAGGAGTACCGATACCCAT
ACGCTCCCAACAGCTTTTTGAAGTGGATTTCACACCACAACAACTCTATTGACTCCACCAAGATC
CCCAACATCTAGAATTGATTTGAGGTGTATTTAAACAAGTTCTTGGAGCCATTGGTGATTAAGAG
AAGCTAGAGAAACAAAAGAGAAAGCCTTAAACATCAAGTTTGAGCAATTCAAGCCAAAATCCATT
CAATATTCAATTTGCTTTAAAGAACACAATTTGTGCTCAATTGTATTCATCTTTGAGTGTTTTTT
CTTTGCTCTAGAATTGTACAAACATCTTACCTTGTGAGGTTTTTCTGTAAGTTTGCAAAGTTTGT
AATTTTCTCTTTGAGAATAGAGTGTTCTCGAGAATTTGGGGTATAATTCTTTGTTCTCAAGAC
Found at i:1775144 original size:7 final size:7
Alignment explanation
Indices: 1775128--1775180 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
1775118 TTTTAGTTTG
1775128 TTTT-AA
1 TTTTCAA
1775134 TTTTCAA
1 TTTTCAA
1775141 TTTTCAA
1 TTTTCAA
*
1775148 TTTTTAA
1 TTTTCAA
* *
1775155 TTTTTAG
1 TTTTCAA
1775162 TTTTCAA
1 TTTTCAA
*
1775169 TTTTTAA
1 TTTTCAA
1775176 TTTTC
1 TTTTC
1775181 GTTCGTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
6 4 0.10
7 36 0.90
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (7 bp):
TTTTCAA
Found at i:1775151 original size:14 final size:14
Alignment explanation
Indices: 1775128--1775180 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
1775118 TTTTAGTTTG
1775128 TTTTAATTTTCAAT
1 TTTTAATTTTCAAT
* *
1775142 TTTCAATTTTTAAT
1 TTTTAATTTTCAAT
*
1775156 TTTTAGTTTTCAAT
1 TTTTAATTTTCAAT
1775170 TTTTAATTTTC
1 TTTTAATTTTC
1775181 GTTCGTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTAATTTTCAAT
Found at i:1775154 original size:21 final size:21
Alignment explanation
Indices: 1775128--1775180 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1775118 TTTTAGTTTG
1775128 TTTTAATTTTCAATTTTCAAT
1 TTTTAATTTTCAATTTTCAAT
* *
1775149 TTTTAATTTTTAGTTTTCAAT
1 TTTTAATTTTCAATTTTCAAT
1775170 TTTTAATTTTC
1 TTTTAATTTTC
1775181 GTTCGTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTCAATTTTCAAT
Found at i:1788610 original size:17 final size:18
Alignment explanation
Indices: 1788588--1788624 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1788578 TAATTATAAT
1788588 TTTTAAATT-TATTTT-TA
1 TTTT-AATTATATTTTATA
1788605 TTTTAATTATATTTTATA
1 TTTTAATTATATTTTATA
1788623 TT
1 TT
1788625 AAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTAATTATATTTTATA
Found at i:1789917 original size:21 final size:21
Alignment explanation
Indices: 1789891--1789938 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1789881 GTTTACCATG
**
1789891 ATTGTGGACGTTGCAGGCGCT
1 ATTGTGGACGTCACAGGCGCT
* *
1789912 ATTGTGGCCGTCACAGGTGCT
1 ATTGTGGACGTCACAGGCGCT
1789933 ATTGTG
1 ATTGTG
1789939 AGTGTAGCGG
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:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (21 bp):
ATTGTGGACGTCACAGGCGCT
Found at i:1790332 original size:2 final size:2
Alignment explanation
Indices: 1790325--1790375 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1790315 CTAGTAATAA
1790325 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
1790367 AT AT AT AT A
1 AT AT AT AT A
1790376 AATGATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1793259 original size:111 final size:111
Alignment explanation
Indices: 1793060--1793266 Score: 319
Period size: 111 Copynumber: 1.9 Consensus size: 111
1793050 CGAAGTGCCG
* *
1793060 AAATGGTCATTCACCTTTTATGAATACCATGAGTGACACCTTTTATGCCGAAAATGTACCGTTAT
1 AAATGGTAATTCACCTTTTATGAATACCATGAGTGACACCTTTTATGCCGAAAATGCACCGTTAT
1793125 ACATTACACAAAATCGATCGATAACTTTCATACATGAAGTATGTCA
66 ACATTACACAAAATCGATCGATAACTTTCATACATGAAGTATGTCA
* *
1793171 AAATGGTAATTCACCTTTTATGAATACCATTG-GTGGCACCTTTTATGCCGATAATGCACCGTTA
1 AAATGGTAATTCACCTTTTATGAATACCA-TGAGTGACACCTTTTATGCCGAAAATGCACCGTTA
* * *
1793235 TGCATTTA-ACAAAATTGATTGATAACTTTCAT
65 TACA-TTACACAAAATCGATCGATAACTTTCAT
1793267 TATTAGCACC
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
111 82 0.94
112 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (111 bp):
AAATGGTAATTCACCTTTTATGAATACCATGAGTGACACCTTTTATGCCGAAAATGCACCGTTAT
ACATTACACAAAATCGATCGATAACTTTCATACATGAAGTATGTCA
Found at i:1793476 original size:16 final size:17
Alignment explanation
Indices: 1793449--1793484 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1793439 ATATCATTCC
1793449 CATACAATTTAACAAAA
1 CATACAATTTAACAAAA
1793466 CATAC-ATTTAACAAAA
1 CATACAATTTAACAAAA
1793482 CAT
1 CAT
1793485 TCGAGGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (17 bp):
CATACAATTTAACAAAA
Found at i:1793825 original size:22 final size:22
Alignment explanation
Indices: 1793798--1793873 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
1793788 TACCCTTACC
1793798 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
1793820 ATGGTA-CTGATAC-TC---CCT
1 ATGGTATC-GATACTTCTATACT
1793838 -TCGGTATCGATACTTCTATACT
1 AT-GGTATCGATACTTCTATACT
*
1793860 ATGGTACCGATACT
1 ATGGTATCGATACT
1793874 CCCTTTAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
17 1 0.02
18 11 0.26
19 3 0.07
21 3 0.07
22 24 0.56
23 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:1793844 original size:40 final size:40
Alignment explanation
Indices: 1793800--1793878 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
1793790 CCCTTACCAT
*
1793800 GGTATCGATACTTCTATACTATGGTACTGATACTCCCTTC
1 GGTATCGATACTTCTATACTATGGTACCGATACTCCCTTC
1793840 GGTATCGATACTTCTATACTATGGTACCGATACTCCCTT
1 GGTATCGATACTTCTATACTATGGTACCGATACTCCCTT
1793879 TAGTATCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (40 bp):
GGTATCGATACTTCTATACTATGGTACCGATACTCCCTTC
Found at i:1793885 original size:40 final size:40
Alignment explanation
Indices: 1793801--1793890 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
1793791 CCTTACCATG
* *
1793801 GTATCGATACTTCTATACTATGGTACTGATACTCCCTTCG
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCTTCA
*
1793841 GTATCGATACTTCTATACTATGGTACCGATACTCCCTTTA
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCTTCA
*
1793881 GTATCAATAC
1 GTATCGATAC
1793891 CATTTCAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (40 bp):
GTATCGATACTTCTATACTATGGTACCGATACTCCCTTCA
Found at i:1808655 original size:21 final size:22
Alignment explanation
Indices: 1808631--1808689 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1808621 TTGTACTCAA
* *
1808631 AAAAATCAAGATAAATA-AATT
1 AAAAATAAAAATAAATAGAATT
1808652 AAAAA-AAAACATAAATAGGAATT
1 AAAAATAAAA-ATAAATA-GAATT
*
1808675 AAAAATGAAAATAAA
1 AAAAATAAAAATAAA
1808690 AATTAGGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.06
21 12 0.39
23 14 0.45
24 3 0.10
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAAATAAAAATAAATAGAATT
Found at i:1810124 original size:141 final size:141
Alignment explanation
Indices: 1809865--1810144 Score: 400
Period size: 141 Copynumber: 2.0 Consensus size: 141
1809855 ATTTACCTCG
* * * * *
1809865 ATCTTGCGAAATGTTTCAAGAATTTCTTTCTCTTCTGCTTCTTTCTTAGACTTAACAAATCTAGT
1 ATCTCGCGAAATGTCTCAAGAATTTCTTTCGCTTCTGATTCTTTCTTAGACTTAACAAATCTAGA
*
1809930 GAGATAAGGAGATTTTATGACAAATTCATTCGGTTGTTCACTTTTGAGTCCTTTAGGTTGGTCTT
66 GAGATAAGGAGATTTTATGACAAATTCATTCGGTTGTTAACTTTTGAGTCCTTTAGGTTGGTCTT
*
1809995 TTTGAGTCTCA
131 TCTGAGTCTCA
* * * *
1810006 ATCTCGCGAAATGTCTCAAGAATTTCTTTCGCTTCTGATTGTTTCTTGGATTTAGCAAATCTAGA
1 ATCTCGCGAAATGTCTCAAGAATTTCTTTCGCTTCTGATTCTTTCTTAGACTTAACAAATCTAGA
* * * * *
1810071 GGGA-AGAGGAGGTTTTATGACAAATTCCTTTGGTTGTTAACTTTTGAGTCCTTTGGGTTGGTCT
66 GAGATA-AGGAGATTTTATGACAAATTCATTCGGTTGTTAACTTTTGAGTCCTTTAGGTTGGTCT
1810135 TTCTGAGTCT
130 TTCTGAGTCT
1810145 GGGGAGCAAC
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
140 1 0.01
141 121 0.99
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (141 bp):
ATCTCGCGAAATGTCTCAAGAATTTCTTTCGCTTCTGATTCTTTCTTAGACTTAACAAATCTAGA
GAGATAAGGAGATTTTATGACAAATTCATTCGGTTGTTAACTTTTGAGTCCTTTAGGTTGGTCTT
TCTGAGTCTCA
Found at i:1818461 original size:69 final size:69
Alignment explanation
Indices: 1818336--1818512 Score: 268
Period size: 69 Copynumber: 2.6 Consensus size: 69
1818326 ATATCTATGA
* ** *
1818336 AAAAGTTCGATACTTTGCAACCTTCTTATTTTTCATG-TTTTTTAATTCGAAAATATCGATCTTT
1 AAAAGTTTGATACTTTGCCGCCTTCTCATTTTTCATGTTTTTTTAATTCGAAAATATCGATCTTT
1818400 AAAG
66 AAAG
* *
1818404 AAAAGTTTGATACTTTGCCGTCTTCTCATTTTTCATGTTTTTTTAATTCTAAAATATCGATCTTT
1 AAAAGTTTGATACTTTGCCGCCTTCTCATTTTTCATGTTTTTTTAATTCGAAAATATCGATCTTT
*
1818469 ATAG
66 AAAG
*
1818473 AAAAGTTTGATACTTTGTCGCCTTCTCATTTTTCAT-TTTT
1 AAAAGTTTGATACTTTGCCGCCTTCTCATTTTTCATGTTTT
1818513 ATAAATTCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 36 0.36
69 63 0.64
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (69 bp):
AAAAGTTTGATACTTTGCCGCCTTCTCATTTTTCATGTTTTTTTAATTCGAAAATATCGATCTTT
AAAG
Found at i:1819394 original size:29 final size:30
Alignment explanation
Indices: 1819361--1819426 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1819351 AGGCTGACAA
*
1819361 TGAACCGGCTG-AAACCGGTAAAACTGGGG
1 TGAACCGGCTGAAAACCGGCAAAACTGGGG
**
1819390 TGAACCGGCTGAAAACCGGCAAAACTGGTT
1 TGAACCGGCTGAAAACCGGCAAAACTGGGG
1819420 TGAACCG
1 TGAACCG
1819427 CCGGTTCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.15
Consensus pattern (30 bp):
TGAACCGGCTGAAAACCGGCAAAACTGGGG
Found at i:1820316 original size:18 final size:19
Alignment explanation
Indices: 1820283--1820318 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1820273 TAAAAAAAGT
*
1820283 GAGGATCTTCATTTTATTG
1 GAGGATATTCATTTTATTG
1820302 GAGGATATT-ATTTTATT
1 GAGGATATTCATTTTATT
1820319 AATACGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (19 bp):
GAGGATATTCATTTTATTG
Found at i:1821285 original size:48 final size:48
Alignment explanation
Indices: 1821214--1821327 Score: 156
Period size: 48 Copynumber: 2.4 Consensus size: 48
1821204 TTAATGTAAA
* * * *
1821214 ACTTATTAGTTTTACATAGTGTAAGTAGATCATACCTTAATGTAAAATC
1 ACTT-TTAGTTTTACATAATGTAAGCAGATCATACCCTAATGTAAAAGC
* *
1821263 ACTTTTAATTTTACATAATGTAAGCAGATCCTACCCTAATGTAAAAGC
1 ACTTTTAGTTTTACATAATGTAAGCAGATCATACCCTAATGTAAAAGC
*
1821311 TCTTTTAGTTTTACATA
1 ACTTTTAGTTTTACATA
1821328 GTTTTATGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 53 0.93
49 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (48 bp):
ACTTTTAGTTTTACATAATGTAAGCAGATCATACCCTAATGTAAAAGC
Found at i:1840693 original size:23 final size:23
Alignment explanation
Indices: 1840666--1840717 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1840656 TAACTAGAAC
1840666 AATAAAATAAATATCCTAGAGCA
1 AATAAAATAAATATCCTAGAGCA
*
1840689 AATAAAATAAATATCCTAGAGCT
1 AATAAAATAAATATCCTAGAGCA
1840712 AATAAA
1 AATAAA
1840718 TTGAAAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (23 bp):
AATAAAATAAATATCCTAGAGCA
Found at i:1855919 original size:21 final size:21
Alignment explanation
Indices: 1855894--1856043 Score: 119
Period size: 21 Copynumber: 6.8 Consensus size: 21
1855884 ATTTTGGACT
1855894 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1855915 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1855936 ATCGCAACGAAAC--GCGAACTTCGACT
1 ATCGCAACG-AACTTG-GAA--T--A-A
*
1855962 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1855983 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1856004 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1856025 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1856044 CTATCGCAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.10
20 1 0.01
21 51 0.50
22 3 0.03
23 20 0.20
24 1 0.01
25 3 0.03
26 12 0.12
27 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1855943 original size:42 final size:42
Alignment explanation
Indices: 1855894--1856052 Score: 146
Period size: 42 Copynumber: 3.7 Consensus size: 42
1855884 ATTTTGGACT
*
1855894 ATCGCAA-CGAACTTGGAATAAATCGCAATGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAAT-AATCGCAACGAATTTGGAATAA
* *
1855936 ATCGCAACGAAACGCGAACTTCGACT-ATCGCAACGAATTTGGAATAA
1 ATCG---C--AAC-CGAACTTGGAATAATCGCAACGAATTTGGAATAA
* * *
1855983 ATCGCAACGCGAACTTCGACT-ATCGCAACGAACTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATAATCGCAACGAATTTGGAATAA
*
1856025 ATCGCAACGCGAACTTGGACT-ATCGCAA
1 ATCGCAAC-CGAACTTGGAATAATCGCAA
1856053 TGCGAATATG
Statistics
Matches: 105, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
42 67 0.64
44 1 0.01
45 1 0.01
47 26 0.25
49 10 0.10
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACCGAACTTGGAATAATCGCAACGAATTTGGAATAA
Found at i:1855968 original size:47 final size:46
Alignment explanation
Indices: 1855915--1856052 Score: 184
Period size: 42 Copynumber: 3.2 Consensus size: 46
1855905 CTTGGAATAA
*
1855915 ATCGCAATGAATTTGGAATAAATCGCAACGAAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACG-AACGCGAACTTCGACT
1855962 ATCGCAACGAATTTGGAATAAATCG---C-AACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGAACGCGAACTTCGACT
* *
1856004 ATCGCAACGAACTTGGAATAAATCG---C-AACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGAACGCGAACTTCGACT
1856046 ATCGCAA
1 ATCGCAA
1856053 TGCGAATATG
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
42 63 0.72
44 1 0.01
47 24 0.27
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (46 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGAACGCGAACTTCGACT
Found at i:1856049 original size:21 final size:21
Alignment explanation
Indices: 1855946--1856058 Score: 108
Period size: 21 Copynumber: 5.4 Consensus size: 21
1855936 ATCGCAACGA
*
1855946 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
* *
1855967 AA--CGAATTTGGAATAAATCGC
1 AACGCGAACTTGGACT--ATCGC
*
1855988 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
*
1856009 AA--CGAACTTGGAATAAATCGC
1 AACGCGAACTTGGACT--ATCGC
1856030 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
*
1856051 AATGCGAA
1 AACGCGAA
1856059 TATGTAAATC
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
19 19 0.26
21 35 0.47
23 20 0.27
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
AACGCGAACTTGGACTATCGC
Found at i:1864920 original size:30 final size:31
Alignment explanation
Indices: 1864852--1864921 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1864842 TTAAGAATAA
*
1864852 TATATTTTAACTACTTATATTATTGATTTAT
1 TATATTTTAACTACTTACATTATTGATTTAT
*
1864883 T-TAATTTTAA-TCACTTACGTTATTGA-TTAT
1 TAT-ATTTTAACT-ACTTACATTATTGATTTAT
1864913 TATATTTTA
1 TATATTTTA
1864922 GTTAGTGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (31 bp):
TATATTTTAACTACTTACATTATTGATTTAT
Found at i:1869110 original size:30 final size:29
Alignment explanation
Indices: 1869071--1869169 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 29
1869061 TAAATTTGAA
* * *
1869071 GGACAAAAATAATAAAAACAGAAACTAAAG
1 GGACTAAAATAATAAAAATAGAAAC-ATAG
*** *
1869101 GGACTAAAATGGCAAAAATAAAAACATAG
1 GGACTAAAATAATAAAAATAGAAACATAG
* *
1869130 GGAGTAAAACAATAAAAATAGAAACATAG
1 GGACTAAAATAATAAAAATAGAAACATAG
1869159 AGGACTAAAAT
1 -GGACTAAAAT
1869170 GTCAACAACA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 26 0.49
30 27 0.51
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (29 bp):
GGACTAAAATAATAAAAATAGAAACATAG
Found at i:1869132 original size:29 final size:29
Alignment explanation
Indices: 1869099--1869170 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1869089 CAGAAACTAA
*
1869099 AGGGACTAAAATGGCAAAAATAAAAACAT
1 AGGGACTAAAATGACAAAAATAAAAACAT
* ** * *
1869128 AGGGAGTAAAACAATAAAAATAGAAACAT
1 AGGGACTAAAATGACAAAAATAAAAACAT
1869157 AGAGGACTAAAATG
1 AG-GGACTAAAATG
1869171 TCAACAACAG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.14
Consensus pattern (29 bp):
AGGGACTAAAATGACAAAAATAAAAACAT
Found at i:1870559 original size:3 final size:3
Alignment explanation
Indices: 1870553--1870598 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
1870543 ACATAATTAT
1870553 TAA TAA TAA TAA -ACA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1870599 ATTTAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.03
3 35 0.88
4 4 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1870567 original size:22 final size:22
Alignment explanation
Indices: 1870542--1870598 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1870532 ATATATATGT
*
1870542 AACATAATTATTAAT-AATAATA
1 AACATAA-TAATAATAAATAATA
1870564 AACATAATAATAATAAATAATA
1 AACATAATAATAATAAATAATA
1870586 ATA-ATAATAATAA
1 A-ACATAATAATAA
1870599 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.19
22 25 0.78
23 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
AACATAATAATAATAAATAATA
Found at i:1870605 original size:25 final size:25
Alignment explanation
Indices: 1870545--1870598 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1870535 TATATGTAAC
* *
1870545 ATAATTATTAATAATAATAAACATA
1 ATAATAATAAATAATAATAAACATA
1870570 ATAATAATAAATAATAATAATA-ATA
1 ATAATAATAAATAATAATAA-ACATA
1870595 ATAA
1 ATAA
1870599 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATAATAAATAATAATAAACATA
Found at i:1871065 original size:28 final size:29
Alignment explanation
Indices: 1871033--1871103 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
1871023 GGTTTTAAGG
*
1871033 GAAACCGACTCAAAGATTTGTTTCAA-AA
1 GAAACAGACTCAAAGATTTGTTTCAAGAA
1871061 GAAACAGACTCAAAGATTTGTTTCAAGAA
1 GAAACAGACTCAAAGATTTGTTTCAAGAA
*
1871090 -AAACATACTCAAAG
1 GAAACAGACTCAAAG
1871104 GTGATGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (29 bp):
GAAACAGACTCAAAGATTTGTTTCAAGAA
Found at i:1871117 original size:31 final size:28
Alignment explanation
Indices: 1871033--1871120 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 28
1871023 GGTTTTAAGG
* *
1871033 GAAACCGACTCAAAGATTTGTTTCAAAA
1 GAAACAGACTCAAAGATGTGTTTCAAAA
*
1871061 GAAACAGACTCAAAGATTTGTTTCAAGAA
1 GAAACAGACTCAAAGATGTGTTTCAA-AA
*
1871090 -AAACATACTCAAAGGTGATGTGTTTCAAAA
1 GAAACAGACTCAAA---GATGTGTTTCAAAA
1871120 G
1 G
1871121 TAACTGTCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 37 0.71
29 2 0.04
30 2 0.04
31 11 0.21
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (28 bp):
GAAACAGACTCAAAGATGTGTTTCAAAA
Found at i:1871360 original size:36 final size:32
Alignment explanation
Indices: 1871240--1871377 Score: 118
Period size: 38 Copynumber: 4.0 Consensus size: 32
1871230 CAAAGATCGG
*
1871240 TGTTTCGAGAGAAACAAACTCAAAGATGTTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTT
* *
1871272 TGTTTCAAGAAAAACACACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG--T-TTT
*
1871310 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTT
*
1871346 TGTTTTCAA-AGAAACAAACTTAAAGAT-TTTT
1 TG-TTTCAAGAGAAACAAACTCAAAGATGTTTT
1871377 T
1 T
1871378 CTCAAAGAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
31 4 0.05
32 23 0.26
34 2 0.02
35 3 0.03
36 22 0.25
37 7 0.08
38 26 0.30
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTT
Found at i:1871565 original size:66 final size:67
Alignment explanation
Indices: 1871454--1871602 Score: 221
Period size: 66 Copynumber: 2.3 Consensus size: 67
1871444 CGTTTTAAGT
* * *
1871454 GAGACGAAATTTG-TTTCAAATGAAACAATCTCAAAGGTTGGTTTTTCATTAAAAATTATCTCAA
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
1871518 GA
66 GA
* * * *
1871520 GAGACAAAATTTGTTTTCAAA-GAAACAATCTCAAATGTTTATTTTTCATTAGAAACTGTCTCAA
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
1871584 GA
66 GA
1871586 GAGACAAAATTTGTTTT
1 GAGACAAAATTTGTTTT
1871603 TGAAGAAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 68 0.91
67 7 0.09
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (67 bp):
GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
GA
Found at i:1871640 original size:66 final size:66
Alignment explanation
Indices: 1871454--1871641 Score: 175
Period size: 66 Copynumber: 2.8 Consensus size: 66
1871444 CGTTTTAAGT
* * * * ** * * *
1871454 GAGACGAAATTTG-TTTCAAATGAAACAATCTCAAAGGTTGGTTTTTCATTAAAAATTATCTCAA
1 GAGACAAAATTTGTTTTCAAA-GAAACAATCTCAAATGATGATTTTTCAAGAGAAACTGTCTCAA
1871518 GA
65 GA
* * **
1871520 GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAATGTTTATTTTTCATTAGAAACTGTCTCAAG
1 GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAATGATGATTTTTCAAGAGAAACTGTCTCAAG
1871585 A
66 A
** * *
1871586 GAGACAAAATTTGTTTTTGAAGAAATAGA-CTCAAAT-ATGATTTTGTTAAGAGAAAC
1 GAGACAAAATTTGTTTTCAAAGAAACA-ATCTCAAATGATGATTTT-TCAAGAGAAAC
1871642 AAACTCAAAG
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 6 0.06
66 90 0.87
67 8 0.08
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (66 bp):
GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAATGATGATTTTTCAAGAGAAACTGTCTCAAG
A
Found at i:1871781 original size:67 final size:68
Alignment explanation
Indices: 1871664--1871827 Score: 178
Period size: 68 Copynumber: 2.5 Consensus size: 68
1871654 TTTTTTTTAA
* * * * *
1871664 AAAG-AACATACTCAAAGA-TTTGTT-TC-AAAAGAAACTGTCTCAAGAGAGACAAAA-ATTGTT
1 AAAGAAACAGACTCAAAGAGTTTTTTCTCAAAAAAAAATTCTCTCAAGAGAGACAAAATATTGTT
*
1871724 T-T
66 TCC
* * *
1871726 AAGAGTAACAGGCTCAAAGAGTTTTTTCTCAAAAAAAAATTCTCTCAAGAGAGACAAAATTTTGT
1 AA-AGAAACAGACTCAAAGAGTTTTTTCTCAAAAAAAAATTCTCTCAAGAGAGACAAAATATTGT
1871791 TTCC
65 TTCC
* *
1871795 AAAGAAACAGACTCAAAGATTTTTTTTTCAAAA
1 AAAGAAACAGACTCAAAGAGTTTTTTCTCAAAA
1871828 GAAACGACTC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 12 0.14
65 5 0.06
66 2 0.02
67 25 0.30
68 33 0.40
69 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (68 bp):
AAAGAAACAGACTCAAAGAGTTTTTTCTCAAAAAAAAATTCTCTCAAGAGAGACAAAATATTGTT
TCC
Found at i:1871811 original size:68 final size:63
Alignment explanation
Indices: 1871664--1871820 Score: 172
Period size: 67 Copynumber: 2.4 Consensus size: 63
1871654 TTTTTTTTAA
* * * * *
1871664 AAAGAACATACTCAAAGATTTGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAAATTGTTTT
1 AAAGAACAGACTCAAAGATTTTTTTCAAAAAAAAACTCTCTCAAGAGAGACAAAAATTGTTTC
* * *
1871726 AAGAGTAACAGGCTCAAAGAGTTTTTTCTCAAAAAAAAATTCTCTCAAGAGAGACAAAATTTTGT
1 AA-AG-AACAGACTCAAAGA-TTTTTT-TCAAAAAAAAACTCTCTCAAGAGAGACAAAA-ATTGT
1871791 TTCC
61 TT-C
1871795 AAAGAAACAGACTCAAAGATTTTTTT
1 AAAG-AACAGACTCAAAGATTTTTTT
1871821 TTCAAAAGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 12 0.15
65 5 0.06
66 3 0.04
67 31 0.40
68 21 0.27
69 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (63 bp):
AAAGAACAGACTCAAAGATTTTTTTCAAAAAAAAACTCTCTCAAGAGAGACAAAAATTGTTTC
Found at i:1871816 original size:29 final size:28
Alignment explanation
Indices: 1871780--1871846 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
1871770 TCAAGAGAGA
*
1871780 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTGTTTCAAAAGAAAC-GACT
*
1871808 CAAAGATTTTTTTTTCAAAAGAAACGACT
1 CAAAGA-TTTTGTTTCAAAAGAAACGACT
1871837 CAAAGATTTT
1 CAAAGATTTT
1871847 TTCACGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 8 0.23
29 11 0.31
30 16 0.46
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (28 bp):
CAAAGATTTTGTTTCAAAAGAAACGACT
Done.