Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:1620538 original size:24 final size:24
Alignment explanation
Indices: 1620506--1620552 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1620496 TTGAGTTAAA
*
1620506 ATTTAGGTTCTGATTCGGGTTTGG
1 ATTTAGGTTCGGATTCGGGTTTGG
* *
1620530 ATTTGGGTTCGGGTTCGGGTTTG
1 ATTTAGGTTCGGATTCGGGTTTG
1620553 TGTTTAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.45
Consensus pattern (24 bp):
ATTTAGGTTCGGATTCGGGTTTGG
Found at i:1620570 original size:19 final size:19
Alignment explanation
Indices: 1620546--1620588 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1620536 GTTCGGGTTC
*
1620546 GGGTTTGTGTTT-AGATTTA
1 GGGTTTGAGTTTGAG-TTTA
1620565 GGGTTTGAGTTTGAGTTTA
1 GGGTTTGAGTTTGAGTTTA
1620584 GGGTT
1 GGGTT
1620589 CAAGTTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (19 bp):
GGGTTTGAGTTTGAGTTTA
Found at i:1621396 original size:12 final size:12
Alignment explanation
Indices: 1621354--1621396 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
1621344 ATAAACTATT
1621354 TTATAATTAATA
1 TTATAATTAATA
1621366 TTAAAATAATTATATA
1 TT---ATAATTA-ATA
1621382 TTATAATTAATA
1 TTATAATTAATA
1621394 TTA
1 TTA
1621397 ATATGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 8 0.30
13 7 0.26
15 7 0.26
16 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATTAATA
Found at i:1621409 original size:28 final size:26
Alignment explanation
Indices: 1621330--1621483 Score: 95
Period size: 28 Copynumber: 5.8 Consensus size: 26
1621320 TTCATCCCTA
* * *
1621330 TATAATTTATATTAATA-AACTATTT
1 TATAATTAATATTAATATAATTATAT
*
1621355 TATAATTAATATTAAAATAATTATATAT
1 TATAATTAATATTAATATAA-T-TATAT
1621383 TATAATTAATATTAATATGAAGTTATAT
1 TATAATTAATATTAATAT-AA-TTATAT
* * *
1621411 TAATAA--AATA-TAGT-TTATAAT-T
1 T-ATAATTAATATTAATATAATTATAT
*
1621433 TGTAATTAATATTAATATAAAATATAATAT
1 TATAATTAATATTAATAT--AAT-T-ATAT
*
1621463 ATAAAATTAATATTAATATAA
1 -TATAATTAATATTAATATAA
1621484 ACTATATGTT
Statistics
Matches: 99, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
21 3 0.03
22 2 0.02
23 7 0.07
24 4 0.04
25 17 0.17
26 5 0.05
27 6 0.06
28 27 0.27
29 11 0.11
30 1 0.01
31 16 0.16
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
TATAATTAATATTAATATAATTATAT
Found at i:1621497 original size:31 final size:30
Alignment explanation
Indices: 1621436--1621505 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
1621426 TATAATTTGT
1621436 AATTAATATTAATATAAAATATAATATATAA
1 AATTAATATTAATATAAAATATAATATAT-A
* *
1621467 AATTAATATTAATATAAACTAT-ATGTTATA
1 AATTAATATTAATATAAAATATAAT-ATATA
1621497 AATT-ATATT
1 AATTAATATT
1621506 GTATAGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 5 0.14
30 7 0.19
31 24 0.67
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATAATATATA
Found at i:1621690 original size:20 final size:22
Alignment explanation
Indices: 1621667--1621725 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
1621657 GGTTACATAT
1621667 ATAGTTTATATA-ACATATA-A
1 ATAGTTTATATATACATATACA
*
1621687 ATAGATTTGTATATATACATATACT
1 ATAG--TT-TATATATACATATACA
*
1621712 ATAGGTTATATATA
1 ATAGTTTATATATA
1621726 TATAGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.12
22 10 0.31
23 7 0.22
24 7 0.22
25 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (22 bp):
ATAGTTTATATATACATATACA
Found at i:1621729 original size:15 final size:16
Alignment explanation
Indices: 1621705--1621745 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1621695 GTATATATAC
1621705 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
1621721 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
1621736 ATATACTATA
1 ATATACTATA
1621746 CATATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:1621745 original size:20 final size:19
Alignment explanation
Indices: 1621663--1621755 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
1621653 TATAGGTTAC
*
1621663 ATATATAGTTTATATAACAT
1 ATATATAGTTTATAT-ATAT
* *
1621683 ATAAATAGATTTGTATATAT
1 ATATATAG-TTTATATATAT
* * *
1621703 ACATATACTATAGGT-TATAT
1 ATATATAGTTTA--TATATAT
1621723 ATATATAGTTTATATATACT
1 ATATATAGTTTATATATA-T
* *
1621743 ATACATATTTTAT
1 ATATATAGTTTAT
1621756 TAATACATGT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
18 1 0.02
19 6 0.11
20 41 0.75
21 7 0.13
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (19 bp):
ATATATAGTTTATATATAT
Found at i:1621985 original size:17 final size:17
Alignment explanation
Indices: 1621965--1622011 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
1621955 ATATGATTTA
1621965 TATATATATATATAGGT
1 TATATATATATATAGGT
*
1621982 TATATATATATATAGTT
1 TATATATATATATAGGT
1621999 TATATATACTATA
1 TATATATA-TATA
1622012 CATAGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (17 bp):
TATATATATATATAGGT
Found at i:1622046 original size:16 final size:16
Alignment explanation
Indices: 1622025--1622085 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
1622015 AGTTTATACA
1622025 TACATATACTATAAGT
1 TACATATACTATAAGT
* *
1622041 TACATATATGGTTTACATGT
1 TACATATA--CTATA-A-GT
1622061 ATACATATACTATAAGT
1 -TACATATACTATAAGT
*
1622078 TATATATA
1 TACATATA
1622086 ATAACAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 15 0.43
17 2 0.06
18 4 0.11
19 4 0.11
20 2 0.06
21 8 0.23
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TACATATACTATAAGT
Found at i:1622219 original size:14 final size:14
Alignment explanation
Indices: 1622200--1622237 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1622190 TAGTTTATAA
1622200 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAG
*
1622214 AGTTTATGGTTTAG
1 AGTTTAGGGTTTAG
1622228 -GTTTTAGGGT
1 AG-TTTAGGGT
1622238 CTAGTGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
AGTTTAGGGTTTAG
Found at i:1622367 original size:17 final size:19
Alignment explanation
Indices: 1622333--1622372 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1622323 ATAGATTACT
1622333 TATATTAGTTATACATACA
1 TATATTAGTTATACATACA
*
1622352 TATA-TAGTT-TATATACA
1 TATATTAGTTATACATACA
1622369 TATA
1 TATA
1622373 CATACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 4 0.20
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATTAGTTATACATACA
Found at i:1622438 original size:15 final size:15
Alignment explanation
Indices: 1622418--1622553 Score: 97
Period size: 13 Copynumber: 9.0 Consensus size: 15
1622408 ATATACTTTT
1622418 TATAGTTTATATATA
1 TATAGTTTATATATA
1622433 TATAG-TT-TATATA
1 TATAGTTTATATATA
*
1622446 CATAG-TT-TATATA
1 TATAGTTTATATATA
* *
1622459 TATAGTTCATATAAA
1 TATAGTTTATATATA
* *
1622474 CATA-ATT-TATATA
1 TATAGTTTATATATA
*
1622487 -ATAGCTTATAATAATTA
1 TATAGTTTAT-AT-A-TA
1622504 TATAGTTTATAATATAAA
1 TATAGTTTAT-ATAT--A
1622522 TATAGTTTATATATAAA
1 TATAGTTTATATAT--A
1622539 TATAGTTTATATATA
1 TATAGTTTATATATA
1622554 AACTTATATT
Statistics
Matches: 101, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
12 3 0.03
13 29 0.29
14 5 0.05
15 16 0.16
16 2 0.02
17 24 0.24
18 22 0.22
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATATATA
Found at i:1622471 original size:28 final size:26
Alignment explanation
Indices: 1622427--1622497 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 26
1622417 TTATAGTTTA
* *
1622427 TATATATATAGTTTATATACATAGTT
1 TATATATATAGTTTATAAACATAATT
1622453 TATATATATAGTTCATATAAACATAATT
1 TATATATATAGTT--TATAAACATAATT
*
1622481 TATATA-ATAGCTTATAA
1 TATATATATAGTTTATAA
1622498 TAATTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 5 0.12
26 13 0.32
27 5 0.12
28 17 0.43
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (26 bp):
TATATATATAGTTTATAAACATAATT
Found at i:1622513 original size:18 final size:18
Alignment explanation
Indices: 1622482--1622554 Score: 89
Period size: 17 Copynumber: 4.1 Consensus size: 18
1622472 AACATAATTT
*
1622482 ATATAATAGCTTATA-ATA
1 ATAT-ATAGTTTATATATA
1622500 ATTATATAGTTTATAATATA
1 A-TATATAGTTTAT-ATATA
1622520 A-ATATAGTTTATATATA
1 ATATATAGTTTATATATA
1622537 A-ATATAGTTTATATATA
1 ATATATAGTTTATATATA
1622554 A
1 A
1622555 ACTTATATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
17 23 0.45
18 20 0.39
19 4 0.08
20 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATATAGTTTATATATA
Found at i:1622537 original size:17 final size:17
Alignment explanation
Indices: 1622503--1622555 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
1622493 TATAATAATT
1622503 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
1622521 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
1622538 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
1622555 A
1 A
1622556 CTTATATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 24 0.69
18 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:1622565 original size:17 final size:16
Alignment explanation
Indices: 1622418--1622575 Score: 83
Period size: 17 Copynumber: 10.2 Consensus size: 16
1622408 ATATACTTTT
*
1622418 TATAGTT-TATATATA
1 TATAGTTATATATAAA
1622433 TATAGTT-TATAT--A
1 TATAGTTATATATAAA
*
1622446 CATAGTT-TATAT--A
1 TATAGTTATATATAAA
*
1622459 TATAGTT-CATATAAA
1 TATAGTTATATATAAA
* *
1622474 CATAATT-TATAT--A
1 TATAGTTATATATAAA
1622487 -ATAGCTTATA-ATAATTA
1 TATAG-TTATATATAA--A
1622504 TATAGTTTATAATATAAA
1 TATAG-TTAT-ATATAAA
1622522 TATAGTTTATATATAAA
1 TATAG-TTATATATAAA
1622539 TATAGTTTATATATAAA
1 TATAG-TTATATATAAA
*
1622556 CTTATA-TTATATATATA
1 --TATAGTTATATATAAA
1622573 TAT
1 TAT
1622576 TATAATTTTT
Statistics
Matches: 121, Mismatches: 9, Indels: 26
0.78 0.06 0.17
Matches are distributed among these distances:
12 3 0.02
13 28 0.23
14 2 0.02
15 25 0.21
17 35 0.29
18 19 0.16
19 5 0.04
20 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (16 bp):
TATAGTTATATATAAA
Found at i:1622566 original size:34 final size:34
Alignment explanation
Indices: 1622503--1622575 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
1622493 TATAATAATT
1622503 ATATAGTTTATAATATAAATATAGTTTATATATAA
1 ATATAGTTTATAATATAAATATAG-TTATATATAA
*
1622538 ATATAGTTTAT-ATATAAACTTATA-TTATATATAT
1 ATATAGTTTATAATATAAA--TATAGTTATATATAA
1622572 ATAT
1 ATAT
1622576 TATAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 20 0.57
35 11 0.31
36 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (34 bp):
ATATAGTTTATAATATAAATATAGTTATATATAA
Found at i:1624932 original size:12 final size:12
Alignment explanation
Indices: 1624915--1624998 Score: 82
Period size: 12 Copynumber: 7.0 Consensus size: 12
1624905 CGAAAATCAA
1624915 AACAGAATTCAG
1 AACAGAATTCAG
1624927 AACAG-ATATCAG
1 AACAGAAT-TCAG
1624939 AACAGAATTCAG
1 AACAGAATTCAG
*
1624951 AATAG-ATATCAG
1 AACAGAAT-TCAG
*
1624963 AACAGAATCCAG
1 AACAGAATTCAG
* * *
1624975 ATCAGAAATAAG
1 AACAGAATTCAG
*
1624987 AACAAAATTCAG
1 AACAGAATTCAG
1624999 GTCATGTATC
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 4 0.07
12 49 0.86
13 4 0.07
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:1624939 original size:7 final size:6
Alignment explanation
Indices: 1624917--1624981 Score: 50
Period size: 5 Copynumber: 10.8 Consensus size: 6
1624907 AAAATCAAAA
1624917 CAGAATT CAGAA- CAGATAT CAGAA- CAGAATT CAGAAT -AGATAT CAGAA-
1 CAGAA-T CAGAAT CAGA-AT CAGAAT CAGAA-T CAGAAT CAGA-AT CAGAAT
1624965 CAGAAT CCAG-AT CAGAA
1 CAGAAT -CAGAAT CAGAA
1624982 ATAAGAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
5 20 0.41
6 9 0.18
7 20 0.41
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
CAGAAT
Found at i:1624942 original size:24 final size:24
Alignment explanation
Indices: 1624910--1625021 Score: 118
Period size: 24 Copynumber: 4.7 Consensus size: 24
1624900 GATATCGAAA
*
1624910 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGAACAGAT
*
1624934 ATCAGAACAGAATTCAGAATAGAT
1 ATCAGAACAGAATTCAGAACAGAT
* * *
1624958 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGAACAGAT
* * **
1624982 ATAAGAACAAAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAGAACA-GAT
*
1625006 ATCAGAATAGAATTCA
1 ATCAGAACAGAATTCA
1625022 AGTCAGAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
24 72 0.99
25 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACAGAT
Found at i:1625033 original size:24 final size:24
Alignment explanation
Indices: 1624910--1625035 Score: 98
Period size: 24 Copynumber: 5.2 Consensus size: 24
1624900 GATATCGAAA
* *
1624910 ATCAAAACAGAATTC-AGAACAGAT
1 ATCAGAACAGAATTCAAG-TCAGAT
*
1624934 ATCAGAACAGAATTCAGAAT-AGAT
1 ATCAGAACAGAATTCA-AGTCAGAT
* *
1624958 ATCAGAACAGAA-TCCAGATCAGAA
1 ATCAGAACAGAATTCAAG-TCAGAT
* * *
1624982 ATAAGAACAAAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCA-GAT
* *
1625006 ATCAGAATAGAATTCAAGTCAGAA
1 ATCAGAACAGAATTCAAGTCAGAT
1625030 ATCAGA
1 ATCAGA
1625036 TAAAATATTA
Statistics
Matches: 79, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
22 1 0.01
23 4 0.05
24 69 0.87
25 4 0.05
26 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCAGAT
Found at i:1625517 original size:19 final size:19
Alignment explanation
Indices: 1625493--1625531 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1625483 TCGAATGCAT
1625493 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
**
1625512 TCCATGCATTGATGCACTC
1 TCCATGCACCGATGCACTC
1625531 T
1 T
1625532 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1625553 original size:64 final size:64
Alignment explanation
Indices: 1625473--1625640 Score: 200
Period size: 64 Copynumber: 2.6 Consensus size: 64
1625463 TCAATGAATA
* * *
1625473 AATTGAAACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATTGATGCACTC-TG-ATT
1 AATTAAAACATCGAATGCATT-CATGCATCGATGCACTCTCCATGCATTGATGCAC-CAGGCATT
1625536 T
64 T
* **
1625537 AATTAAAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATTGATGCACCAGGCTATT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCATGCATTGATGCACCAGGC-ATT
1625602 T
64 T
*
1625603 --TTCAAACATCGAATGCACTTCATGCATCGATGCACTCT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCT
1625641 TAGTGCACCA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 82 0.92
65 2 0.02
66 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (64 bp):
AATTAAAACATCGAATGCATTCATGCATCGATGCACTCTCCATGCATTGATGCACCAGGCATTT
Found at i:1633054 original size:21 final size:21
Alignment explanation
Indices: 1633025--1633083 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
1633015 ACTCCGGGAG
* *
1633025 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
1633046 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
1633067 CT-CCTCCT-TCG-GCTCCT
1 CTAGCTCCTCTCGAGCTCCT
1633084 GCTGATGACG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.18
19 3 0.09
20 5 0.15
21 20 0.59
ACGTcount: A:0.05, C:0.46, G:0.15, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:1634095 original size:21 final size:21
Alignment explanation
Indices: 1634071--1634110 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634061 TTTTCAAAGG
1634071 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1634092 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1634111 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1634160 original size:19 final size:19
Alignment explanation
Indices: 1634124--1634193 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
1634114 TAAATTGAAA
1634124 CATCGAATGCA-T-TCCATG
1 CATCG-ATGCACTCTCCATG
*
1634142 CACCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
1634161 CATCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
1634180 CATCGATGCACTCT
1 CATCGATGCACTCT
1634194 GATTTAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 38 0.79
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.26
Consensus pattern (19 bp):
CATCGATGCACTCTCCATG
Found at i:1634218 original size:83 final size:83
Alignment explanation
Indices: 1634091--1634254 Score: 231
Period size: 83 Copynumber: 2.0 Consensus size: 83
1634081 TGCATCAATA
* **
1634091 CCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACTCT
1 CCATGCATCGATGCATC-ATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAAT
1634156 CCATGCATCGATGCACTCT
65 CCATGCATCGATGCACTCT
* * ** *
1634175 CCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAAT
1 CCATGCATCGATGCA-TCATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAAT
1634239 CCATGCATCGATGCAC
65 CCATGCATCGATGCAC
1634255 CAGGCTATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
83 54 0.76
84 15 0.21
85 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (83 bp):
CCATGCATCGATGCATCATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAATC
CATGCATCGATGCACTCT
Found at i:1634299 original size:17 final size:19
Alignment explanation
Indices: 1634271--1634319 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1634261 ATTTTCCAAA
1634271 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1634289 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
1634308 CACCGATGCACT
1 CATCGATGCACT
1634320 AGGAATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1638883 original size:20 final size:21
Alignment explanation
Indices: 1638855--1638895 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1638845 ATAAAATCAT
*
1638855 TTATGAATA-CAAAATAAAAG
1 TTATCAATATCAAAATAAAAG
1638875 TTATCAATATTCAAAATAAAA
1 TTATCAATA-TCAAAATAAAA
1638896 AAGATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (21 bp):
TTATCAATATCAAAATAAAAG
Found at i:1639513 original size:12 final size:12
Alignment explanation
Indices: 1639496--1639579 Score: 73
Period size: 12 Copynumber: 7.0 Consensus size: 12
1639486 CGGAAATCAA
1639496 AACAGAATTCAG
1 AACAGAATTCAG
*
1639508 AACAG-ATATCAA
1 AACAGAAT-TCAG
*
1639520 AACATAATTCAG
1 AACAGAATTCAG
* *
1639532 AACA-TATATCAT
1 AACAGAAT-TCAG
*
1639544 AACAGAATCCAG
1 AACAGAATTCAG
* *
1639556 ATCAGAAATCAG
1 AACAGAATTCAG
1639568 AACAGAATTCAG
1 AACAGAATTCAG
1639580 GTCATGTATC
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
11 4 0.07
12 47 0.85
13 4 0.07
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:1639518 original size:24 final size:24
Alignment explanation
Indices: 1639491--1639579 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
1639481 CATATCGGAA
1639491 ATCAAAACAGAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGAACAGAT
* *
1639515 ATCAAAACATAATTCAGAACATAT
1 ATCAAAACAGAATTCAGAACAGAT
* * * *
1639539 ATCATAACAGAATCCAGATCAGAA
1 ATCAAAACAGAATTCAGAACAGAT
*
1639563 ATCAGAACAGAATTCAG
1 ATCAAAACAGAATTCAG
1639580 GTCATGTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGAACAGAT
Found at i:1639577 original size:48 final size:48
Alignment explanation
Indices: 1639491--1639616 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 48
1639481 CATATCGGAA
* * * *
1639491 ATCAAAACAGAATTCAGAACAGATATCAAAACATAATTCAGAACATAT
1 ATCAAAACAGAATTCAGATCAGAAATCAGAACAGAATTCAGAACATAT
* * ** *
1639539 ATCATAACAGAATCCAGATCAGAAATCAGAACAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAGATCAGAAATCAGAACAGAATTCAGAACATAT
* *
1639587 ATCAGAATAGAATTCA-AGTCAGAAATCAGA
1 ATCAAAACAGAATTCAGA-TCAGAAATCAGA
1639617 TAAAATATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 64 0.98
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAAAACAGAATTCAGATCAGAAATCAGAACAGAATTCAGAACATAT
Found at i:1639590 original size:24 final size:24
Alignment explanation
Indices: 1639491--1639602 Score: 109
Period size: 24 Copynumber: 4.7 Consensus size: 24
1639481 CATATCGGAA
*
1639491 ATCAAAACAGAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1639515 ATCAAAACATAATTCAGAACATAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1639539 ATCATAACAGAATCCAGATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
* *
1639563 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1639587 ATCAGAATAGAATTCA
1 ATCAAAACAGAATTCA
1639603 AGTCAGAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 73 0.99
25 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1639614 original size:24 final size:24
Alignment explanation
Indices: 1639539--1639616 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
1639529 CAGAACATAT
* *
1639539 ATCATAACAGAA-TCCAGATCAGAA
1 ATCAGAACAGAATTCAAG-TCAGAA
* *
1639563 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCA-GAA
*
1639587 ATCAGAATAGAATTCAAGTCAGAA
1 ATCAGAACAGAATTCAAGTCAGAA
1639611 ATCAGA
1 ATCAGA
1639617 TAAAATATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCAGAA
Found at i:1642112 original size:13 final size:13
Alignment explanation
Indices: 1642094--1642145 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1642084 TGTCAACGCC
1642094 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* * *
1642107 GGTCAATGGATTG
1 GGTCAACGGGTCG
1642120 GGT---CGGGTCG
1 GGTCAACGGGTCG
1642130 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1642143 GGT
1 GGT
1642146 GGGTTGTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
10 7 0.23
13 23 0.77
ACGTcount: A:0.13, C:0.17, G:0.48, T:0.21
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1642145 original size:23 final size:23
Alignment explanation
Indices: 1642100--1642149 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1642090 CGCCGGTCAA
* *
1642100 CGGGTCGGGTCAATGGATTGGGT
1 CGGGTCGGGTCAACGGATCGGGT
*
1642123 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGATCGGGT
1642146 -GGGT
1 CGGGT
1642150 TGTAACCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.10, C:0.16, G:0.52, T:0.22
Consensus pattern (23 bp):
CGGGTCGGGTCAACGGATCGGGT
Found at i:1644283 original size:24 final size:24
Alignment explanation
Indices: 1644251--1644344 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
1644241 ACGGAGATAT
*
1644251 CAGAAATCAAAATAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* *
1644275 CAGATATCAAAATAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * *
1644299 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCAGAA
*
1644323 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAAAACAGAATTCAG
1644345 GTCATGTATC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:1644333 original size:36 final size:37
Alignment explanation
Indices: 1644249--1644344 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 37
1644239 AAACGGAGAT
* *
1644249 ATCAGAAATCAAAATAGAATTCAGAACAGATATCAAA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAAA
* * *
1644286 AT-AGAATTCAGAACAG-ATATCAGAACAGA-ATCCAG
1 ATCAGAAATCAGAACAGAAT-TCAGAACAGATATCAAA
1644321 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
1644345 GTCATGTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 8 0.16
36 38 0.76
37 4 0.08
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.18
Consensus pattern (37 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAAA
Found at i:1644344 original size:12 final size:12
Alignment explanation
Indices: 1644264--1644344 Score: 85
Period size: 12 Copynumber: 6.8 Consensus size: 12
1644254 AAATCAAAAT
1644264 AGAATTCAGAAC
1 AGAATTCAGAAC
* *
1644276 AG-ATATCAAAAT
1 AGAAT-TCAGAAC
1644288 AGAATTCAGAAC
1 AGAATTCAGAAC
1644300 AG-ATATCAGAAC
1 AGAAT-TCAGAAC
* *
1644312 AGAATCCAGATC
1 AGAATTCAGAAC
*
1644324 AGAAATCAGAAC
1 AGAATTCAGAAC
1644336 AGAATTCAG
1 AGAATTCAG
1644345 GTCATGTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 4 0.07
12 47 0.85
13 4 0.07
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.17
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:1644355 original size:24 final size:24
Alignment explanation
Indices: 1644249--1644357 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1644239 AAACGGAGAT
* * * *
1644249 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGATATCAGAACAGAATCCAG
* * * *
1644273 AACAGATATCAAAATAGAATTCAG
1 ATCAGATATCAGAACAGAATCCAG
*
1644297 AACAGATATCAGAACAGAATCCAG
1 ATCAGATATCAGAACAGAATCCAG
* *
1644321 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATCCAG
*
1644345 GTCATG-TATCAGA
1 ATCA-GATATCAGA
1644358 TAAAATATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 73 0.99
25 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATCCAG
Found at i:1651524 original size:3 final size:3
Alignment explanation
Indices: 1651516--1651602 Score: 138
Period size: 3 Copynumber: 29.0 Consensus size: 3
1651506 CCATATTGAT
*
1651516 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1651564 TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1651603 AATATATATA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1651948 original size:18 final size:17
Alignment explanation
Indices: 1651927--1651964 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1651917 ACCACACCGG
1651927 AGAGAC-AGAGAACACAAC
1 AGAGACGAG-GAA-ACAAC
1651945 AGAGACGAGGAAACAAC
1 AGAGACGAGGAAACAAC
1651962 AGA
1 AGA
1651965 CCCCAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.55, C:0.18, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAGACGAGGAAACAAC
Found at i:1651962 original size:17 final size:18
Alignment explanation
Indices: 1651927--1651964 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1651917 ACCACACCGG
1651927 AGAGACAGAGAACACAAC
1 AGAGACAGAGAACACAAC
1651945 AGAGAC-GAGGAA-ACAAC
1 AGAGACAGA-GAACACAAC
1651962 AGA
1 AGA
1651965 CCCCAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.55, C:0.18, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAGACAGAGAACACAAC
Found at i:1652963 original size:15 final size:16
Alignment explanation
Indices: 1652945--1652975 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1652935 TATAATAAAT
1652945 AAAT-ATTTATTTTAA
1 AAATAATTTATTTTAA
1652960 AAATAATTTATTTTAA
1 AAATAATTTATTTTAA
1652976 TATCGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATAATTTATTTTAA
Found at i:1653655 original size:24 final size:23
Alignment explanation
Indices: 1653615--1653664 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1653605 TTAATTTATA
*
1653615 ATTTTTTTATATATATACATATT
1 ATTTTTATATATATATACATATT
* *
1653638 ATTTTTATAGTATTTATATATATT
1 ATTTTTATA-TATATATACATATT
1653662 ATT
1 ATT
1653665 AATATTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTTATATATATATACATATT
Found at i:1664303 original size:1 final size:1
Alignment explanation
Indices: 1664297--1664358 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
1664287 ATGATTGAAG
* * * * * * * *
1664297 AAAAAAAAGAAAAAAAAGAAAAAAGAAAAAAAAAGAGAAAAAAGAGAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1664359 GGGGTCAAGG
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:1664308 original size:9 final size:9
Alignment explanation
Indices: 1664294--1664357 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
1664284 ATTATGATTG
1664294 AAGAAAAAA
1 AAGAAAAAA
1664303 AAGAAAAAA
1 AAGAAAAAA
1664312 AAGAAAAAA
1 AAGAAAAAA
*
1664321 GA-AAAAAA
1 AAGAAAAAA
*
1664329 AAGAGAAAA
1 AAGAAAAAA
*
1664338 AAGAGAAAA
1 AAGAAAAAA
1664347 AAGAAAAAA
1 AAGAAAAAA
1664356 AA
1 AA
1664358 AGGGGTCAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
8 7 0.14
9 43 0.86
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1664374 original size:28 final size:28
Alignment explanation
Indices: 1664297--1664359 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1664287 ATGATTGAAG
1664297 AAAAAAAAGA-AAAAAA-AGAAAAAAGA
1 AAAAAAAAGAGAAAAAAGAGAAAAAAGA
1664323 AAAAAAAAGAGAAAAAAGAGAAAAAAGA
1 AAAAAAAAGAGAAAAAAGAGAAAAAAGA
1664351 AAAAAAAAG
1 AAAAAAAAG
1664360 GGGTCAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 10 0.29
27 6 0.17
28 19 0.54
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (28 bp):
AAAAAAAAGAGAAAAAAGAGAAAAAAGA
Found at i:1665659 original size:83 final size:83
Alignment explanation
Indices: 1665510--1666390 Score: 1584
Period size: 83 Copynumber: 10.6 Consensus size: 83
1665500 AAATGCAATG
*
1665510 TGCTCATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1665575 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* *
1665593 TGC-CAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
* *
1665657 TGAATTTGGAAGATGAATG
65 TGAATTTAGAAGATGAATT
1665676 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* *
1665741 GAATTTGGAAGATGAATG
66 GAATTTAGAAGATGAATT
1665759 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* *
1665824 GAATTTGGAAGATGAATG
66 GAATTTAGAAGATGAATT
*
1665842 TGCTCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1665907 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
1665925 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1665990 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
1666008 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* *
1666073 GAATTTGGAAGATGAATG
66 GAATTTAGAAGATGAATT
*
1666091 TGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1666156 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
1666174 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1666239 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
*
1666257 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* *
1666322 GGATTTAAAAGATGAATT
66 GAATTTAGAAGATGAATT
* *
1666340 TGCTCATAGCATCTTCTGGAAGTGATCTTTGAATTATCTGATCTGGTTTGG
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1666391 TAGGAACTAC
Statistics
Matches: 774, Mismatches: 22, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
82 1 0.00
83 772 1.00
84 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAATTTAGAAGATGAATT
Found at i:1667452 original size:113 final size:113
Alignment explanation
Indices: 1667115--1667681 Score: 827
Period size: 113 Copynumber: 5.0 Consensus size: 113
1667105 TAGCAAAGAT
* * * *
1667115 TCAAATCTATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGA-TCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * * *
1667179 AAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * *
1667228 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCAT
1667292 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1667344 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1667409 AGAAGGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1667457 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1667522 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1667570 -CTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * *
1667633 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1667682 ATAATTCTAT
Statistics
Matches: 415, Mismatches: 32, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
112 76 0.18
113 238 0.57
114 1 0.00
115 1 0.00
116 98 0.24
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1667536 original size:229 final size:228
Alignment explanation
Indices: 1667115--1667681 Score: 858
Period size: 229 Copynumber: 2.5 Consensus size: 228
1667105 TAGCAAAGAT
* * *
1667115 TCAAATCTATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGA-TCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* * ** *
1667179 AAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCATTTG
*
1667244 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGA
130 ATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAGA
*
1667309 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
194 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
1667344 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
* * *
1667409 AGAAGGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCATTTGA
* * *
1667474 TGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAA
131 TGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAA
1667536 GTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
195 GTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * *
1667570 -CTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
*
1667633 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
1667682 ATAATTCTAT
Statistics
Matches: 310, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
225 72 0.23
226 85 0.27
227 1 0.00
228 2 0.01
229 149 0.48
230 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (228 bp):
TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCATTTGA
TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:1668016 original size:3 final size:3
Alignment explanation
Indices: 1668008--1668094 Score: 129
Period size: 3 Copynumber: 29.0 Consensus size: 3
1667998 CCATATTGAT
* *
1668008 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1668056 TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1668095 AATATATATA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1668492 original size:18 final size:17
Alignment explanation
Indices: 1668469--1668506 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1668459 AAAAGAACGG
1668469 AGAGAC-AGAGAACACAAC
1 AGAGACGAG-GAA-ACAAC
1668487 AGAGACGAGGAAACAAC
1 AGAGACGAGGAAACAAC
1668504 AGA
1 AGA
1668507 CCCCAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.55, C:0.18, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAGACGAGGAAACAAC
Found at i:1668504 original size:17 final size:18
Alignment explanation
Indices: 1668469--1668506 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1668459 AAAAGAACGG
1668469 AGAGACAGAGAACACAAC
1 AGAGACAGAGAACACAAC
1668487 AGAGAC-GAGGAA-ACAAC
1 AGAGACAGA-GAACACAAC
1668504 AGA
1 AGA
1668507 CCCCAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.55, C:0.18, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAGACAGAGAACACAAC
Found at i:1671715 original size:20 final size:21
Alignment explanation
Indices: 1671692--1671735 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1671682 TATCGATATT
*
1671692 GAGGG-TTCGGTATCGAGACC
1 GAGGGCTTCGGTATCAAGACC
* *
1671712 GAGGGCTTTGTTATCAAGACC
1 GAGGGCTTCGGTATCAAGACC
1671733 GAG
1 GAG
1671736 ATTCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
GAGGGCTTCGGTATCAAGACC
Found at i:1673116 original size:3 final size:3
Alignment explanation
Indices: 1673108--1673196 Score: 78
Period size: 3 Copynumber: 30.0 Consensus size: 3
1673098 CCATTTGCTT
*
1673108 TTA TTA TTA TTA -TA TTA TTA TT- TTA TT- TATA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * * *
1673151 TT- TTA TTTA TTA GTTT TTA TTA TTA ATA ATA TTA TTA TTA CTA TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1673197 CAGGTCCAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
2 7 0.10
3 59 0.83
4 5 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1673144 original size:31 final size:29
Alignment explanation
Indices: 1673106--1673189 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 29
1673096 ATCCATTTGC
1673106 TTTTATTATTATTATATTATTATTTTA-T
1 TTTTATTATTATTATATTATTATTTTAGT
* *
1673134 TTATACTATTATTATTATTTTATT-TATTAGT
1 TT-T--TATTATTATTATATTATTATTTTAGT
*
1673165 TTTTATTATTAATAATATTATTATT
1 TTTTATTATT-ATTATATTATTATT
1673190 ACTATTACAG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
28 9 0.20
29 10 0.22
30 6 0.13
31 20 0.44
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTTATTATTATTATATTATTATTTTAGT
Found at i:1673151 original size:34 final size:36
Alignment explanation
Indices: 1673108--1673196 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 36
1673098 CCATTTGCTT
*
1673108 TTATTATTATTATATTATTA--TTTTATT-TATACTA
1 TTATTATTATTATATTATTAGTTTTTATTAT-TAATA
*
1673142 TTATTATTATTTTATTTATTAGTTTTTATTATTAATA
1 TTATTATTATTATA-TTATTAGTTTTTATTATTAATA
*
1673179 ATATTATTATTACTATTA
1 TTATTATTATTA-TATTA
1673197 CAGGTCCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 13 0.28
35 6 0.13
37 24 0.52
38 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (36 bp):
TTATTATTATTATATTATTAGTTTTTATTATTAATA
Found at i:1673188 original size:28 final size:27
Alignment explanation
Indices: 1673107--1673190 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
1673097 TCCATTTGCT
*
1673107 TTTATTATTATTATATTATTATT-TTA
1 TTTATTATTATTATAATATTATTATTA
* *
1673133 TTTATACTATTATTATTATTTTATTTATTA
1 TTTAT--TATTATTATAATATTA-TTATTA
1673163 GTTT-TTATTATTAATAATATTATTATTA
1 -TTTATTATTATT-ATAATATTATTATTA
1673191 CTATTACAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 5 0.11
28 26 0.55
29 9 0.19
30 4 0.09
31 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTATTATTATTATAATATTATTATTA
Found at i:1674584 original size:29 final size:30
Alignment explanation
Indices: 1674515--1674585 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
1674505 TTTTAGCCAC
* *
1674515 TATTTAGTTATAT-TTTAATTTTATATGTT
1 TATTTAGTCATATATTTAATTTTATATGAT
1674544 TATTT--TCAATATATTTAATTATTAT-T-AT
1 TATTTAGTC-ATATATTTAATT-TTATATGAT
1674572 TATTTAGTCATATA
1 TATTTAGTCATATA
1674586 AATATGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
27 1 0.03
28 10 0.29
29 18 0.51
30 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTAGTCATATATTTAATTTTATATGAT
Found at i:1674990 original size:2 final size:2
Alignment explanation
Indices: 1674943--1674980 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1674933 ATTTATAAAA
*
1674943 AT AT AT A- AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1674981 ATTAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1675899 original size:29 final size:30
Alignment explanation
Indices: 1675811--1675899 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 30
1675801 CAAAATATAT
* *
1675811 AACTTTTAAAAAATTACATTTTTAGTCCCTA
1 AACTTTTAAAAAATTACA-TTTTGGTCACTA
** * * *
1675842 AACTTTTCCAAATTTATACTTTGGTCACTA
1 AACTTTTAAAAAATTACATTTTGGTCACTA
*
1675872 AACTTTT-AAAACTTACATTTTGGTCACT
1 AACTTTTAAAAAATTACATTTTGGTCACT
1675900 GGTCAGATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
29 17 0.36
30 16 0.34
31 14 0.30
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAAAATTACATTTTGGTCACTA
Found at i:1678131 original size:16 final size:16
Alignment explanation
Indices: 1678110--1678141 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1678100 TTAACGTTAT
1678110 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
1678126 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
1678142 ATTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:1678365 original size:12 final size:12
Alignment explanation
Indices: 1678350--1678374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1678340 GAATAAATAA
1678350 ATAAATAAAATT
1 ATAAATAAAATT
1678362 ATAAATAAAATT
1 ATAAATAAAATT
1678374 A
1 A
1678375 AAAAAAAGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATAAAATT
Found at i:1678842 original size:15 final size:15
Alignment explanation
Indices: 1678824--1678857 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1678814 AGGACAACAA
* *
1678824 TGATGATGGTGGTTG
1 TGATGATAGTGGTGG
1678839 TGATGATAGTGGTGG
1 TGATGATAGTGGTGG
1678854 TGAT
1 TGAT
1678858 AATAAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (15 bp):
TGATGATAGTGGTGG
Found at i:1679359 original size:24 final size:24
Alignment explanation
Indices: 1679332--1679377 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1679322 AGATATATAA
* *
1679332 TTTTTATATTTGT-AGTTATGTAT
1 TTTTTTTATTTCTAAGTTATGTAT
*
1679355 TTTTTTTCTTTCTAAGTTATGTA
1 TTTTTTTATTTCTAAGTTATGTA
1679378 AAATGAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTTTATTTCTAAGTTATGTAT
Found at i:1680278 original size:3 final size:3
Alignment explanation
Indices: 1680258--1680314 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
1680248 TTTTTTCATA
* * * * *
1680258 ATT ATA ATT ATA ATT ATT ATT AAT ATA ATAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
1680304 ATTT ATT ATT A
1 A-TT ATT ATT A
1680315 AATAAATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1680813 original size:18 final size:18
Alignment explanation
Indices: 1680786--1680820 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1680776 AACTACAGAG
*
1680786 AAAAAAATAACCCACAAC
1 AAAAAAATAAACCACAAC
*
1680804 AAAAACATAAACCACAA
1 AAAAAAATAAACCACAA
1680821 GCAGAGAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.26, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAATAAACCACAAC
Found at i:1681646 original size:27 final size:27
Alignment explanation
Indices: 1681628--1681679 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1681618 TATTTAGTTA
1681628 TATTTTAATTTAAATATTAATTATTAT
1 TATTTTAATTTAAATATTAATTATTAT
* * *
1681655 TATTTTATTTTTAATATAAATTATT
1 TATTTTAATTTAAATATTAATTATT
1681680 TTAATCATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTAATTTAAATATTAATTATTAT
Found at i:1682958 original size:9 final size:9
Alignment explanation
Indices: 1682944--1682972 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1682934 AGCTCTAGCT
1682944 TTTAATTTA
1 TTTAATTTA
1682953 TTTAATTTA
1 TTTAATTTA
1682962 TTTAATTTA
1 TTTAATTTA
1682971 TT
1 TT
1682973 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTAATTTA
Found at i:1687467 original size:6 final size:6
Alignment explanation
Indices: 1687441--1687513 Score: 89
Period size: 6 Copynumber: 12.5 Consensus size: 6
1687431 TCCAGTAAAG
* * *
1687441 AAAGAA GAAGGAA AAAAAA AAAGAA AAA-AA AAAGAA AAAGGA AAAGAA
1 AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
1687489 AAAGAA AAAG-A AAAG-A AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1687514 AAGGAAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
5 15 0.26
6 38 0.66
7 5 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1687467 original size:11 final size:11
Alignment explanation
Indices: 1687453--1687515 Score: 83
Period size: 11 Copynumber: 5.6 Consensus size: 11
1687443 AGAAGAAGGA
1687453 AAAAAAAAAAG
1 AAAAAAAAAAG
1687464 AAAAAAAAAAG
1 AAAAAAAAAAG
*
1687475 AAAAAGGAAAAG
1 AAAAA-AAAAAG
1687487 AAAAAGAAAAAG
1 AAAAA-AAAAAG
*
1687499 -AAAAGAAAAG
1 AAAAAAAAAAG
1687509 AAAAAAA
1 AAAAAAA
1687516 GGAAAATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
10 5 0.11
11 25 0.54
12 16 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1687477 original size:23 final size:23
Alignment explanation
Indices: 1687437--1687515 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
1687427 CTCATCCAGT
* * * *
1687437 AAAGAAAGAAGAAGGAAAAAAAA
1 AAAGAAAAAAAAAAGAAAAAAGA
*
1687460 AAAGAAAAAAAAAAGAAAAAGGA
1 AAAGAAAAAAAAAAGAAAAAAGA
1687483 AAAGAAAAAGAAAAAG--AAAAGA
1 AAAGAAAAA-AAAAAGAAAAAAGA
1687505 AAAGAAAAAAA
1 AAAGAAAAAAA
1687516 GGAAAATTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 14 0.29
23 27 0.55
24 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAAAAAGAAAAAAGA
Found at i:1687516 original size:30 final size:30
Alignment explanation
Indices: 1687437--1687521 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
1687427 CTCATCCAGT
*
1687437 AAAG-AAAGAAGAAGGAAAAAA-AAAAAGAA
1 AAAGAAAAGAA-AAGAAAAAAAGAAAAAGAA
* **
1687466 AAAAAAAAGAAAA-AGGAAAAGAAAAAGAA
1 AAAGAAAAGAAAAGAAAAAAAGAAAAAGAA
*
1687495 AAAGAAAAGAAAAGAAAAAAAGGAAAA
1 AAAGAAAAGAAAAGAAAAAAAGAAAAA
1687522 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
28 4 0.09
29 25 0.56
30 16 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (30 bp):
AAAGAAAAGAAAAGAAAAAAAGAAAAAGAA
Found at i:1687521 original size:6 final size:5
Alignment explanation
Indices: 1687437--1687521 Score: 61
Period size: 6 Copynumber: 16.6 Consensus size: 5
1687427 CTCATCCAGT
* *
1687437 AAAG- AAAGA AGAAGG AAA-A AAA-A AAAGAA AAAAA AAAGAA AAAGGA
1 AAAGA AAAGA A-AAGA AAAGA AAAGA AAAG-A AAAGA AAAG-A AAA-GA
*
1687483 AAAGAA AAAGAA AAAGA AAAGA AAAGA AAA-A AAGGA AAA
1 AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1687522 TTGAATCAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
4 14 0.21
5 25 0.37
6 27 0.40
7 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1692184 original size:22 final size:22
Alignment explanation
Indices: 1692158--1692234 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1692148 ATCTACACTC
1692158 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1692180 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1692202 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1692224 TTCAAATATGA
1 TTCAAAGATGA
1692235 AAGCTTTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1693042 original size:76 final size:76
Alignment explanation
Indices: 1692912--1694010 Score: 1874
Period size: 76 Copynumber: 14.5 Consensus size: 76
1692902 CTATTTCCCA
*
1692912 CATCTGTAAGTCTTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1692977 AGTCTTAGGGT
66 AGCCTTAGGGT
*
1692988 CATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693053 AGCCTTAAGGT
66 AGCCTTAGGGT
* *
1693064 CATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAAGCCATCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693129 AGCCTTAGGAT
66 AGCCTTAGGGT
* *
1693140 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693205 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
1693216 CATCTGTAAGTCTTATAGTGCATGCTGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693281 AGCCTTAGGGC
66 AGCCTTAGGGT
* * *
1693292 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCATCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693357 AGCCTTAGGAT
66 AGCCTTAGGGT
*
1693368 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693433 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1693444 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693509 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1693520 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693585 AGCCTTAGGAT
66 AGCCTTAGGGT
* *
1693596 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTGGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693661 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1693672 CATATGTAACTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693737 GGCCTTAGGGT
66 AGCCTTAGGGT
* *
1693748 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1693813 AGCCTTAGGAT
66 AGCCTTAGGGT
*
1693824 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693889 AGCCTTAGGGT
66 AGCCTTAGGGT
1693900 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1693965 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
1693976 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1694011 CATTTCCATC
Statistics
Matches: 959, Mismatches: 64, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 959 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1694152 original size:3 final size:3
Alignment explanation
Indices: 1694132--1694188 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
1694122 TTTTTTCATA
* * * * *
1694132 ATT ATA ATT ATA ATT ATT ATT AAT ATA ATAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
1694178 ATTT ATT ATT A
1 A-TT ATT ATT A
1694189 AATAAATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1695505 original size:27 final size:27
Alignment explanation
Indices: 1695487--1695538 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1695477 TATTTAGTTA
1695487 TATTTTAATTTAAATATTAATTATTAT
1 TATTTTAATTTAAATATTAATTATTAT
* *
1695514 TATTTTATTTTTAATATTAATTATT
1 TATTTTAATTTAAATATTAATTATT
1695539 TTAATCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTTAATTTAAATATTAATTATTAT
Found at i:1695551 original size:27 final size:25
Alignment explanation
Indices: 1695494--1695575 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 25
1695484 TTATATTTTA
* **
1695494 ATTTAAATATTAATTATTATTATTTT
1 ATTTTAATATTAATTATT-TTATCAT
1695520 ATTTTTAATATTAATTATTTTAATCAT
1 A-TTTTAATATTAATTATTTT-ATCAT
* *
1695547 GTTTTAATATTTATTTATTTT-TCAAT
1 ATTTTAATA-TTAATTATTTTATC-AT
1695573 ATT
1 ATT
1695576 AAGAAAGGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.04
26 15 0.33
27 29 0.63
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (25 bp):
ATTTTAATATTAATTATTTTATCAT
Found at i:1698603 original size:6 final size:6
Alignment explanation
Indices: 1698562--1698632 Score: 52
Period size: 6 Copynumber: 11.8 Consensus size: 6
1698552 ACTACTACCC
* * * * * * *
1698562 CCACCC CCACCT CCTCCG CCGCCG CCACCA CCACCT CCACCT CCTCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* * *
1698610 CCGCCT CCTCCT CCACCA CCACC
1 CCACCT CCACCT CCACCT CCACC
1698633 ACCTCCACCG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.13, C:0.69, G:0.06, T:0.13
Consensus pattern (6 bp):
CCACCT
Found at i:1698613 original size:33 final size:33
Alignment explanation
Indices: 1698562--1698638 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
1698552 ACTACTACCC
* *
1698562 CCACCCCCACCTCCTCCGCCGCCGCCACCACCA
1 CCACCACCTCCTCCTCCGCCGCCGCCACCACCA
* * * *
1698595 CCTCCACCTCCTCCTCCGCCTCCTCCTCCACCA
1 CCACCACCTCCTCCTCCGCCGCCGCCACCACCA
1698628 CCACCACCTCC
1 CCACCACCTCC
1698639 ACCGCCCCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.13, C:0.69, G:0.05, T:0.13
Consensus pattern (33 bp):
CCACCACCTCCTCCTCCGCCGCCGCCACCACCA
Found at i:1698650 original size:30 final size:30
Alignment explanation
Indices: 1698562--1698650 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
1698552 ACTACTACCC
* * * *
1698562 CCACCCCCACCTCCTCCGCCGCCGCCACCA
1 CCACCACCACCTCCTCCACCGCCCCCTCCA
* * * *
1698592 CCACCTCCACCTCCTCCTCCGCCTCCTCCT
1 CCACCACCACCTCCTCCACCGCCCCCTCCA
*
1698622 CCACCACCACCACCTCCACCGCCCCCTCC
1 CCACCACCACCTCCTCCACCGCCCCCTCC
1698651 CCCAGAAGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.12, C:0.70, G:0.06, T:0.12
Consensus pattern (30 bp):
CCACCACCACCTCCTCCACCGCCCCCTCCA
Found at i:1701319 original size:41 final size:41
Alignment explanation
Indices: 1701274--1701599 Score: 343
Period size: 41 Copynumber: 8.0 Consensus size: 41
1701264 TGTCCTATTA
*
1701274 CGGCGTTTGTATAAAAATGCCACTAAAGTAAGAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
* * * *
1701315 CGGCGTTTTTATAAAAATGCCGCTAAAGTACGAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
* * * **
1701356 CGGTGTTTGTATAAAAACGCCACTAAAGTATGATTGGTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
* * ** *
1701397 CGGCATTTGTATAAAAACGCCACTAAAGTACGAGTGGTTAA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
** * *
1701438 CGATGTTTGTATAGAAACGCCACTAAAGTACA-AGTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTA-AGAGTCTTTAG
* * *
1701479 TGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
* * * *
1701520 CTGCATTTGTATACAAATGCCACTAAAGTATA-A-TCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTA-AGAGTCTTTAG
* * * *
1701560 CGGCGTTTATATAAAAACACCACTAAAGTATGAGTATTTA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTA
1701600 ATGGTGTTTT
Statistics
Matches: 233, Mismatches: 47, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
40 32 0.14
41 201 0.86
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (41 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTCTTTAG
Found at i:1701411 original size:123 final size:123
Alignment explanation
Indices: 1701274--1701608 Score: 395
Period size: 123 Copynumber: 2.7 Consensus size: 123
1701264 TGTCCTATTA
* * * *
1701274 CGGCGTTTGTATAAAAATGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTTTATAAAAATGCCGCT
1 CGGCATTTGTATAAAAATGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTATATAAAAACGCCACT
* * * * *
1701339 AAAGTACGAGTCTTTAGCGGTGTTTGTATAAAAACGCCACTAAAGTATGATTGGTTAG
66 AAAGTACGAGTCTTTAGTGGTGTTTGTATAAAAACACCACTAAAGTACGAGTCGTTAG
* * ** * ** * *
1701397 CGGCATTTGTATAAAAACGCCACTAAAGTACGAGTGGTTAACGATGTTTGTATAGAAACGCCACT
1 CGGCATTTGTATAAAAATGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTATATAAAAACGCCACT
* * * *
1701462 AAAGTACAAGTCTATAGTGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTAG
66 AAAGTACGAGTCTTTAGTGGTGTTTGTATAAAAACACCACTAAAGTACGAGTCGTTAG
* * *
1701520 CTGCATTTGTATACAAATGCCACTAAAGTATA-A-TCTTTAGCGGCGTTTATATAAAAACACCAC
1 CGGCATTTGTATAAAAATGCCACTAAAGTA-AGAGTCTTTAGCGGCGTTTATATAAAAACGCCAC
* * *
1701583 TAAAGTATGAGTATTTAATGGTGTTT
65 TAAAGTACGAGTCTTTAGTGGTGTTT
1701609 TTGCTTAAAA
Statistics
Matches: 172, Mismatches: 39, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
122 42 0.24
123 130 0.76
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (123 bp):
CGGCATTTGTATAAAAATGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTATATAAAAACGCCACT
AAAGTACGAGTCTTTAGTGGTGTTTGTATAAAAACACCACTAAAGTACGAGTCGTTAG
Found at i:1703384 original size:27 final size:29
Alignment explanation
Indices: 1703341--1703401 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1703331 AAGATAAGTG
*
1703341 TTTTAGAGATATATTTGA-A-AAATGAGT
1 TTTTAGAGAAATATTTGATATAAATGAGT
*
1703368 TTTTAGATGAAAT-TTTGATATGAATGAGT
1 TTTTAGA-GAAATATTTGATATAAATGAGT
1703397 TTTTA
1 TTTTA
1703402 AAGTTTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.41
28 5 0.17
29 12 0.41
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (29 bp):
TTTTAGAGAAATATTTGATATAAATGAGT
Found at i:1704223 original size:18 final size:18
Alignment explanation
Indices: 1704200--1704234 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1704190 AGGGTTATAC
*
1704200 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGAGACAT
1704218 AGTGGTCATTCGAGACA
1 AGTGGTCATTCGAGACA
1704235 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:1708362 original size:12 final size:12
Alignment explanation
Indices: 1708343--1708376 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1708333 AAAAGTTAGT
1708343 ATAA-ATAAAAA
1 ATAATATAAAAA
*
1708354 ATAGTATAAAAA
1 ATAATATAAAAA
1708366 ATAATATAAAA
1 ATAATATAAAA
1708377 GTTAGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:1722656 original size:13 final size:15
Alignment explanation
Indices: 1722621--1722658 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1722611 TCTTAAAGAG
*
1722621 GAAGGGAGACAAAAA
1 GAAGAGAGACAAAAA
1722636 GAAGAGAGACAAAAA
1 GAAGAGAGACAAAAA
1722651 GAAGAGAG
1 GAAGAGAG
1722659 GAAGAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.61, C:0.05, G:0.34, T:0.00
Consensus pattern (15 bp):
GAAGAGAGACAAAAA
Found at i:1724721 original size:3 final size:3
Alignment explanation
Indices: 1724713--1724753 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1724703 AGTGAGGTAT
*
1724713 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1724754 TAATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:1724754 original size:6 final size:6
Alignment explanation
Indices: 1724711--1724786 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
1724701 TTAGTGAGGT
* * * * * *
1724711 ATAACA ACAACA ACAACA ACAACA ACAACA ACAACA ATAACA ATAATA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA
* * * *
1724759 ATAATA ATAATA ATAATA ATAATA ATAA
1 ATAACA ATAACA ATAACA ATAACA ATAA
1724787 AAAATATAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAACA
Found at i:1724758 original size:3 final size:3
Alignment explanation
Indices: 1724746--1724802 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
1724736 CAACAACAAC
*
1724746 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1724792 -AT AAT GAT AAT
1 AAT AAT AAT AAT
1724803 GCCAGAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1724758 original size:9 final size:9
Alignment explanation
Indices: 1724711--1724759 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
1724701 TTAGTGAGGT
1724711 ATAACAACA
1 ATAACAACA
*
1724720 ACAACAACA
1 ATAACAACA
*
1724729 ACAACAACA
1 ATAACAACA
*
1724738 ACAACAACA
1 ATAACAACA
*
1724747 ATAACAATA
1 ATAACAACA
1724756 ATAA
1 ATAA
1724760 TAATAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.67, C:0.24, G:0.00, T:0.08
Consensus pattern (9 bp):
ATAACAACA
Found at i:1725048 original size:23 final size:23
Alignment explanation
Indices: 1725029--1725084 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1725019 ACATAGAATT
**
1725029 ACACCGAAGTGTTGCGTAGAGAA
1 ACACCGAAGTGCCGCGTAGAGAA
1725052 ACACCGAAGTGCCGCGTAGAGAA
1 ACACCGAAGTGCCGCGTAGAGAA
*
1725075 ACATCGAAGT
1 ACACCGAAGT
1725085 ACCATATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (23 bp):
ACACCGAAGTGCCGCGTAGAGAA
Found at i:1725127 original size:22 final size:22
Alignment explanation
Indices: 1725085--1725136 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
1725075 ACATCGAAGT
* *
1725085 ACCATATAAGATGTCCCTAAGG
1 ACCATATAAAATGTCCCTAAGA
*
1725107 ACCATATAGAAAT-TCCTTAAGA
1 ACCATATA-AAATGTCCCTAAGA
*
1725129 ATCATATA
1 ACCATATA
1725137 CATATGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (22 bp):
ACCATATAAAATGTCCCTAAGA
Found at i:1731703 original size:3 final size:3
Alignment explanation
Indices: 1731695--1731769 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
1731685 TTAGTGAGGT
1731695 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1731743 ATA ATA ATA ATA A-A AT- ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1731770 GCCAGAATGA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1732491 original size:26 final size:26
Alignment explanation
Indices: 1732455--1732507 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1732445 ATGCACTCAC
1732455 CTAGATCTCTTTGTCTTTCCCTCGAT
1 CTAGATCTCTTTGTCTTTCCCTCGAT
1732481 CTAGATCTCTTTGTCTTTCCCTCGAT
1 CTAGATCTCTTTGTCTTTCCCTCGAT
1732507 C
1 C
1732508 GATCTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.45
Consensus pattern (26 bp):
CTAGATCTCTTTGTCTTTCCCTCGAT
Found at i:1736279 original size:40 final size:40
Alignment explanation
Indices: 1736216--1736334 Score: 188
Period size: 40 Copynumber: 3.0 Consensus size: 40
1736206 ATTCGATATT
* *
1736216 TGCACCGTAGTG--TTACACATAAGGTCGTGTCCACCATA
1 TGCACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
*
1736254 TGCACCGAAGTGTATTACACATAAGGTCATGCCCACCATA
1 TGCACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
*
1736294 TACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1 TGCACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1736334 T
1 T
1736335 ACACTTAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
38 11 0.15
40 63 0.85
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (40 bp):
TGCACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
Found at i:1736353 original size:40 final size:40
Alignment explanation
Indices: 1736228--1736338 Score: 195
Period size: 40 Copynumber: 2.8 Consensus size: 40
1736218 CACCGTAGTG
* *
1736228 TTACACATAAGGTCGTGTCCACCATATGCACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
*
1736268 TTACACATAAGGTCATGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1736308 TTACACATAAGGTCGTGCCCACCATATACAC
1 TTACACATAAGGTCGTGCCCACCATATACAC
1736339 TTAGTGTCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
Found at i:1738723 original size:17 final size:17
Alignment explanation
Indices: 1738697--1738737 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1738687 TGGTAGTCTT
*
1738697 CTTGGACTTTAGGGGCC
1 CTTGGCCTTTAGGGGCC
1738714 CTTGGCCTTTAGGGGCC
1 CTTGGCCTTTAGGGGCC
1738731 CTTGGCC
1 CTTGGCC
1738738 CTATTTGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.29, G:0.34, T:0.29
Consensus pattern (17 bp):
CTTGGCCTTTAGGGGCC
Found at i:1743340 original size:24 final size:24
Alignment explanation
Indices: 1743313--1743394 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 24
1743303 ATTCATAATA
1743313 ATTTTTATATTAATTTTAAAAAAT
1 ATTTTTATATTAATTTTAAAAAAT
*
1743337 ATTTTTATATTAACTTATT-AAATAT
1 ATTTTTATATTAA-TT-TTAAAAAAT
1743362 ATTTTATTATTAACTTAATTTTAAAAAAT
1 A-TTT-TTA-T-A-TTAATTTTAAAAAAT
1743391 ATTT
1 ATTT
1743395 CATTTTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
24 13 0.27
25 8 0.17
26 5 0.10
27 3 0.06
28 6 0.12
29 9 0.19
30 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTATATTAATTTTAAAAAAT
Found at i:1743563 original size:31 final size:29
Alignment explanation
Indices: 1743456--1743660 Score: 129
Period size: 31 Copynumber: 7.0 Consensus size: 29
1743446 TTAAGATGAG
*
1743456 AATAAAATATA-TTTAATAATTTAAATTAAT
1 AATAAAATATATTTTAA-AA-TTAAAATAAT
* * *
1743486 AATATAATATAATTTAGTAAATTAAGA-AA-
1 AATAAAATATATTTTA--AAATTAAAATAAT
*
1743515 AAT---ATATAGTTTGAAAAGTTAAAATAAT
1 AATAAAATATA-TTTTAAAA-TTAAAATAAT
* * *
1743543 AATAAAATATATTTTCAAAAGTTCAGATAAG
1 AATAAAATATATTTT-AAAA-TTAAAATAAT
* * *
1743574 AATAAAATAAATATTTTTAAATAAAAATAAA
1 AATAAAAT--ATATTTTAAAATTAAAATAAT
* *
1743605 AATAAAATAT-TTTT-AAATTATATTAAT
1 AATAAAATATATTTTAAAATTAAAATAAT
*
1743632 AATAAAATATATTTTATAAATTAATATAA
1 AATAAAATATATTTTA-AAATTAAAATAA
1743661 AAAATATTTC
Statistics
Matches: 137, Mismatches: 22, Indels: 32
0.72 0.12 0.17
Matches are distributed among these distances:
25 3 0.02
26 10 0.07
27 24 0.18
28 11 0.08
29 5 0.04
30 24 0.18
31 47 0.34
32 5 0.04
33 8 0.06
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (29 bp):
AATAAAATATATTTTAAAATTAAAATAAT
Found at i:1743620 original size:27 final size:27
Alignment explanation
Indices: 1743569--1743647 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
1743559 AAAAGTTCAG
*
1743569 ATAAGAAT-AAAAT-AAATATTTTTAA
1 ATAAAAATAAAAATAAAATATTTTTAA
1743594 ATAAAAATAAAAATAAAATATTTTTAA
1 ATAAAAATAAAAATAAAATATTTTTAA
* * * *
1743621 ATTATATTAATAATAAAATATATTTTA
1 ATAAAAATAAAAATAAAATAT-TTTTA
1743648 TAAATTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 7 0.15
26 5 0.11
27 29 0.63
28 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
ATAAAAATAAAAATAAAATATTTTTAA
Found at i:1743667 original size:24 final size:24
Alignment explanation
Indices: 1743608--1743695 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 24
1743598 AAATAAAAAT
1743608 AAAATATTT-TTAAATTATATTAATAA
1 AAAATATTTCTTAAATTA-A-T-ATAA
*
1743634 TAAAATATATTTTATAAATTAATATAA
1 -AAAATAT-TTCT-TAAATTAATATAA
1743661 AAAATATTTCTTAAAGTTAATATGAAA
1 AAAATATTTCTTAAA-TTAATAT--AA
1743688 AAAATATT
1 AAAATATT
1743696 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
24 4 0.07
25 10 0.19
26 7 0.13
27 21 0.39
28 3 0.06
29 2 0.04
30 7 0.13
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAATATTTCTTAAATTAATATAA
Found at i:1748616 original size:15 final size:15
Alignment explanation
Indices: 1748592--1748623 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1748582 TGGCAGATCG
*
1748592 AAATCTAGAACGGGA
1 AAATCAAGAACGGGA
1748607 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1748622 AA
1 AA
1748624 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1755862 original size:35 final size:35
Alignment explanation
Indices: 1755816--1755910 Score: 190
Period size: 35 Copynumber: 2.7 Consensus size: 35
1755806 CTTTAATGAG
1755816 TAAGGATAAAGACAGACCACAGTAAGGATAGGTGA
1 TAAGGATAAAGACAGACCACAGTAAGGATAGGTGA
1755851 TAAGGATAAAGACAGACCACAGTAAGGATAGGTGA
1 TAAGGATAAAGACAGACCACAGTAAGGATAGGTGA
1755886 TAAGGATAAAGACAGACCACAGTAA
1 TAAGGATAAAGACAGACCACAGTAA
1755911 TAACAATGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.47, C:0.13, G:0.26, T:0.14
Consensus pattern (35 bp):
TAAGGATAAAGACAGACCACAGTAAGGATAGGTGA
Found at i:1758319 original size:16 final size:16
Alignment explanation
Indices: 1758298--1758352 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1758288 GGTATTACCC
1758298 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
** *
1758314 GACCTGTGATGAACCT
1 GACCTGTTTTCAACCT
* *
1758330 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1758346 GACCTGT
1 GACCTGT
1758353 AAATGATCCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1758367 original size:32 final size:32
Alignment explanation
Indices: 1758302--1758369 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1758292 TTACCCGACC
* *
1758302 TGTTTTCAACCTGACCTGTGATGAACCTGACT
1 TGTTTTCAACCTGACCTGTAATGAACCTAACT
* *
1758334 TGTTTTTAACCTGACCTGTAAATGATCC-AACT
1 TGTTTTCAACCTGACCTGT-AATGAACCTAACT
1758366 TGTT
1 TGTT
1758370 AATGACCTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTTTTCAACCTGACCTGTAATGAACCTAACT
Found at i:1758405 original size:16 final size:17
Alignment explanation
Indices: 1758384--1758421 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1758374 ACCTGATCTG
1758384 ATATTTACCAGACTTA-
1 ATATTTACCAGACTTAT
*
1758400 ATATTTACCTGACTTAT
1 ATATTTACCAGACTTAT
1758417 ATATT
1 ATATT
1758422 ATCATGGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATTTACCAGACTTAT
Found at i:1758686 original size:190 final size:191
Alignment explanation
Indices: 1758347--1758727 Score: 692
Period size: 190 Copynumber: 2.0 Consensus size: 191
1758337 TTTTAACCTG
*
1758347 ACCTGTAAATGATCCAACTTGTTAATGACCTGATCTGATATTTACCAGACTTAATATTTACCTGA
1 ACCTGTAAATGATCCAACTTGTTAATGACATGATCTGATATTTACCAGACTTAATATTTACCTGA
1758412 CTTATATATTATCATGGACGAAATTATAAGATTTTAATAAAATTATGAGTTTTTTAATTTAAGAT
66 CTTATATATTATCATGGACGAAATTATAAGATTTTAATAAAATTATGAGTTTTTTAATTTAAGAT
*
1758477 GTAATTAAAAAATTAATATGATTACTTTTTACATGTTATAATAAATATTTATTATGATAAT
131 GTAATTAAAAAATTAATATGATTACTTTTTAAATGTTATAATAAATATTTATTATGATAAT
* * * * *
1758538 ACCTGTTAATGAT-CGACTTGTTAATGACATGATCTGATATTTATCAGACTTGATATTTACCTTA
1 ACCTGTAAATGATCCAACTTGTTAATGACATGATCTGATATTTACCAGACTTAATATTTACCTGA
1758602 CTTATATATTATCATGGACGAAATTATAAGATTTTAATAAAATTATGAGTTTTTTAATTTAAGAT
66 CTTATATATTATCATGGACGAAATTATAAGATTTTAATAAAATTATGAGTTTTTTAATTTAAGAT
1758667 GTAATTAAAAAATTAATATGATTACTTTTTAAATGTTATAATAAATATTTATTATGATAAT
131 GTAATTAAAAAATTAATATGATTACTTTTTAAATGTTATAATAAATATTTATTATGATAAT
1758728 TAAATTAATA
Statistics
Matches: 183, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
190 171 0.93
191 12 0.07
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (191 bp):
ACCTGTAAATGATCCAACTTGTTAATGACATGATCTGATATTTACCAGACTTAATATTTACCTGA
CTTATATATTATCATGGACGAAATTATAAGATTTTAATAAAATTATGAGTTTTTTAATTTAAGAT
GTAATTAAAAAATTAATATGATTACTTTTTAAATGTTATAATAAATATTTATTATGATAAT
Found at i:1759258 original size:33 final size:33
Alignment explanation
Indices: 1759219--1759282 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
1759209 TAATTTACTT
1759219 TATATAGTTATATATA-TATACA-GGTTATATATA
1 TATATAGTT-TATATACTATACATGGTT-TATATA
1759252 TATATAGTTTATATACTATACATGGTTTATA
1 TATATAGTTTATATACTATACATGGTTTATA
1759283 CATGCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 6 0.21
33 19 0.66
34 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (33 bp):
TATATAGTTTATATACTATACATGGTTTATATA
Found at i:1759266 original size:19 final size:17
Alignment explanation
Indices: 1759225--1759282 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1759215 ACTTTATATA
1759225 GTTATATATATATACAG
1 GTTATATATATATACAG
*
1759242 GTTATATATATATATA-
1 GTTATATATATATACAG
1759258 GTT-TATATACTATACATG
1 GTTATATATA-TATACA-G
1759276 GTT-TATA
1 GTTATATA
1759283 CATGCATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 6 0.17
16 8 0.22
17 15 0.42
18 7 0.19
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (17 bp):
GTTATATATATATACAG
Found at i:1759660 original size:21 final size:20
Alignment explanation
Indices: 1759636--1759744 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 20
1759626 TTATATTAAG
1759636 GTTTATGGTTTAGGATTTAGA
1 GTTTATGGTTTAGG-TTTAGA
*
1759657 GTTTATGATTTATGGTTTAGA
1 GTTTATGGTTTA-GGTTTAGA
* * *
1759678 ATTTAGGGTTTAGTGTTTAGT
1 GTTTATGGTTTAG-GTTTAGA
* * *
1759699 GTTTATAGTTTAAAGTTTAGG
1 GTTTATGGTTT-AGGTTTAGA
* *
1759720 GTTTATGATTTAGGGTTTAGG
1 GTTTATGGTTTA-GGTTTAGA
1759741 GTTT
1 GTTT
1759745 CTATAAACTA
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 66 0.93
22 3 0.04
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (20 bp):
GTTTATGGTTTAGGTTTAGA
Found at i:1759741 original size:7 final size:7
Alignment explanation
Indices: 1759635--1759744 Score: 76
Period size: 7 Copynumber: 15.7 Consensus size: 7
1759625 TTTATATTAA
*
1759635 GGTTTAT
1 GGTTTAG
1759642 GGTTTAG
1 GGTTTAG
*
1759649 GATTTAG
1 GGTTTAG
* *
1759656 AGTTTAT
1 GGTTTAG
* *
1759663 GATTTAT
1 GGTTTAG
1759670 GGTTTAG
1 GGTTTAG
**
1759677 AATTTAG
1 GGTTTAG
1759684 GGTTTAG
1 GGTTTAG
*
1759691 TGTTTAG
1 GGTTTAG
* *
1759698 TGTTTAT
1 GGTTTAG
* *
1759705 AGTTTAA
1 GGTTTAG
*
1759712 AGTTTAG
1 GGTTTAG
*
1759719 GGTTTAT
1 GGTTTAG
*
1759726 GATTTAG
1 GGTTTAG
1759733 GGTTTAG
1 GGTTTAG
1759740 GGTTT
1 GGTTT
1759745 CTATAAACTA
Statistics
Matches: 80, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 80 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (7 bp):
GGTTTAG
Found at i:1759918 original size:23 final size:25
Alignment explanation
Indices: 1759892--1759949 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
1759882 ATACATACAT
*
1759892 ATTATATAAAATTGTTT-AATA-AA
1 ATTATATAAAATTATTTAAATATAA
1759915 ATTA-ATAAAATTATTTAAATATAA
1 ATTATATAAAATTATTTAAATATAA
1759939 ATTATATAAAA
1 ATTATATAAAA
1759950 AATGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 8 0.26
24 6 0.19
25 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTATATAAAATTATTTAAATATAA
Found at i:1764545 original size:137 final size:138
Alignment explanation
Indices: 1764321--1764824 Score: 542
Period size: 137 Copynumber: 3.7 Consensus size: 138
1764311 TAGGAGGATA
* * * * * *
1764321 TTTAATTTAGTCTTTTCCTTTGCTCGAGGTTCTCAAATTAATTATTCGATTCAATAAATTGCTAA
1 TTTAATTTGGTCCTTACCTTTGCTCGAGGTTATCAAATTAATTATTCGATTCAATAAATGGTTAA
* ** * * * * *
1764386 AATTTATTAGGATTTAATATTAGAGCCTTAACTCT-GAGTTTAATTACACCTTAGTCCTTTAATT
66 AAATGGTTAGGTTTTAATATTAGAGCCTCAATTTTAG-GTTTAATTTCACCTTAGTCC-TTAATT
1764450 TAGG-GAAATT
129 TAGGTG-AATT
* * * * *
1764460 TTTAATTTGGTCATTGCC-TTGCTTGTGGTT-TCAAATTAATTATTTGATTCAATAAATGGTTAA
1 TTTAATTTGGTCCTTACCTTTGCTCGAGGTTATCAAATTAATTATTCGATTCAATAAATGGTTAA
*
1764523 AAATGGTTAGGTTTTAATATTAGGGCCTCAATTTTAGGTTTAATTTCACCTTAGTACC-TAATTT
66 AAATGGTTAGGTTTTAATATTAGAGCCTCAATTTTAGGTTTAATTTCACCTTAGT-CCTTAATTT
1764587 AGGTGAATT
130 AGGTGAATT
* * * * * * *
1764596 TTTAAATTGGTCCTCACCTTTGTTTC-AGGTT-CCAAAGTATTTTTTCGATTCAATAAATGGTT-
1 TTTAATTTGGTCCTTACCTTTG-CTCGAGGTTATCAAATTAATTATTCGATTCAATAAATGGTTA
* * *
1764658 AAAATTGTTAGGTTTTAATATTAGAGCCTCCATTTTAGGTTTAATTTCACCTTAGCCCCTTAATT
65 AAAATGGTTAGGTTTTAATATTAGAGCCTCAATTTTAGGTTTAATTTCACCTTAG-TCCTTAATT
* *
1764723 TTGGTGACTT
129 TAGGTGAATT
* **
1764733 TTTAATTTGATCCTTAATTTTGCTCGAGGTTAT-AAATTAATTATTCG-TCTCAATAAATGGTTA
1 TTTAATTTGGTCCTTACCTTTGCTCGAGGTTATCAAATTAATTATTCGAT-TCAATAAATGGTTA
* *
1764796 AAAATGGTTAGATTTTAATATAAGAGCCT
65 AAAATGGTTAGGTTTTAATATTAGAGCCT
1764825 TCTTCTTAGT
Statistics
Matches: 306, Mismatches: 48, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
136 84 0.27
137 167 0.55
138 40 0.13
139 15 0.05
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (138 bp):
TTTAATTTGGTCCTTACCTTTGCTCGAGGTTATCAAATTAATTATTCGATTCAATAAATGGTTAA
AAATGGTTAGGTTTTAATATTAGAGCCTCAATTTTAGGTTTAATTTCACCTTAGTCCTTAATTTA
GGTGAATT
Found at i:1768201 original size:30 final size:31
Alignment explanation
Indices: 1768167--1768226 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1768157 ACTAGCTTTA
**
1768167 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
1768197 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1768227 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:1769617 original size:23 final size:26
Alignment explanation
Indices: 1769569--1769634 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
1769559 TCCATCTTTC
*
1769569 TTTCATTTCATTTCTTATCTTTATTA
1 TTTCATTTCATTTCTTACCTTTATTA
1769595 TTTCA-TT-ATTTCTT-CCTTTATTA
1 TTTCATTTCATTTCTTACCTTTATTA
* *
1769618 -ATCATATTCTTTTCTTA
1 TTTCAT-TTCATTTCTTA
1769635 TCTATGTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.09
23 8 0.24
24 9 0.27
25 8 0.24
26 5 0.15
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTCATTTCATTTCTTACCTTTATTA
Found at i:1771090 original size:15 final size:15
Alignment explanation
Indices: 1771070--1771100 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1771060 GAGAGTGAAG
1771070 AACAATTTTTATCTA
1 AACAATTTTTATCTA
1771085 AACAATTTTTATCTA
1 AACAATTTTTATCTA
1771100 A
1 A
1771101 CCTTACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (15 bp):
AACAATTTTTATCTA
Done.