Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2280343 original size:37 final size:36
Alignment explanation
Indices: 2280267--2280343 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
2280257 CCTTTTTTAT
*
2280267 ATTTAATTTTGTAAAAAAATTATATAAATATTATGA
1 ATTTAATTTTGTAAAAAAATTATATAAATATTATCA
* *
2280303 ATTTAATTTTTTAAAGAAAA-TATATAAATATTTTACA
1 ATTTAATTTTGTAAA-AAAATTATATAAATATTAT-CA
2280340 ATTT
1 ATTT
2280344 GTAATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
ATTTAATTTTGTAAAAAAATTATATAAATATTATCA
Found at i:2280526 original size:19 final size:18
Alignment explanation
Indices: 2280484--2280526 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
2280474 CAATAATCAT
**
2280484 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
2280502 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
2280522 ATTCC
1 ATTCC
2280527 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:2282452 original size:15 final size:15
Alignment explanation
Indices: 2282432--2282466 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2282422 GGAGGTCAAG
*
2282432 AAGGGTCGAAAGAAA
1 AAGGGTCAAAAGAAA
*
2282447 AAGGGTCAAAAGAAG
1 AAGGGTCAAAAGAAA
2282462 AAGGG
1 AAGGG
2282467 GTTGATGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.37, T:0.06
Consensus pattern (15 bp):
AAGGGTCAAAAGAAA
Found at i:2287866 original size:23 final size:23
Alignment explanation
Indices: 2287823--2287866 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
2287813 TGTATAATTA
*
2287823 TAAATTAATTAAAAATTTATAGG
1 TAAATTAATTAAAAATATATAGG
*
2287846 TAAA-TAATTTAAAATAATATA
1 TAAATTAATTAAAAAT-ATATA
2287867 TTAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
TAAATTAATTAAAAATATATAGG
Found at i:2288464 original size:6 final size:6
Alignment explanation
Indices: 2288455--2288479 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2288445 AATAAATTAA
2288455 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
2288480 CATTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:2288722 original size:21 final size:20
Alignment explanation
Indices: 2288688--2288726 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2288678 TCAATGATGG
*
2288688 ATATAAAATTTTAAAAAATT
1 ATATAAAATATTAAAAAATT
2288708 ATATAAAAATATTAAAAAA
1 ATAT-AAAATATTAAAAAA
2288727 ATGTGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAAATATTAAAAAATT
Found at i:2288728 original size:22 final size:20
Alignment explanation
Indices: 2288688--2288728 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2288678 TCAATGATGG
*
2288688 ATATAAAATTTTAAAAAATT
1 ATATAAAATTTAAAAAAATT
2288708 ATATAAAAATATTAAAAAAAT
1 ATAT-AAAAT-TTAAAAAAAT
2288729 GTGAAATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATAAAATTTAAAAAAATT
Found at i:2288778 original size:49 final size:48
Alignment explanation
Indices: 2288720--2288822 Score: 161
Period size: 49 Copynumber: 2.1 Consensus size: 48
2288710 ATAAAAATAT
**
2288720 TAAAAAAATGTGAAATTAGACCATCAATAAGAAAATATTTAAATTATA
1 TAAAAAAATGTGAAATTAGAAAATCAATAAGAAAATATTTAAATTATA
**
2288768 TAAAAGAAATGTGAAATTAGAAAATTGATAAGAAAATATTTAAATTATA
1 TAAAA-AAATGTGAAATTAGAAAATCAATAAGAAAATATTTAAATTATA
2288817 TAAAAA
1 TAAAAA
2288823 TTAAATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 6 0.12
49 44 0.88
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (48 bp):
TAAAAAAATGTGAAATTAGAAAATCAATAAGAAAATATTTAAATTATA
Found at i:2290499 original size:18 final size:19
Alignment explanation
Indices: 2290478--2290513 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2290468 GGGTAAAATA
2290478 TAAAATAAAATAA-AAAAG
1 TAAAATAAAATAATAAAAG
*
2290496 TAAATTAAAATAATAAAA
1 TAAAATAAAATAATAAAA
2290514 TTAACGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (19 bp):
TAAAATAAAATAATAAAAG
Found at i:2290504 original size:13 final size:12
Alignment explanation
Indices: 2290471--2290514 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2290461 AAGTGAAGGG
*
2290471 TAAAATATAAAA
1 TAAAATAAAAAA
2290483 TAAAATAAAAAA
1 TAAAATAAAAAA
*
2290495 GTAAATTAAAATAA
1 -TAAAATAAAA-AA
2290509 TAAAAT
1 TAAAAT
2290515 TAACGGGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.41
13 14 0.52
14 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:2290577 original size:16 final size:16
Alignment explanation
Indices: 2290539--2290580 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2290529 TAGATAAATA
*
2290539 AAAAGTAAAT-TGCAG
1 AAAATTAAATATGCAG
* *
2290554 AAATTTAAATATGCAT
1 AAAATTAAATATGCAG
2290570 AAAATTAAATA
1 AAAATTAAATA
2290581 GCAAAAGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (16 bp):
AAAATTAAATATGCAG
Found at i:2292677 original size:22 final size:22
Alignment explanation
Indices: 2292649--2292705 Score: 84
Period size: 20 Copynumber: 2.7 Consensus size: 22
2292639 TGAGCAGGTA
2292649 GTATCGATACCATTTGAAGAA-G
1 GTATCGATACCATTTG-AGAATG
2292671 GTATCGATACCA--TGAGAATG
1 GTATCGATACCATTTGAGAATG
2292691 GTATCGATACCATTT
1 GTATCGATACCATTT
2292706 TCAAGATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.47
22 13 0.41
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATTTGAGAATG
Found at i:2292695 original size:42 final size:41
Alignment explanation
Indices: 2292609--2292705 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 41
2292599 CTAAAGGTAA
* *
2292609 TATCGATACCGTTTGAAAAGGTATCGATACTGAGCAGGTAG
1 TATCGATACCATTTGAAAAGGTATCGATACTGAGCAGATAG
*
2292650 TATCGATACCATTTGAAGAAGGTATCGATACCATGAG-A-ATGG
1 TATCGATACCATTTGAA-AAGGTATCGATA-C-TGAGCAGATAG
2292692 TATCGATACCATTT
1 TATCGATACCATTT
2292706 TCAAGATGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 16 0.32
42 28 0.56
43 2 0.04
44 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (41 bp):
TATCGATACCATTTGAAAAGGTATCGATACTGAGCAGATAG
Found at i:2293569 original size:21 final size:21
Alignment explanation
Indices: 2293543--2293613 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
2293533 CGAGGGGTTT
2293543 TATGTGGTCATTCGGGACAAA
1 TATGTGGTCATTCGGGACAAA
2293564 TATGTGG-CACTTCGGTG-CAAA
1 TATGTGGTCA-TTCGG-GACAAA
* * * *
2293585 CCTATATGGTCTTTCGAGACAAT
1 --TATGTGGTCATTCGGGACAAA
2293608 TATGTG
1 TATGTG
2293614 ACACTTCGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.05
21 21 0.54
22 2 0.05
23 13 0.33
24 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAA
Found at i:2298464 original size:43 final size:42
Alignment explanation
Indices: 2298350--2298597 Score: 309
Period size: 43 Copynumber: 5.8 Consensus size: 42
2298340 TTAATTACCG
2298350 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTT-CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *** * *
2298393 TTACAGTTTCCCAGGTTTTTTTGTTGTGTGCAATGGTAAGCC
1 TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
2298435 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTT-CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
2298478 TTATAGATTCCCCAGGTTCCTTTTCTGTGTGCAAGGGTAAGCC
1 TTACAG-TTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
2298521 TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAAGGTAAGCC
1 TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2298563 TTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
1 TTACAG-TTCCCCAGGTC-CCTTTGCTGTGTGCAAG
2298598 TATAAGACCT
Statistics
Matches: 177, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
42 74 0.42
43 101 0.57
44 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (42 bp):
TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2298534 original size:85 final size:85
Alignment explanation
Indices: 2298350--2298597 Score: 356
Period size: 85 Copynumber: 2.9 Consensus size: 85
2298340 TTAATTACCG
* *
2298350 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTTTTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCTTTT
* *
2298415 GTTGTGTGCAATGGTAAGCC
66 GCTGTGTGCAAGGGTAAGCC
*
2298435 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGATTCCCCAGGTTCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTCCCCAGGTT-CTT
2298500 TT-CTGTGTGCAAGGGTAAGCC
64 TTGCTGTGTGCAAGGGTAAGCC
* * * * *
2298521 TTACAGTT-TCCCAGGTTCTTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCAGGCTCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTCCCCAGGTTCTTT
*
2298585 TGCTATGTGCAAG
65 TGCTGTGTGCAAG
2298598 TATAAGACCT
Statistics
Matches: 147, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
84 5 0.03
85 103 0.70
86 35 0.24
87 4 0.03
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (85 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCTTTT
GCTGTGTGCAAGGGTAAGCC
Found at i:2298587 original size:128 final size:128
Alignment explanation
Indices: 2298359--2298597 Score: 390
Period size: 128 Copynumber: 1.9 Consensus size: 128
2298349 GTTACAGTTC
* *
2298359 CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTTTTTTGTTGTGTGC
1 CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTGCTGTGTGC
* *
2298424 AATGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGATT
66 AAAGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTATAGATT
* *
2298487 CCCCAGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTGCTGTGTGC
1 CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTGCTGTGTGC
* *
2298552 AAAGGTAAGCCTTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
66 AAAGGTAAGCCTTACAGTTCCCCCAGGTC-CCTTTGCTATGTGCAAG
2298598 TATAAGACCT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
127 1 0.01
128 101 0.99
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (128 bp):
CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTGCTGTGTGC
AAAGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTATAGATT
Found at i:2300622 original size:57 final size:57
Alignment explanation
Indices: 2300534--2300653 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 57
2300524 ATGGTCCAAA
* *
2300534 TGACCGGTTTGATAGGTTACAACCCGACCCGACCCGTTGACCGACGTTGACCACTGT
1 TGACCAGTTTGACAGGTTACAACCCGACCCGACCCGTTGACCGACGTTGACCACTGT
* *
2300591 TGACCAGTTTGACCGGTTACAACCTGACCCGACCCGTTGACCGACGTTGACCACTGT
1 TGACCAGTTTGACAGGTTACAACCCGACCCGACCCGTTGACCGACGTTGACCACTGT
2300648 TGACCA
1 TGACCA
2300654 AAACTTTGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.23
Consensus pattern (57 bp):
TGACCAGTTTGACAGGTTACAACCCGACCCGACCCGTTGACCGACGTTGACCACTGT
Found at i:2303106 original size:43 final size:43
Alignment explanation
Indices: 2303058--2303305 Score: 340
Period size: 43 Copynumber: 5.8 Consensus size: 43
2303048 TTAATTATCG
*
2303058 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2303101 TTACAGTTT-CCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2303143 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGTC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
2303186 TTATAGTTTCCCTAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
2303229 ATACA-TTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2303271 TTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
1 TTACAGTTTCCCCAGGTC-CCTTTGCTGTGTGCAAG
2303306 TATAAGACCT
Statistics
Matches: 181, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 77 0.43
43 104 0.57
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2303242 original size:85 final size:85
Alignment explanation
Indices: 2303059--2303305 Score: 379
Period size: 85 Copynumber: 2.9 Consensus size: 85
2303049 TAATTATCGT
2303059 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTG
1 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTG
*
2303124 CTGTGTGCAAGGGTAAGCCT
66 CTGTGTGCAAGGGTAAGCCA
* * *
2303144 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGTCTTATAGTTTCCCTAGGTTCCTTT
1 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC-AGGTTCTTTT
2303209 GCTGTGTGCAAGGGTAAGCCA
65 GCTGTGTGCAAGGGTAAGCCA
** * * *
2303230 TACA-TTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCTCTTTT
1 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCTTTT
*
2303294 GCTATGTGCAAG
65 GCTGTGTGCAAG
2303306 TATAAGACCT
Statistics
Matches: 147, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
85 111 0.76
86 36 0.24
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (85 bp):
TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTG
CTGTGTGCAAGGGTAAGCCA
Found at i:2303304 original size:128 final size:128
Alignment explanation
Indices: 2303062--2303305 Score: 400
Period size: 128 Copynumber: 1.9 Consensus size: 128
2303052 TTATCGTTAC
*
2303062 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTTGCTG
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCATACAGTTTCCCAGGTTCTTTTGCTG
*
2303127 TGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGTCTTAT
66 TGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAAGTCTTAT
* * * *
2303190 AGTTTCCCTAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCATACATTTTCCCAGGTTCTTTTGCTG
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCATACAGTTTCCCAGGTTCTTTTGCTG
* *
2303255 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
66 TGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTC-CCTTTGCTATGTGCAAG
2303306 TATAAGACCT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
127 1 0.01
128 106 0.99
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (128 bp):
AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCATACAGTTTCCCAGGTTCTTTTGCTG
TGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAAGTCTTAT
Found at i:2306949 original size:42 final size:42
Alignment explanation
Indices: 2306899--2306998 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
2306889 GATTTGCTAG
* *
2306899 AGGTAGTATTGATACCGTTTGAAGAAGGTATCGATACTGAGC
1 AGGTAGTATCGATACCGTTTGAAGAAGATATCGATACTGAGC
* *
2306941 AGGTAGTATCAATACCGTTTGAAGAATATATCGATACTGAGC
1 AGGTAGTATCGATACCGTTTGAAGAAGATATCGATACTGAGC
*
2306983 TGGTAGTATCGATACC
1 AGGTAGTATCGATACC
2306999 ATGGGTATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (42 bp):
AGGTAGTATCGATACCGTTTGAAGAAGATATCGATACTGAGC
Found at i:2307937 original size:23 final size:22
Alignment explanation
Indices: 2307877--2307947 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
2307867 CCTTCAGGAC
* *
2307877 AATTATATGGTCATTCGGGGCA
1 AATTATGTGGTCATTCGGTGCA
*
2307899 AA-TATGTTG-CACTTCGGTGCA
1 AATTATGTGGTCA-TTCGGTGCA
2307920 AATCTATGTGGTCATTCGGTGCA
1 AAT-TATGTGGTCATTCGGTGCA
2307943 AATTA
1 AATTA
2307948 CGAGTTGTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
21 15 0.37
22 4 0.10
23 18 0.44
24 2 0.05
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (22 bp):
AATTATGTGGTCATTCGGTGCA
Found at i:2309801 original size:2 final size:2
Alignment explanation
Indices: 2309796--2309823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2309786 CGTGCGCACG
2309796 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
2309824 TTGAAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2311324 original size:13 final size:13
Alignment explanation
Indices: 2311308--2311340 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2311298 CATCTCCATC
*
2311308 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
2311321 TTTCTTTCATTAT
1 TTTCTTTCATTAT
2311334 TTTCTTT
1 TTTCTTT
2311341 TCACAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:2315075 original size:35 final size:36
Alignment explanation
Indices: 2315029--2315101 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 36
2315019 ATTTCCAAAA
* ** * *
2315029 TGGTATTGATACTTGCCTTATGGTATCGGTAC-CCT
1 TGGTATCGATACTACCCCTATGGTATCGATACTCCT
2315064 TGGTATCGATACTACCCCTATGGTATCGATACTCCT
1 TGGTATCGATACTACCCCTATGGTATCGATACTCCT
2315100 TG
1 TG
2315102 AATAACTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 27 0.84
36 5 0.16
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (36 bp):
TGGTATCGATACTACCCCTATGGTATCGATACTCCT
Found at i:2315242 original size:18 final size:18
Alignment explanation
Indices: 2315219--2315261 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2315209 CAGTACCGAT
2315219 ACTCCTTGCCCAGAAGTC
1 ACTCCTTGCCCAGAAGTC
2315237 ACTCCTTGCCCAGAAGTC
1 ACTCCTTGCCCAGAAGTC
2315255 ACTCCTT
1 ACTCCTT
2315262 ACACCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.26
Consensus pattern (18 bp):
ACTCCTTGCCCAGAAGTC
Found at i:2317897 original size:13 final size:13
Alignment explanation
Indices: 2317881--2317910 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2317871 TTATTCAATA
2317881 TTTATTTACTTAT
1 TTTATTTACTTAT
*
2317894 TTTATTTATTTAT
1 TTTATTTACTTAT
2317907 TTTA
1 TTTA
2317911 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTACTTAT
Found at i:2319647 original size:13 final size:13
Alignment explanation
Indices: 2319620--2319677 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
2319610 CCATTAGTAG
2319620 AAACCCAA-ATCAT
1 AAACCCAATAT-AT
2319633 AAACCCAATATAT
1 AAACCCAATATAT
* * *
2319646 -AACCTAACAGA-
1 AAACCCAATATAT
2319657 AAACCCAATATAT
1 AAACCCAATATAT
*
2319670 TAACCCAA
1 AAACCCAA
2319678 ACAAAATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
12 16 0.46
13 17 0.49
14 2 0.06
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (13 bp):
AAACCCAATATAT
Found at i:2319683 original size:24 final size:23
Alignment explanation
Indices: 2319621--2319683 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
2319611 CATTAGTAGA
2319621 AACCCAAATCATAAACCCAATATAT
1 AACCCAAA-CA-AAACCCAATATAT
* *
2319646 AACCTAACAGAAAACCCAATATATT
1 AACCCAA-ACAAAACCCAATATA-T
2319671 AACCCAAACAAAA
1 AACCCAAACAAAA
2319684 TATAAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 17 0.53
25 14 0.44
26 1 0.03
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.16
Consensus pattern (23 bp):
AACCCAAACAAAACCCAATATAT
Found at i:2321869 original size:45 final size:45
Alignment explanation
Indices: 2321815--2322010 Score: 254
Period size: 45 Copynumber: 4.4 Consensus size: 45
2321805 CATAATATAT
* * * *
2321815 TTTTATGTTGATAATGCACTCATATGCATTTCAA-TAATAGCATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACT-ATAGCATAC
*
2321860 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * *
2321905 TTTACTGTTGATGATGTACCCATATACATTTCAACTAGT-GCTTAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTA-TAGCATAC
2321950 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT-C
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* *
2321994 ATTTCATGCTGATAATG
1 TTTTC-TGTTGATAATG
2322011 CACATGCATG
Statistics
Matches: 133, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
44 6 0.05
45 125 0.94
46 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (45 bp):
TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
Found at i:2328537 original size:45 final size:45
Alignment explanation
Indices: 2328488--2328600 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
2328478 TAGTCATAAT
* * *
2328488 ATACTTTTATGTTGAGAATGCACTCATATGCATTTCAACAATAGC
1 ATACTTTTATGTTGATAATGCACCCATATACATTTCAACAATAGC
* * *
2328533 ATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGC
1 ATACTTTTATGTTGATAATGCACCCATATACATTTCAACAATAGC
2328578 AT-CTTTTCATGTTGATAATGCAC
1 ATACTTTT-ATGTTGATAATGCAC
2328601 ATGTATGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 5 0.08
45 54 0.92
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (45 bp):
ATACTTTTATGTTGATAATGCACCCATATACATTTCAACAATAGC
Found at i:2335695 original size:122 final size:119
Alignment explanation
Indices: 2335470--2335695 Score: 258
Period size: 122 Copynumber: 1.9 Consensus size: 119
2335460 AATCTGACTA
* *
2335470 TTTAAATTAAAACAAAAGTATGAGGTAGTGTAATTTAGCGATGTATATTAAAACATAAACTTACT
1 TTTAAATTAAAACAAAAGTATGAGGTAGTGTAATTTAGCGATGTATATTAAAACAGAAACATACT
*
2335535 TCGTCTAAAATCTAAATGGGAGAAACTATGCGGCGTTTCATGAAATTTGACCGT
66 TCGTCTAAAATCTAAATGGAAGAAACTATGCGGCGTTTCATGAAATTTGACCGT
* * * * *
2335589 TTTAAATTAAAACACAATTATGGGGGAATAGTGTAATTTAGAC-ATGTTTATTAAAACAGACACA
1 TTTAAATTAAAACAAAAGTAT-GAGG--TAGTGTAATTTAG-CGATGTATATTAAAACAGAAACA
* * * * * * *
2335653 TGCGTTTGTCTAAAATTTATATGGAATAAATTATG-GGGGTTTC
62 TAC-TTCGTCTAAAATCTAAATGGAAGAAACTATGCGGCGTTTC
2335696 CATACAATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
119 19 0.22
120 3 0.03
122 39 0.45
123 26 0.30
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTAAATTAAAACAAAAGTATGAGGTAGTGTAATTTAGCGATGTATATTAAAACAGAAACATACT
TCGTCTAAAATCTAAATGGAAGAAACTATGCGGCGTTTCATGAAATTTGACCGT
Found at i:2342601 original size:12 final size:12
Alignment explanation
Indices: 2342586--2342616 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
2342576 TTGAAATTAT
2342586 AAATATATTTTA
1 AAATATATTTTA
2342598 AAATTATATTTTA
1 AAA-TATATTTTA
2342611 AAATAT
1 AAATAT
2342617 CAAAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:2342755 original size:2 final size:2
Alignment explanation
Indices: 2342748--2342794 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2342738 CATCATAATT
* *
2342748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2342790 TA TA T
1 TA TA T
2342795 TTCTGATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2344058 original size:26 final size:26
Alignment explanation
Indices: 2344011--2344060 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2344001 GTTTTAAGGG
* * *
2344011 ATTTTTAAAGATTTGGATTTTTTATC
1 ATTTTTAAAGAATTAGAGTTTTTATC
2344037 ATTTTTAAAGAATTAGAGTTTTTA
1 ATTTTTAAAGAATTAGAGTTTTTA
2344061 AAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (26 bp):
ATTTTTAAAGAATTAGAGTTTTTATC
Found at i:2344709 original size:18 final size:19
Alignment explanation
Indices: 2344675--2344710 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2344665 AGCAAACATT
*
2344675 TTTAATACTTGAATTTAAC
1 TTTAATACTTCAATTTAAC
2344694 TTTAATA-TTCAATTTAA
1 TTTAATACTTCAATTTAA
2344711 TCCGTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAATACTTCAATTTAAC
Found at i:2347806 original size:54 final size:54
Alignment explanation
Indices: 2347673--2348100 Score: 462
Period size: 54 Copynumber: 8.2 Consensus size: 54
2347663 TATGGTTTTT
* * * * * **
2347673 CACACGTAGTGCCGATACGATAATTCACAAACTCATTATGAATTGCGTGGGGTTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTC-TTAGGTTG
* * *
2347728 CACACATAGTGTCAATACGGAAATTCACAAACTTATTATGAATTTATTAGGTTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
** *
2347782 CACACATAGTAACAATACGAAAATTCAAAAACTTATTATGAATTTCTTAGGTTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
* *
2347836 CACACATAGTACCAATACGAAAATTCACAAACGTATTATGAATTTCTTAGGTTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
* *
2347890 CACACACAGTGCCAATACGGAAATTCACAAACTTATTATGAATTTCTTAGGTT-
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
* *
2347943 -ACACATAGTGCCAATACGAAAATTCATAAACTTATAATGAATTTGC--A-----
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTT-CTTAGGTTG
* * * *
2347990 CACACA-A-TGTCAATACGAAAATTTATAAACTTATAATGAA-----T---TTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
* * * *
2348034 CACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTG
1 CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
2348088 CACACATAGTGCC
1 CACACATAGTGCC
2348101 TATTCGGTAA
Statistics
Matches: 324, Mismatches: 33, Indels: 33
0.83 0.08 0.08
Matches are distributed among these distances:
44 6 0.02
45 1 0.00
46 60 0.19
47 1 0.00
48 5 0.02
51 2 0.01
52 40 0.12
53 1 0.00
54 170 0.52
55 38 0.12
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
CACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTAGGTTG
Found at i:2348010 original size:46 final size:46
Alignment explanation
Indices: 2347887--2348078 Score: 224
Period size: 46 Copynumber: 4.0 Consensus size: 46
2347877 ATTTCTTAGG
* * * *
2347887 TTGCACACACAGTGCCAATACGGAAATTCACAAACTTATTATGAAT
1 TTGCACACACAATGCCAATACGAAAATTCATAAACTTATAATGAAT
*
2347933 TT-CTTAGGTTACACATAGTGCCAATACGAAAATTCATAAACTTATAATGAAT
1 TTGC--A---CACACA-A-TGCCAATACGAAAATTCATAAACTTATAATGAAT
* *
2347985 TTGCACACACAATGTCAATACGAAAATTTATAAACTTATAATGAAT
1 TTGCACACACAATGCCAATACGAAAATTCATAAACTTATAATGAAT
* * *
2348031 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAAT
1 TTGCACACACAATGCCAATACGAAAATTCATAAACTTATAATGAAT
2348077 TT
1 TT
2348079 CTTAAGTTGC
Statistics
Matches: 125, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
45 1 0.01
46 77 0.62
47 2 0.02
48 5 0.04
50 5 0.04
51 1 0.01
52 33 0.26
53 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (46 bp):
TTGCACACACAATGCCAATACGAAAATTCATAAACTTATAATGAAT
Found at i:2360425 original size:26 final size:27
Alignment explanation
Indices: 2360389--2360458 Score: 124
Period size: 26 Copynumber: 2.6 Consensus size: 27
2360379 ATCTATGTTT
2360389 AAATTGTTAAATGAACGTGTAT-AAAA
1 AAATTGTTAAATGAACGTGTATAAAAA
*
2360415 AAATTGTTAAATGAACGTTTATAAAAA
1 AAATTGTTAAATGAACGTGTATAAAAA
2360442 AAATTGTTAAATGAACG
1 AAATTGTTAAATGAACG
2360459 GGTGGAGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 21 0.50
27 21 0.50
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.31
Consensus pattern (27 bp):
AAATTGTTAAATGAACGTGTATAAAAA
Found at i:2360727 original size:3 final size:3
Alignment explanation
Indices: 2360721--2360763 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
2360711 TTCTTCTTCT
* *
2360721 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2360764 TTTTATAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:2361253 original size:3 final size:3
Alignment explanation
Indices: 2361245--2361313 Score: 129
Period size: 3 Copynumber: 22.7 Consensus size: 3
2361235 AGAATTGCAA
2361245 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
2361291 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
2361314 CAACAACAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2361450 original size:25 final size:25
Alignment explanation
Indices: 2361414--2361463 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2361404 ATCATTCTTC
2361414 TAAATACCCACACAATAAATGGAGA
1 TAAATACCCACACAATAAATGGAGA
2361439 TAAAT-CCTCACACAATAAATGGAGA
1 TAAATACC-CACACAATAAATGGAGA
2361464 AGAAGAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.18
Consensus pattern (25 bp):
TAAATACCCACACAATAAATGGAGA
Found at i:2361832 original size:12 final size:12
Alignment explanation
Indices: 2361804--2361832 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2361794 GCAATGATGA
2361804 GATTTTTGAAAT
1 GATTTTTGAAAT
2361816 G-TTTTTGAAAT
1 GATTTTTGAAAT
2361827 GATTTT
1 GATTTT
2361833 AATGAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (12 bp):
GATTTTTGAAAT
Found at i:2364668 original size:20 final size:19
Alignment explanation
Indices: 2364645--2364704 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
2364635 ATTAAAAATC
*
2364645 AATAATAAAATAACAATAAA
1 AATAAAAAAATAA-AATAAA
**
2364665 AATAAAAAAATAAAATGGA
1 AATAAAAAAATAAAATAAA
2364684 AATAAAATAAATAAAAATAAA
1 AATAAAA-AAAT-AAAATAAA
2364705 TTATAAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 11 0.33
20 16 0.48
21 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (19 bp):
AATAAAAAAATAAAATAAA
Found at i:2364688 original size:11 final size:9
Alignment explanation
Indices: 2364664--2364705 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
2364654 ATAACAATAA
2364664 AAATAAAA-
1 AAATAAAAT
2364672 AAATAAAAT
1 AAATAAAAT
2364681 GGAAATAAAAT
1 --AAATAAAAT
2364692 AAATAAAAAT
1 AAAT-AAAAT
2364702 AAAT
1 AAAT
2364706 TATAAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.27
9 4 0.13
10 9 0.30
11 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2364817 original size:30 final size:32
Alignment explanation
Indices: 2364772--2364830 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
2364762 AACTAGACTG
*
2364772 TTTTGCAAATTGTTTT-CAAAACTATATACTA
1 TTTTGCAAAATGTTTTCCAAAACTATATACTA
2364803 TTTT-CAAAATGTTTTCCAAAACTATATA
1 TTTTGCAAAATGTTTTCCAAAACTATATA
2364831 ATATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (32 bp):
TTTTGCAAAATGTTTTCCAAAACTATATACTA
Found at i:2365326 original size:44 final size:44
Alignment explanation
Indices: 2365217--2365331 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
2365207 TGGTATTAAC
* ** * * * *
2365217 CCAACTCCCTATGTGATGGAGCCAAGTGAAGTGTTGGTATTGTT
1 CCAACTCCTTATGTGATGGAATCGAGTGAAATGTTGGTACTGAT
* *
2365261 CTAACTTCTTATGTGATGGAATCGAGTGAAATGTT-GTCACTGAT
1 CCAACTCCTTATGTGATGGAATCGAGTGAAATGTTGGT-ACTGAT
*
2365305 CCAACTCCTTATGTGATGGAATTGAGT
1 CCAACTCCTTATGTGATGGAATCGAGT
2365332 AGAATATCAG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (44 bp):
CCAACTCCTTATGTGATGGAATCGAGTGAAATGTTGGTACTGAT
Found at i:2375197 original size:18 final size:18
Alignment explanation
Indices: 2375151--2375197 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2375141 ATTAACATGT
* *
2375151 TTATCATCACTTATTTTA
1 TTATCATTAATTATTTTA
2375169 TTATCATTAATTATTTT-
1 TTATCATTAATTATTTTA
2375186 TTATCATATAAT
1 TTATCAT-TAAT
2375198 CATATACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATCATTAATTATTTTA
Found at i:2376431 original size:16 final size:18
Alignment explanation
Indices: 2376412--2376478 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 18
2376402 AACAAAATGC
2376412 TAAAAAATAA-AAAAT-A
1 TAAAAAATAATAAAATAA
2376428 TAAAAAATAATAATAATAA
1 TAAAAAATAATAA-AATAA
* *
2376447 TAAAAGA-AA-GAAATAA
1 TAAAAAATAATAAAATAA
2376463 TAAAATAATAATAAAA
1 TAAAA-AATAATAAAA
2376479 GGTTAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
16 20 0.49
17 4 0.10
18 7 0.17
19 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAAAATAATAAAATAA
Found at i:2376501 original size:24 final size:24
Alignment explanation
Indices: 2376461--2376519 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2376451 AGAAAGAAAT
* * * *
2376461 AATAAAATAATA-ATAAAAGGTTA
1 AATAAAAAAATATTTAAAAAGTAA
*
2376484 AATTAAAAAATATTTAAAAAGTAA
1 AATAAAAAAATATTTAAAAAGTAA
2376508 AATAAAAAAATA
1 AATAAAAAAATA
2376520 AAGATAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (24 bp):
AATAAAAAAATATTTAAAAAGTAA
Found at i:2377669 original size:16 final size:16
Alignment explanation
Indices: 2377650--2377686 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2377640 AGACCAAAAC
2377650 AATAAAATAAAATAA-A
1 AATAAAAT-AAATAATA
2377666 AATAAAATAAATAATA
1 AATAAAATAAATAATA
2377682 AATAA
1 AATAA
2377687 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATAAATAATA
Found at i:2377686 original size:11 final size:11
Alignment explanation
Indices: 2377653--2377683 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2377643 CCAAAACAAT
2377653 AAAATAAAATA
1 AAAATAAAATA
2377664 AAAATAAAATA
1 AAAATAAAATA
2377675 AATAATAAA
1 AA-AATAAA
2377684 TAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:2377836 original size:36 final size:36
Alignment explanation
Indices: 2377700--2377993 Score: 208
Period size: 36 Copynumber: 7.9 Consensus size: 36
2377690 ATATATACAT
*
2377700 AAATATTTTCAAAAAC-ATATAATATATAAA-TTT-CA
1 AAATGTTTT-AAAAACTATAT-ATATATAAATTTTCCA
* * *
2377735 AAATGTTTT-TAAACTATATAATATATGAATTTTTTCA
1 AAATGTTTTAAAAACTATAT-ATATAT-AAATTTTCCA
* ** * *
2377772 ACATGTTTTCAAAAAAAAAAGATTATATAAATTTTCCCA
1 AAATGTTTT-AAAAACTATATA-TATATAAATTTT-CCA
* *
2377811 AAACGTTTTAAAAACTATATA-ATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATATATATAAAT-TTTCCA
* ** *
2377847 AAATGTTTTCAAAACTATA-ATATATATGTTTTCAA
1 AAATGTTTTAAAAACTATATATATATAAATTTTCCA
2377882 AAATGTTTTCAAAAACTATATATATATATAAGTTTT-CA
1 AAATGTTTT-AAAAACTATATATATATA-AA-TTTTCCA
* * *
2377920 AAATGATTTTAAAAATTATATATTATATATATTTTCTA
1 AAATG-TTTTAAAAACTATATA-TATATAAATTTTCCA
*
2377958 AAATGTTTTTTTTAAAACTATATAT-TATATAATTTT
1 AAATG---TTTTAAAAACTATATATATATA-AATTTT
2377994 AAAAACTATT
Statistics
Matches: 204, Mismatches: 35, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
33 4 0.02
34 11 0.05
35 24 0.12
36 45 0.22
37 24 0.12
38 43 0.21
39 39 0.19
40 14 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATATATATAAATTTTCCA
Found at i:2377845 original size:75 final size:72
Alignment explanation
Indices: 2377722--2377934 Score: 193
Period size: 73 Copynumber: 2.9 Consensus size: 72
2377712 AAACATATAA
* * * *
2377722 TATATAAATTTCAAAATGTTTTTAAACTATATAATATATGAATTTTTTCAACATGTTTTCAAAAA
1 TATATAAATTTCAAAACGTTTTAAAACTATATAATATA-GAATGTTTTCAAAATGTTTTCAAAAA
2377787 AAAAAGAT
65 AAAAAGAT
2377795 TATATAAATTTTCCCAAAACGTTTTAAAAACTATATAATATA-AATGTTTTCAAAATGTTTTCAA
1 TATATAAA-TTT--CAAAACGTTTT-AAAACTATATAATATAGAATGTTTTCAAAATGTTTTCAA
** * *
2377859 AACTATAATA-
62 AAAAAAAAGAT
** * *
2377869 TATAT-GTTTTCAAAAATGTTTTCAAAAACTATATATATATATAA-GTTTTCAAAATGATTTT-A
1 TATATAAATTTC-AAAACGTTTT--AAAACTATATA-ATATAGAATGTTTTCAAAATG-TTTTCA
2377931 AAAA
61 AAAA
2377935 TTATATATTA
Statistics
Matches: 119, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
70 1 0.01
71 9 0.08
72 15 0.13
73 29 0.24
74 14 0.12
75 26 0.22
76 10 0.08
77 15 0.13
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (72 bp):
TATATAAATTTCAAAACGTTTTAAAACTATATAATATAGAATGTTTTCAAAATGTTTTCAAAAAA
AAAAGAT
Found at i:2377852 original size:11 final size:11
Alignment explanation
Indices: 2377836--2377860 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2377826 TATATAATAT
2377836 AAATGTTTTCA
1 AAATGTTTTCA
2377847 AAATGTTTTCA
1 AAATGTTTTCA
2377858 AAA
1 AAA
2377861 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2377889 original size:12 final size:12
Alignment explanation
Indices: 2377872--2377896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2377862 TATAATATAT
2377872 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2377884 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2377896 A
1 A
2377897 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2377911 original size:111 final size:108
Alignment explanation
Indices: 2377704--2377966 Score: 266
Period size: 110 Copynumber: 2.4 Consensus size: 108
2377694 ATACATAAAT
* * *
2377704 ATTTTCAAAAAC-ATATAATATATAA-ATTTCAAAATGTTTTTAAACTATATAATATATGAATTT
1 ATTTT-AAAAACTATATAATATA-AATTTTTCAAAATGTTTTAAAAC-ATATAATATAT-AATGT
*
2377767 TTTCAACATGTTTTCAAAAAAAAAAGATTATATAAATTTTCCCAAAACG
62 TTTCAAAATGTTTTCAAAAAAAAAAGATTATATAAATTTT--CAAAACG
2377816 -TTTTAAAAACTATATAATATAAATGTTTTCAAAATGTTTTCAAAAC-TATAATATAT-ATGTTT
1 ATTTTAAAAACTATATAATATAAAT-TTTTCAAAATGTTTT-AAAACATATAATATATAATGTTT
** * * * *
2377878 TCAAAAATGTTTTCAAAAACTATATATATATATAAGTTTTCAAAATG
64 TC-AAAATGTTTTCAAAAAAAAAAGAT-TATATAAATTTTCAAAACG
* * *
2377925 ATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTT
1 ATTTTAAAAACTATATAATATAAAT-TTTTC-AAAATGTTTT
2377967 TTTTAAAACT
Statistics
Matches: 129, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
109 13 0.10
110 53 0.41
111 45 0.35
112 14 0.11
113 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (108 bp):
ATTTTAAAAACTATATAATATAAATTTTTCAAAATGTTTTAAAACATATAATATATAATGTTTTC
AAAATGTTTTCAAAAAAAAAAGATTATATAAATTTTCAAAACG
Found at i:2379040 original size:164 final size:164
Alignment explanation
Indices: 2378609--2379103 Score: 697
Period size: 164 Copynumber: 3.0 Consensus size: 164
2378599 ACTCGACAAT
* * * * * * * *
2378609 TTTATTGACAAATAGCCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGT
1 TTTATTAACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGT
* * * * *
2378674 GTAATCGAAC-TCGGGAGTCTTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATA
66 GTAATCGAACTTAGGG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
2378738 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
130 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
** * * * **
2378773 TTTGATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGAG
1 TTT-ATTAACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAG
* **
2378838 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
65 TGTAATCGAACTTAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
*
2378903 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
130 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * *
2378938 TTT-TCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAG
1 TTTAT-TAACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAG
*
2379002 TGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
65 TGTAATCGAACTTAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
2379067 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
130 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
2379102 TT
1 TT
2379104 GGTGGCAGGT
Statistics
Matches: 292, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
163 1 0.00
164 149 0.51
165 139 0.48
166 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (164 bp):
TTTATTAACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGT
GTAATCGAACTTAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
Found at i:2384278 original size:8 final size:8
Alignment explanation
Indices: 2384222--2384280 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
2384212 AAAATGCTAA
2384222 AAAATAA-
1 AAAATAAT
*
2384229 AAAATATAA
1 AAAATA-AT
2384238 AAAATAAT
1 AAAATAAT
2384246 AATAATAAT
1 AA-AATAAT
* *
2384255 GAAAGAA-
1 AAAATAAT
2384262 AGAAATAAT
1 A-AAATAAT
2384271 AAAATAAT
1 AAAATAAT
2384279 AA
1 AA
2384281 TAAAAGGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.14
8 22 0.52
9 14 0.33
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:2384308 original size:24 final size:24
Alignment explanation
Indices: 2384268--2384326 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2384258 AGAAAGAAAT
* * * *
2384268 AATAAAATAATA-ATAAAAGGTTA
1 AATAAAAAAATATTTAAAAAGTAA
*
2384291 AATTAAAAAATATTTAAAAAGTAA
1 AATAAAAAAATATTTAAAAAGTAA
2384315 AATAAAAAAATA
1 AATAAAAAAATA
2384327 AAGATAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (24 bp):
AATAAAAAAATATTTAAAAAGTAA
Found at i:2385476 original size:16 final size:16
Alignment explanation
Indices: 2385457--2385493 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2385447 AGACCAAAAC
2385457 AATAAAATAAAATAA-A
1 AATAAAAT-AAATAATA
2385473 AATAAAATAAATAATA
1 AATAAAATAAATAATA
2385489 AATAA
1 AATAA
2385494 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATAAATAATA
Found at i:2385493 original size:11 final size:11
Alignment explanation
Indices: 2385460--2385490 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2385450 CCAAAACAAT
2385460 AAAATAAAATA
1 AAAATAAAATA
2385471 AAAATAAAATA
1 AAAATAAAATA
2385482 AATAATAAA
1 AA-AATAAA
2385491 TAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:2385642 original size:36 final size:36
Alignment explanation
Indices: 2385507--2385774 Score: 165
Period size: 36 Copynumber: 7.2 Consensus size: 36
2385497 ATATATACAT
* *
2385507 AAATATTTTCAAAAAC-ATATAATATATAA-ATTT-CA
1 AAATGTTTT-AAAAACTATATAATATA-AATGTTTCCA
* * *
2385542 AAATGTTTT-TAAACTATATAATATATGAATTTTTTCA
1 AAATGTTTTAAAAACTATATAATATA--AATGTTTCCA
* ** * *
2385579 ACATGTTTTCAAAAAAAAAGATTATATAAAT-TTTCCCA
1 AAATGTTTT--AAAAACTATATAATATAAATGTTT-CCA
* *
2385617 AAACGTTTTAAAAACTATATAATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATATAAATGTTTCCA
* * *
2385653 AAATGTTTTCAAAAC--TATAATATATATGTTTTCAA
1 AAATGTTTTAAAAACTATATAATATAAATG-TTTCCA
* *
2385688 AAATGTTTTCAAAAACTATATATATATATATAAGTTTTCA
1 AAATGTTTT-AAAAACTATATA-ATATA-A-ATGTTTCCA
* * *
2385728 AAATGATTTTAAAAATTATATATTATATATAT-TTTCTA
1 AAATG-TTTTAAAAACTATATA--ATATAAATGTTTCCA
2385766 AAATGTTTT
1 AAATGTTTT
2385775 TTTTAAAACT
Statistics
Matches: 182, Mismatches: 33, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
33 4 0.02
34 22 0.12
35 23 0.13
36 39 0.21
37 20 0.11
38 25 0.14
39 6 0.03
40 31 0.17
41 12 0.07
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATAATATAAATGTTTCCA
Found at i:2385651 original size:74 final size:71
Alignment explanation
Indices: 2385529--2385666 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 71
2385519 AAACATATAA
* * * *
2385529 TATATAAATTTCAAAATGTTTTTAAACTATATAATATATGAATTTTTTCAACATGTTTTCAAAAA
1 TATATAAATTTCAAAACGTTTTAAAACTATATAATATA-GAATGTTTTCAAAATGTTTTCAAAAA
2385594 AAAAGAT
65 AAAAGAT
2385601 TATATAAATTTTCCCAAAACGTTTTAAAAACTATATAATATA-AATGTTTTCAAAATGTTTTCAA
1 TATATAAA-TTT--CAAAACGTTTT-AAAACTATATAATATAGAATGTTTTCAAAATGTTTTCAA
2385665 AA
62 AA
2385667 CTATAATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
72 8 0.14
73 3 0.05
74 22 0.38
75 10 0.17
76 15 0.26
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (71 bp):
TATATAAATTTCAAAACGTTTTAAAACTATATAATATAGAATGTTTTCAAAATGTTTTCAAAAAA
AAAGAT
Found at i:2385658 original size:11 final size:11
Alignment explanation
Indices: 2385642--2385666 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2385632 TATATAATAT
2385642 AAATGTTTTCA
1 AAATGTTTTCA
2385653 AAATGTTTTCA
1 AAATGTTTTCA
2385664 AAA
1 AAA
2385667 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2385679 original size:74 final size:74
Alignment explanation
Indices: 2385507--2385798 Score: 265
Period size: 72 Copynumber: 3.9 Consensus size: 74
2385497 ATATATACAT
* * *
2385507 AAATATTTTCAAAAAC-ATATAATATATAAA-TTT-CAAAATGTTTT-TAAACTATATAATATAT
1 AAATGTTTTC-AAAACTATATATTATATAAATTTTCCAAAATGTTTTAAAAACTATATAATATAT
*
2385568 GAATTTTTTCA
65 -AATGTTTTCA
* ** * * *
2385579 ACATGTTTTCAAAAAAAAAGATTATATAAATTTTCCCAAAACGTTTTAAAAACTATATAATATA-
1 AAATGTTTTCAAAACTATATATTATATAAATTTT-CCAAAATGTTTTAAAAACTATATAATATAT
2385643 AATGTTTTCA
65 AATGTTTTCA
** *
2385653 AAATGTTTTCAAAACTATA-A-TATATATGTTTTCAAAAATGTTTTCAAAAACTATATATATATA
1 AAATGTTTTCAAAACTATATATTATATAAATTTTCCAAAATGTTTT-AAAAACTATATA-ATATA
*
2385716 TATAAGTTTTCA
64 TA-ATGTTTTCA
* * * * * *
2385728 AAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTTTTTAAAACTATATATTA
1 AAATG-TTTTCAAAACTATATATTATATAAATTTTCCAAAATG---TTTTAAAAACTATATAATA
2385793 TATAAT
62 TATAAT
2385799 TTTAAAAACT
Statistics
Matches: 180, Mismatches: 25, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
71 14 0.08
72 41 0.23
73 9 0.05
74 25 0.14
75 23 0.13
76 27 0.15
77 1 0.01
78 19 0.11
79 6 0.03
80 11 0.06
81 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (74 bp):
AAATGTTTTCAAAACTATATATTATATAAATTTTCCAAAATGTTTTAAAAACTATATAATATATA
ATGTTTTCA
Found at i:2385695 original size:12 final size:12
Alignment explanation
Indices: 2385678--2385702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2385668 TATAATATAT
2385678 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2385690 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2385702 A
1 A
2385703 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2385779 original size:41 final size:37
Alignment explanation
Indices: 2385493--2385844 Score: 233
Period size: 34 Copynumber: 9.5 Consensus size: 37
2385483 ATAATAAATA
* * * * *
2385493 ATATATATATACATAAATATTTTCAAAAAC-ATATAAT
1 ATATATATTTTCA-AAATGTTTTTAAAAACTATATATT
* *
2385530 ATATA-AATTTCAAAATGTTTTT--AAACTATATAAT
1 ATATATATTTTCAAAATGTTTTTAAAAACTATATATT
* * * * * *
2385564 ATATGAATTTTTTCAACATGTTTTCAAAAA-AAAAGATT
1 ATAT--ATATTTTCAAAATGTTTTTAAAAACTATATATT
* * *
2385602 ATATAAATTTTCCCAAAACG-TTTTAAAAACTATATAAT
1 ATATATATTTT--CAAAATGTTTTTAAAAACTATATATT
* * *
2385640 ATAAATGTTTTCAAAATG-TTTTCAAAACTATA-A-T
1 ATATATATTTTCAAAATGTTTTTAAAAACTATATATT
* *
2385674 ATATATGTTTTCAAAAATGTTTTCAAAAACTATATATAT
1 ATATATATTTTC-AAAATGTTTTTAAAAACTATATAT-T
* *
2385713 ATATATAAGTTTTCAAAATGATTTTAAAAATTATATATT
1 ATATAT-A-TTTTCAAAATGTTTTTAAAAACTATATATT
*
2385752 ATATATATTTTCTAAAATGTTTTTTTTAAAACTATATATT
1 ATATATATTTTC-AAAATG--TTTTTAAAAACTATATATT
** * *
2385792 ATATA-ATTTT-AAAA-ACTATTAAAAATTATATATT
1 ATATATATTTTCAAAATGTTTTTAAAAACTATATATT
*
2385826 ATATACGTAGTTTCAAAAT
1 ATATA--TATTTTCAAAAT
2385845 ATGTATATAT
Statistics
Matches: 248, Mismatches: 43, Indels: 46
0.74 0.13 0.14
Matches are distributed among these distances:
33 4 0.02
34 43 0.17
35 15 0.06
36 41 0.17
37 40 0.16
38 36 0.15
39 22 0.09
40 42 0.17
41 5 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
ATATATATTTTCAAAATGTTTTTAAAAACTATATATT
Found at i:2387435 original size:10 final size:10
Alignment explanation
Indices: 2387413--2387449 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2387403 CAAGAAGAAG
2387413 AGAAGAAAT-A
1 AGAA-AAATAA
2387423 AGAAAAATAA
1 AGAAAAATAA
2387433 AGAAAAATAA
1 AGAAAAATAA
2387443 AGAAAAA
1 AGAAAAA
2387450 GGTGTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (10 bp):
AGAAAAATAA
Found at i:2390516 original size:9 final size:9
Alignment explanation
Indices: 2390502--2390531 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2390492 TGAGGAATGC
2390502 AAAAATGTA
1 AAAAATGTA
2390511 AAAAATGTA
1 AAAAATGTA
2390520 AAAAATGTA
1 AAAAATGTA
2390529 AAA
1 AAA
2390532 TAATTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (9 bp):
AAAAATGTA
Found at i:2400293 original size:16 final size:16
Alignment explanation
Indices: 2400263--2400293 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2400253 TAATATTGAA
*
2400263 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
2400279 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
2400294 AAAATTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:2403604 original size:35 final size:34
Alignment explanation
Indices: 2403519--2403605 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
2403509 AATATAATTT
*
2403519 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
2403553 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
2403591 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2403606 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:2403671 original size:34 final size:35
Alignment explanation
Indices: 2403596--2403672 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
2403586 AATGGTAATA
* * *
2403596 AACAAAATTAACCAAAATACATTAACAAAAAGTCT
1 AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
2403631 AACAAATTTAA-CAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACCAAAATAAATTAACAA-AAAGTCC
2403664 AACCAAATT
1 AA-CAAATT
2403673 AATGAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.16
34 21 0.57
35 10 0.27
ACGTcount: A:0.61, C:0.16, G:0.01, T:0.22
Consensus pattern (35 bp):
AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
Found at i:2406119 original size:3 final size:3
Alignment explanation
Indices: 2406111--2406153 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2406101 GGTATTAGGT
* * *
2406111 TTA TTA TTA TTA CTA TTA TAA GTA TTA TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2406154 TTTACCTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2409617 original size:185 final size:185
Alignment explanation
Indices: 2409305--2409682 Score: 702
Period size: 185 Copynumber: 2.0 Consensus size: 185
2409295 ATATGATGCT
*
2409305 TATGTGGCATGAGTGTATGTGTTATATATTATTGAATATGTTACAGGAATTGTGTGAATACATGT
1 TATGTGGTATGAGTGTATGTGTTATATATTATTGAATATGTTACAGGAATTGTGTGAATACATGT
* *
2409370 TAGTGTGATAAGCTATGTGAACTAGTATAAATATTTTATGTGATTACATAAGTTATATGATATAA
66 TAGTGTGATAAACTATGTGAACTAGTATAAATATTGTATGTGATTACATAAGTTATATGATATAA
2409435 ACATGTGATATAAGATATAAGCTAAAGAATTATATGATATGAGATAAGACAGACA
131 ACATGTGATATAAGATATAAGCTAAAGAATTATATGATATGAGATAAGACAGACA
*
2409490 TATGTGGTATGAGTGTATGTGTTATATATTATTGCATATGTTACAGGAATTGTGTGAATACATGT
1 TATGTGGTATGAGTGTATGTGTTATATATTATTGAATATGTTACAGGAATTGTGTGAATACATGT
*
2409555 TAGTGTGATAAACTATGTGAATTAGTATAAATATTGTATGTGATTACATAAGTTATATGATATAA
66 TAGTGTGATAAACTATGTGAACTAGTATAAATATTGTATGTGATTACATAAGTTATATGATATAA
*
2409620 ACATGTGATATAAGATATAAGCTAAAGAATTATATGATATGAGATAAGACAGACG
131 ACATGTGATATAAGATATAAGCTAAAGAATTATATGATATGAGATAAGACAGACA
2409675 TATGTGGT
1 TATGTGGT
2409683 TATATGAGAC
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 187 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (185 bp):
TATGTGGTATGAGTGTATGTGTTATATATTATTGAATATGTTACAGGAATTGTGTGAATACATGT
TAGTGTGATAAACTATGTGAACTAGTATAAATATTGTATGTGATTACATAAGTTATATGATATAA
ACATGTGATATAAGATATAAGCTAAAGAATTATATGATATGAGATAAGACAGACA
Found at i:2409751 original size:2 final size:2
Alignment explanation
Indices: 2409744--2409771 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2409734 AAAGTGAACC
2409744 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
2409772 GAATATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2410078 original size:32 final size:31
Alignment explanation
Indices: 2410037--2410128 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
2410027 AGTCGAGGGT
2410037 TTACCTATGTTCTATGGAACATATGGACATAA
1 TTACCTATGTTCTATGGAACATATGGACA-AA
* *
2410069 TTACCTATG-TCTTTCGGGACATATGGAC-AA
1 TTACCTATGTTCTAT-GGAACATATGGACAAA
* * *
2410099 TATACCTATATTCTAAGGAACATATAGACA
1 T-TACCTATGTTCTATGGAACATATGGACA
2410129 GTTTCCCTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 3 0.06
31 22 0.45
32 24 0.49
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTATGGAACATATGGACAAA
Found at i:2411228 original size:51 final size:51
Alignment explanation
Indices: 2411173--2411271 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
2411163 CGCTATACCC
* *
2411173 CACGTGGCGCCAGATCAGTGTAAAGCACGCTGCAGGGGGCACACCTTATCT
1 CACGTGGCGCCAGATCAGCGAAAAGCACGCTGCAGGGGGCACACCTTATCT
* * *
2411224 CACGTGGCGCCAGATTAGCGAAAAGCGCGCTGCAGGGGGCACGCCTTA
1 CACGTGGCGCCAGATCAGCGAAAAGCACGCTGCAGGGGGCACACCTTA
2411272 CTGCAAAGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.15
Consensus pattern (51 bp):
CACGTGGCGCCAGATCAGCGAAAAGCACGCTGCAGGGGGCACACCTTATCT
Found at i:2411501 original size:30 final size:29
Alignment explanation
Indices: 2411460--2411564 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 29
2411450 AACTATATAA
* *
2411460 TATATAATATTTTTAAAATAATTTTTAAAT
1 TATATATTATTTTCAAAAT-ATTTTTAAAT
*
2411490 TATATATTATTTTCAAAAT-GTTTTACAA-
1 TATATATTATTTTCAAAATATTTTTA-AAT
2411518 -ATA-ATGT-TTTT-AAAATATTTTTTTAAAAT
1 TATATAT-TATTTTCAAAATA--TTTTT-AAAT
2411547 TATATATTATTTTCAAAA
1 TATATATTATTTTCAAAA
2411565 GGTTTCTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
25 5 0.08
26 6 0.10
27 4 0.07
28 11 0.18
29 3 0.05
30 21 0.35
31 6 0.10
32 4 0.07
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATATTATTTTCAAAATATTTTTAAAT
Found at i:2411533 original size:14 final size:14
Alignment explanation
Indices: 2411463--2411551 Score: 53
Period size: 13 Copynumber: 6.5 Consensus size: 14
2411453 TATATAATAT
2411463 ATAATATTTTTAAA
1 ATAATATTTTTAAA
2411477 AT-A-ATTTTTAAA
1 ATAATATTTTTAAA
* **
2411489 TTATATATTATTTTCA
1 ATA-ATATT-TTTAAA
*
2411505 A-AAT-GTTTTACAA
1 ATAATATTTTTA-AA
*
2411518 ATAATGTTTTTAAA
1 ATAATATTTTTAAA
*
2411532 AT-ATTTTTTTAAA
1 ATAATATTTTTAAA
*
2411545 ATTATAT
1 ATAATAT
2411552 ATTATTTTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
12 13 0.23
13 16 0.28
14 15 0.26
15 9 0.16
16 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
ATAATATTTTTAAA
Found at i:2411533 original size:55 final size:57
Alignment explanation
Indices: 2411463--2411569 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
2411453 TATATAATAT
*
2411463 ATAATATTTTTAAAATA-ATTTTT-AAATTATATATTATTTTCAAAATGTTTTACAA
1 ATAATATTTTTAAAATATATTTTTAAAATTATATATTATTTTCAAAAGGTTTTACAA
* *
2411518 ATAATGTTTTTAAAATATTTTTTTAAAATTATATATTATTTTCAAAAGGTTT
1 ATAATATTTTTAAAATATATTTTTAAAATTATATATTATTTTCAAAAGGTTT
2411570 CTAAAACTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 16 0.34
56 5 0.11
57 26 0.55
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (57 bp):
ATAATATTTTTAAAATATATTTTTAAAATTATATATTATTTTCAAAAGGTTTTACAA
Found at i:2411605 original size:30 final size:29
Alignment explanation
Indices: 2411538--2411612 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
2411528 TAAAATATTT
* * *
2411538 TTTTAAAATTATATATTATTTTCAAAAGG
1 TTTTAAAACTATATAATATTTTCAAAAGC
2411567 TTTCTAAAACTATATAATATTTTTC-AAAGC
1 TTT-TAAAACTATATAATA-TTTTCAAAAGC
2411597 TATTTAAAAACTATAT
1 T-TTT-AAAACTATAT
2411613 TTTTCCAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 3 0.08
30 19 0.49
31 17 0.44
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTTAAAACTATATAATATTTTCAAAAGC
Found at i:2411665 original size:2 final size:2
Alignment explanation
Indices: 2411658--2411691 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2411648 CCTTTAAACC
2411658 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
2411692 TAGAACCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2412713 original size:19 final size:18
Alignment explanation
Indices: 2412689--2412725 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2412679 ATTATTTTCC
*
2412689 AAAAAGTAATTATAATAAT
1 AAAAAGTAAATA-AATAAT
2412708 AAAAAGTAAATAAATAAT
1 AAAAAGTAAATAAATAAT
2412726 TGTGAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAAAGTAAATAAATAAT
Found at i:2414621 original size:31 final size:31
Alignment explanation
Indices: 2414583--2414659 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
2414573 CTTTTAAAAC
* * *
2414583 TTGCAATATAAT-CTTCCAACATTTAGTCTGT
1 TTGCAATATAATCCCT-CAACATTTAATCCGT
*
2414614 TTGCAATATGATCCCTCAACATTTAATCCGT
1 TTGCAATATAATCCCTCAACATTTAATCCGT
*
2414645 TTGCAATATGATCCC
1 TTGCAATATAATCCC
2414660 CGACGAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (31 bp):
TTGCAATATAATCCCTCAACATTTAATCCGT
Found at i:2415693 original size:63 final size:64
Alignment explanation
Indices: 2415591--2415716 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 64
2415581 CTTCGCTTTG
*** * *
2415591 CTCTTCCTTTTCATATTCATTTTCTATTTCCGGCTGACTGTTCAATTTCTCTTCATC-TCCTTC
1 CTCTTCCTTTTCATATTCATCACCTATTACCGGCCGACTGTTCAATTTCTCTTCATCTTCCTTC
* * *
2415654 CTCTTCCTTTTCATCTTCATCACCTATTACCGGCCGACTGTTCGATTTCTCTTCTTCTTCCTT
1 CTCTTCCTTTTCATATTCATCACCTATTACCGGCCGACTGTTCAATTTCTCTTCATCTTCCTT
2415717 GTCAGGCTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
63 49 0.91
64 5 0.09
ACGTcount: A:0.12, C:0.33, G:0.07, T:0.48
Consensus pattern (64 bp):
CTCTTCCTTTTCATATTCATCACCTATTACCGGCCGACTGTTCAATTTCTCTTCATCTTCCTTC
Found at i:2418504 original size:15 final size:14
Alignment explanation
Indices: 2418473--2418520 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
2418463 CTGGAAAAAC
2418473 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
2418487 ATAAAAAGAAAATAA
1 ATAAAAAGAAAAT-A
*
2418502 ATAAATAATAATAATA
1 ATAAA-AAGAA-AATA
2418518 ATA
1 ATA
2418521 TAATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 13 0.43
15 6 0.20
16 8 0.27
17 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:2418507 original size:22 final size:23
Alignment explanation
Indices: 2418482--2418530 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
2418472 CATAAAAAGA
2418482 AAATAATAAAAAGAAAATAA-AT
1 AAATAATAAAAAGAAAATAATAT
* * *
2418504 AAATAATAATAATAATATAATAT
1 AAATAATAAAAAGAAAATAATAT
2418527 AAAT
1 AAAT
2418531 TATGTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAATAAAAAGAAAATAATAT
Found at i:2418578 original size:36 final size:35
Alignment explanation
Indices: 2418538--2418970 Score: 294
Period size: 34 Copynumber: 12.2 Consensus size: 35
2418528 AATTATGTAA
*
2418538 TATATATATTTCAAAAATATTTTTTAAACTATATA-
1 TATATAT-TTTCAAAAATATTTTTAAAACTATATAT
*
2418573 T-TATATTTT-AAAAA-AGTTTTCAAAACTATATAT
1 TATATATTTTCAAAAATA-TTTTTAAAACTATATAT
* * *
2418606 TATATAGTTTT-TAAAAT-GTTTTAAAAATAT-TA-
1 TATATA-TTTTCAAAAATATTTTTAAAACTATATAT
2418638 TATA-AGTTTTCAAAAA-ATGTTTTAAAAACTATATAT
1 TATATA-TTTTCAAAAATAT-TTTT-AAAACTATATAT
*
2418674 TATATAATTTTTCCAAAAATGTTTTTAAAACTATATA-
1 TATAT-A-TTTT-CAAAAATATTTTTAAAACTATATAT
*
2418711 TATA-ATTTTCCAAAAATGTTTTTAAAACTATAT-T
1 TATATATTTT-CAAAAATATTTTTAAAACTATATAT
*
2418745 TATATAATTTTTC-AAAATGTTTTTAAAACTATATAT
1 TATAT-A-TTTTCAAAAATATTTTTAAAACTATATAT
* * *
2418781 TATATAATTTTTCAAAAATGTTTTTAAAAAATATATAC
1 TATAT-A-TTTTCAAAAATATTTTT-AAAACTATATAT
* *
2418819 TATATAAGTTTTC-AAAATGTTTTCAAAACTATATAT
1 TATAT-A-TTTTCAAAAATATTTTTAAAACTATATAT
** *
2418855 TATATATTTT-AAAAATATATTCAAAAACCATATAAT
1 TATATATTTTCAAAAATAT-TTTTAAAACTATAT-AT
* * *
2418891 ATATAAATTTTC-GAAATCGTTTTCTGAAAA-T-TATA-
1 -TATATATTTTCAAAAAT-ATTTT-T-AAAACTATATAT
* * *
2418926 TATATATTTGTCAAAAACATTTTCACAAACTATATTAC
1 TATATATTT-TCAAAAATATTTTTA-AAACTATA-TAT
2418964 TATATAT
1 TATATAT
2418971 ATATATATAT
Statistics
Matches: 329, Mismatches: 32, Indels: 71
0.76 0.07 0.16
Matches are distributed among these distances:
31 7 0.02
32 27 0.08
33 11 0.03
34 79 0.24
35 52 0.16
36 43 0.13
37 49 0.15
38 46 0.14
39 14 0.04
40 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATATTTTCAAAAATATTTTTAAAACTATATAT
Found at i:2418880 original size:34 final size:35
Alignment explanation
Indices: 2418540--2418870 Score: 319
Period size: 34 Copynumber: 9.5 Consensus size: 35
2418530 TTATGTAATA
* * *
2418540 TATATA-TTTCAAAAATATTTTTTAAACTATATA-
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAT
* *
2418573 T-TATA-TTTTAAAAAAGTTTTCAAAACTATATAT
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAT
* *
2418606 TATATAGTTTTTAAAATG-TTTTAAAAATAT-TA-
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAT
*
2418638 TATA-AGTTTTCAAAAAATGTTTTAAAAACTATATAT
1 TATATAGTTTT--AAAAATGTTTTTAAAACTATATAT
*
2418674 TATATAATTTTTCCAAAAATGTTTTTAAAACTATATA-
1 TATAT-AGTTTT--AAAAATGTTTTTAAAACTATATAT
2418711 TATA-A-TTTTCCAAAAATGTTTTTAAAACTATAT-T
1 TATATAGTTTT--AAAAATGTTTTTAAAACTATATAT
* *
2418745 TATATAATTTTTCAAAATGTTTTTAAAACTATATAT
1 TATAT-AGTTTTAAAAATGTTTTTAAAACTATATAT
* * *
2418781 TATATAATTTTTCAAAAATGTTTTTAAAAAATATATAC
1 TATAT-AGTTTT-AAAAATGTTTTT-AAAACTATATAT
* *
2418819 TATATAAGTTTTCAAAATGTTTTCAAAACTATATAT
1 TATAT-AGTTTTAAAAATGTTTTTAAAACTATATAT
2418855 TATATA-TTTTAAAAAT
1 TATATAGTTTTAAAAAT
2418871 ATATTCAAAA
Statistics
Matches: 256, Mismatches: 25, Indels: 33
0.82 0.08 0.11
Matches are distributed among these distances:
31 6 0.02
32 30 0.12
33 10 0.04
34 65 0.25
35 34 0.13
36 33 0.13
37 29 0.11
38 49 0.19
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATAGTTTTAAAAATGTTTTTAAAACTATATAT
Found at i:2418930 original size:71 final size:69
Alignment explanation
Indices: 2418613--2418942 Score: 224
Period size: 71 Copynumber: 4.6 Consensus size: 69
2418603 TATTATATAG
* * * ** *
2418613 TTTTTAAAATGTTTT-AAAAATAT-TATATAAGTTTTCAAAAA-ATGTTTTAAAAACTATATATT
1 TTTTCAAAATGTTTTCAAAATTATATATAT-A-TTTTCAAAAATATATTCAAAAAAC-ATATAAT
*
2418675 ATATAAT
63 ATATAAA
* * * **
2418682 TTTTCCAAAAATGTTTTTAAAACTATATATATAATTTTCCAAAAATGT-TT-TTAAAAC-TATAT
1 TTTT-C-AAAATGTTTTCAAAATTATATATAT-ATTTT-CAAAAATATATTCAAAAAACATATA-
* *
2418744 TTATATAAT
61 ATATATAAA
* * * * *
2418753 TTTTCAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAAAATATATA
1 TTTTCAAAATGTTTTCAAAA-T-TATA-TATAT-A-TTTTCAAAAATATATTCAAAAAACATATA
* *
2418818 CTATATAAG
61 ATATATAAA
*
2418827 TTTTCAAAATGTTTTCAAAACTATATATTATATATTTT-AAAAATATATTCAAAAACCATATAAT
1 TTTTCAAAATGTTTTCAAAA-T-TATA-TATATATTTTCAAAAATATATTCAAAAAACATATAAT
2418891 ATATAAA
63 ATATAAA
*
2418898 TTTTCGAAATCGTTTTCTGAAAATTATATATATATTTGTCAAAAA
1 TTTTCAAAAT-GTTTTC--AAAATTATATATATATTT-TCAAAAA
2418943 CATTTTCACA
Statistics
Matches: 223, Mismatches: 19, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
69 19 0.09
70 5 0.02
71 71 0.32
72 48 0.22
73 28 0.13
74 48 0.22
75 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (69 bp):
TTTTCAAAATGTTTTCAAAATTATATATATATTTTCAAAAATATATTCAAAAAACATATAATATA
TAAA
Found at i:2418971 original size:2 final size:2
Alignment explanation
Indices: 2418964--2419095 Score: 180
Period size: 2 Copynumber: 67.5 Consensus size: 2
2418954 ACTATATTAC
2418964 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
* * *
2419006 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TG TA TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2419047 TA TA TG TA TA TA TA TG TA TA TA TA TA CA TA TA TA -A TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2419087 TA TA TA TA T
1 TA TA TA TA T
2419096 TTAATAAAAT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
1 3 0.03
2 111 0.97
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2419100 original size:18 final size:18
Alignment explanation
Indices: 2419068--2419106 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2419058 ATATGTATAT
2419068 ATATACATATATAATAAA
1 ATATACATATATAATAAA
* *
2419086 ATATATATATTTAATAAA
1 ATATACATATATAATAAA
2419104 ATA
1 ATA
2419107 ACTCCGGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATACATATATAATAAA
Found at i:2419151 original size:2 final size:2
Alignment explanation
Indices: 2419146--2419172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2419136 TATATATATA
2419146 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2419173 ATATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2419216 original size:19 final size:19
Alignment explanation
Indices: 2419192--2419228 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2419182 TATATGTATA
*
2419192 TATATATATAATAAAATAT
1 TATATATATAACAAAATAT
*
2419211 TATATATTTAACAAAATA
1 TATATATATAACAAAATA
2419229 ACTCCGGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATATATAACAAAATAT
Found at i:2420199 original size:43 final size:43
Alignment explanation
Indices: 2420152--2420447 Score: 458
Period size: 43 Copynumber: 6.9 Consensus size: 43
2420142 CAAAAAAGCA
*
2420152 TGGGGAAACTATAAGGCTTACCCTTGCACACAGAAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACC
2420195 TGGGGAAACTGTAAGGCTTACCCTTGCACACA-ACAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACC
*
2420238 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACC
* * *
2420281 TGGGGAAACTATAAGGCTTACCCTTACACACAGCAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACC
*
2420324 TGGGGAAACTGTAAAGCTTACCCTTGCACACA-ACAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACC
*
2420367 TGGGGAAACTGTAAGGCTTACCCTTGCACACA-ACAAAGGGACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACC
*
2420410 T-GGG-AACTGTAAGGCTTACCCTTGCACACAGCAAAGGA
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGA
2420448 GCCACCAATA
Statistics
Matches: 237, Mismatches: 12, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
41 31 0.13
42 4 0.02
43 202 0.85
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.17
Consensus pattern (43 bp):
TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACC
Found at i:2420285 original size:129 final size:129
Alignment explanation
Indices: 2420125--2420447 Score: 526
Period size: 129 Copynumber: 2.5 Consensus size: 129
2420115 ACGGTAAGTT
* * * * *
2420125 CTTATCCTTGCACATAGCAAA-AAAGCATGGGGAAACTATAAGGCTTACCCTTGCACACAGAAAA
1 CTTACCCTTGCACACAGCAAAGGAA-CCTGGGGAAACTATAAGGCTTACCCTTGCACACAGCAAA
*
2420189 GGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG
65 GGAACCTGGGGAAACTGTAAAGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG
*
2420254 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTATAAGGCTTACCCTTACACACAGCAAAG
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTATAAGGCTTACCCTTGCACACAGCAAAG
2420319 GAACCTGGGGAAACTGTAAAGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG
66 GAACCTGGGGAAACTGTAAAGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG
* * *
2420383 CTTACCCTTGCACACAACAAAGGGACCT-GGG-AACTGTAAGGCTTACCCTTGCACACAGCAAAG
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTATAAGGCTTACCCTTGCACACAGCAAAG
2420446 GA
66 GA
2420448 GCCACCAATA
Statistics
Matches: 182, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
127 32 0.18
128 3 0.02
129 145 0.80
130 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (129 bp):
CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTATAAGGCTTACCCTTGCACACAGCAAAG
GAACCTGGGGAAACTGTAAAGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGG
Found at i:2424805 original size:80 final size:80
Alignment explanation
Indices: 2424404--2424804 Score: 489
Period size: 80 Copynumber: 4.9 Consensus size: 80
2424394 ATGTGTCATC
* ** * * * *
2424404 GAGCTGAATGGAATCGAACTCGACAATTTTTATTGACAGATAACCCTTCTAGCCCTGAGCTATGC
1 GAGCTGAATGGAATCGAACTC--TAAGGTCT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* *
2424469 TGTAAATTTGATATGCCTTT
63 TGCAAA--TGATACGCCTTT
* * *
2424489 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGGAATCGAACTCTAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATG
*
2424554 CTGCAAATGATATGCCTTT
62 CTGCAAATGATACGCCTTT
* * * * * * *
2424573 GAGCCGAGTGGAATCGAACTATAAGGTCTTTAGCAGATAACCC-TCATTGCCTTAAGCTATGCTG
1 GAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTC-TAGCCTTGAGTTATGCTG
*
2424637 CAAATGATACCCCTTT
65 CAAATGATACGCCTTT
*
2424653 GAGCTGAATGGAATCGAACTCTAAGGTTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1 GAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
*
2424718 AAATGATGCGCCTTT
66 AAATGATACGCCTTT
*
2424733 GAGCTGAATGGAATCAAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1 GAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
2424798 AAATGAT
66 AAATGAT
2424805 GTGCCCTCGA
Statistics
Matches: 277, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
79 2 0.01
80 179 0.65
81 3 0.01
83 3 0.01
84 35 0.13
85 20 0.07
86 35 0.13
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (80 bp):
GAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
AAATGATACGCCTTT
Found at i:2424997 original size:37 final size:38
Alignment explanation
Indices: 2424947--2425020 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
2424937 AAGATTGGTG
*
2424947 TTTCAAGAGAAACTATATCAAGAGAGA-TAAAACTTTA
1 TTTCAAGAGAAACTATATCAAGAGAGACAAAAACTTTA
* * * *
2424984 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAAACTTT
1 TTTCAAGAGAAACTATATCAAGAGAGACAAAAACTTT
2425021 CTCAAGAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 23 0.74
38 8 0.26
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (38 bp):
TTTCAAGAGAAACTATATCAAGAGAGACAAAAACTTTA
Found at i:2425027 original size:21 final size:21
Alignment explanation
Indices: 2424993--2425036 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2424983 ATTTCAAGGG
*
2424993 AAACTGTCTTAAGAGAGACAA
1 AAACTGTCTCAAGAGAGACAA
*
2425014 AAACTTTCTCAAGAGAGACAA
1 AAACTGTCTCAAGAGAGACAA
2425035 AA
1 AA
2425037 CTTAGTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (21 bp):
AAACTGTCTCAAGAGAGACAA
Found at i:2425084 original size:58 final size:58
Alignment explanation
Indices: 2424964--2425073 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
2424954 AGAAACTATA
* * ** *
2424964 TCAAGAGAGATAAAACTTTATTTCAAGGGAAACTGTCTTAAGAGAGACAAAAACTTTC
1 TCAAGAGAGACAAAACTTTATTCCAAAAGAAACTGTCTAAAGAGAGACAAAAACTTTC
*
2425022 TCAAGAGAGACAAAAC-TTAGTTCCAAAAGAAACTGTCTAAAGGGAGACAAAA
1 TCAAGAGAGACAAAACTTTA-TTCCAAAAGAAACTGTCTAAAGAGAGACAAAA
2425074 TTTGTTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.07
58 42 0.93
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (58 bp):
TCAAGAGAGACAAAACTTTATTCCAAAAGAAACTGTCTAAAGAGAGACAAAAACTTTC
Found at i:2425154 original size:36 final size:36
Alignment explanation
Indices: 2425103--2425254 Score: 241
Period size: 36 Copynumber: 4.2 Consensus size: 36
2425093 ATTCAAAGAT
*
2425103 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
2425139 TTTGTTTCAACGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
2425175 TTTGTTTAAAGGGAAACTGTATCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
2425211 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2425247 TTTTGTTT
1 -TTTGTTT
2425255 TGAGTAAATT
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
36 98 0.93
37 7 0.07
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:2425222 original size:21 final size:21
Alignment explanation
Indices: 2425160--2425224 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2425150 GGAAACTATC
2425160 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
2425181 T-AA-AG-G--GAAA-CTGTA
1 TCAAGAGAGACAAAATTTGTT
2425196 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
2425217 TCAAGAGA
1 TCAAGAGA
2425225 AACTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 4 0.12
16 5 0.16
17 2 0.06
18 2 0.06
19 2 0.06
20 5 0.16
21 12 0.38
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:2426756 original size:95 final size:95
Alignment explanation
Indices: 2426566--2426829 Score: 345
Period size: 95 Copynumber: 2.7 Consensus size: 95
2426556 TGCTAGCTGG
* * *
2426566 ATCCATAAAGTCGGGGCATTTTAACCAATTGCTCCAGAGGGACAGCTCAA--TATTATTGTAGAG
1 ATCCATAAAGCCAGGGCA-TTTAACCAATTGCTCTAGAGGGACAGCTCAAGCT-TTATTGT----
*
2426629 ATATTATAATCACCTTTATCAGGCTAGCTGAATATT
60 ATATTATAATCACCTTTATCAGGCTAACTGAATATT
** *
2426665 ATCCATAAAGCCAGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTA
*
2426730 TAATCATCC-TTATCAGGCTAACTGAATCTT
66 TAATCA-CCTTTATCAGGCTAACTGAATATT
* *
2426760 ATCTATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAGTTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATAT-T
2426825 ATAAT
65 ATAAT
2426830 ATTAGAATAT
Statistics
Matches: 148, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
95 89 0.60
96 8 0.05
98 29 0.20
99 21 0.14
100 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAACTGAATATT
Found at i:2428771 original size:21 final size:22
Alignment explanation
Indices: 2428728--2428772 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2428718 TTCACATAGT
2428728 CTTATATTTTATTATTATATGA
1 CTTATATTTTATTATTATATGA
* *
2428750 CTTATATTTT-TTCTTCTATGA
1 CTTATATTTTATTATTATATGA
2428771 CT
1 CT
2428773 CTTCATAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.60
Consensus pattern (22 bp):
CTTATATTTTATTATTATATGA
Found at i:2429079 original size:25 final size:25
Alignment explanation
Indices: 2429051--2429104 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2429041 GATGCACTCA
2429051 CCTTGGCCTCACTAAGTTCCAATCC
1 CCTTGGCCTCACTAAGTTCCAATCC
2429076 CCTTGGCCTCACTAAGTTCCAATCC
1 CCTTGGCCTCACTAAGTTCCAATCC
2429101 CCTT
1 CCTT
2429105 TTATGATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.41, G:0.11, T:0.30
Consensus pattern (25 bp):
CCTTGGCCTCACTAAGTTCCAATCC
Found at i:2429411 original size:19 final size:19
Alignment explanation
Indices: 2429385--2429434 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2429375 TAAGGGGGTA
2429385 CATCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
*
2429404 CTTCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
2429423 CATCGATGCACT
1 CATCGATGCACT
2429435 AATTGCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (19 bp):
CATCGATGCACTCCTTATG
Found at i:2432791 original size:23 final size:23
Alignment explanation
Indices: 2432732--2432800 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2432722 CACCACAGCT
* *
2432732 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
2432755 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2432778 CGTAGAAATGCACCGAAGGGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2432801 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2433487 original size:134 final size:135
Alignment explanation
Indices: 2433329--2433598 Score: 524
Period size: 134 Copynumber: 2.0 Consensus size: 135
2433319 TAACGTATAT
2433329 CATATATGTATATAATAACTTATATCATATCATCTAGTTTATGCTCCATTTCTTTGTATTCCCTT
1 CATATATGTATATAATAACTTATATCATATCATCTAGTTTATGCTCCATTTCTTTGTATTCCCTT
2433394 AGATTACATAAATTATGTCGTGTTTTTAAAC-ATATCATTTAATAGTATTTTATTTATGTATTAA
66 AGATTACATAAATTATGTCGTGTTTTTAAACAATATCATTTAATAGTATTTTATTTATGTATTAA
2433458 TTTAA
131 TTTAA
2433463 CATATATGTATATAATAACTTATATCATATCATCTAGTTTATGCTCCATTTCTTTGTATTCCCTT
1 CATATATGTATATAATAACTTATATCATATCATCTAGTTTATGCTCCATTTCTTTGTATTCCCTT
2433528 AGATTACATAAATTATGTCGTGTTTTTAAACATATATCATTTAATAGTATTTTATTTATGTATTA
66 AGATTACATAAATTATGTCGTGTTTTTAAACA-ATATCATTTAATAGTATTTTATTTATGTATTA
2433593 ATTTAA
130 ATTTAA
2433599 TCTATTCATT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
134 96 0.72
136 38 0.28
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (135 bp):
CATATATGTATATAATAACTTATATCATATCATCTAGTTTATGCTCCATTTCTTTGTATTCCCTT
AGATTACATAAATTATGTCGTGTTTTTAAACAATATCATTTAATAGTATTTTATTTATGTATTAA
TTTAA
Found at i:2434525 original size:24 final size:20
Alignment explanation
Indices: 2434468--2434525 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2434458 TTCCCCTTGA
*
2434468 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
2434488 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
2434511 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2434526 CTACTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2438638 original size:14 final size:14
Alignment explanation
Indices: 2438616--2438649 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2438606 GGACCCTGAA
2438616 AAAAT-ATAAAAAG
1 AAAATAATAAAAAG
2438629 AAAATAATAAAAAG
1 AAAATAATAAAAAG
2438643 AAAATAA
1 AAAATAA
2438650 ATTAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAATAATAAAAAG
Found at i:2438822 original size:38 final size:37
Alignment explanation
Indices: 2438691--2439022 Score: 372
Period size: 38 Copynumber: 9.2 Consensus size: 37
2438681 AATATATATA
* *
2438691 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A-T
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
2438724 TTT-AAAAAAGTTTTCAAAACTATATATTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
2438759 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
*
2438790 TTTCAAAAAATGTTTTTAAAACTATATATTATATAATT
1 TTTC-AAAAATGTTTTTAAAACTATATATTATATAAGT
* **
2438828 TTTCCAAAAATGATTTTAAAACTATATATTATATATTT
1 TTT-CAAAAATGTTTTTAAAACTATATATTATATAAGT
*
2438866 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
2438903 TTTCAAAAATGTTTTAAAAAACTATATACTATATAAGT
1 TTTCAAAAATGTTTT-TAAAACTATATATTATATAAGT
2438941 TTTC-AAAATG-TTTTAAGAACTATATATTATATAAGT
1 TTTCAAAAATGTTTTTAA-AACTATATATTATATAAGT
* *
2438977 TTTC--AAATTTTTTTAAAAACTATATAATATATAAATGT
1 TTTCAAAAATGTTTTT-AAAACTATATATTATAT-AA-GT
2439015 TTTCAAAA
1 TTTCAAAA
2439023 CTATATATTA
Statistics
Matches: 260, Mismatches: 18, Indels: 35
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.03
31 8 0.03
32 19 0.07
33 13 0.05
34 11 0.04
35 18 0.07
36 43 0.17
37 58 0.22
38 78 0.30
39 1 0.00
40 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:2438823 original size:75 final size:74
Alignment explanation
Indices: 2438682--2438973 Score: 269
Period size: 75 Copynumber: 4.0 Consensus size: 74
2438672 AAATTATGTA
* * * * * *
2438682 ATATATATATTTCAAAAATATTTTTTAAACTATA-TAT-TATA-TTTT-AAAAAAGTTTTCAAAA
1 ATATATATTTTTCAAAAAT-GTTTTAAAAATATATTATATA-AGTTTTCAAAAATGTTTTTAAAA
2438743 CTATA---TAT
64 CTATATATTAT
*
2438751 -TATATAGTTTTC-AAAATGTTTT-AAAA-ATATTATATAAGTTTTCAAAAAATGTTTTTAAAAC
1 ATATATATTTTTCAAAAATGTTTTAAAAATATATTATATAAGTTTTC-AAAAATGTTTTTAAAAC
2438812 TATATATTAT
65 TATATATTAT
* **
2438822 ATA-AT-TTTTCCAAAAATGATTTTAAAACTATATATTATATATTTTTTCAAAAATGTTTTTAAA
1 ATATATATTTTTCAAAAATG-TTTTAAAA--ATATATTATATAAGTTTTCAAAAATGTTTTTAAA
2438885 ACTATATA-T-T
63 ACTATATATTAT
2438895 ATATA-ATTTTTCAAAAATGTTTTAAAAAACTATATACTATATAAGTTTTC-AAAATG-TTTTAA
1 ATATATATTTTTCAAAAATGTTTT-AAAAA-TATAT--TATATAAGTTTTCAAAAATGTTTTTAA
2438957 GAACTATATATTAT
62 -AACTATATATTAT
2438971 ATA
1 ATA
2438974 AGTTTTCAAA
Statistics
Matches: 186, Mismatches: 13, Indels: 41
0.77 0.05 0.17
Matches are distributed among these distances:
64 3 0.02
65 7 0.04
66 10 0.05
67 5 0.03
68 29 0.16
70 4 0.02
71 11 0.06
72 7 0.04
73 22 0.12
74 33 0.18
75 36 0.19
76 19 0.10
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (74 bp):
ATATATATTTTTCAAAAATGTTTTAAAAATATATTATATAAGTTTTCAAAAATGTTTTTAAAACT
ATATATTAT
Found at i:2439017 original size:29 final size:26
Alignment explanation
Indices: 2438986--2439042 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
2438976 TTTTCAAATT
2438986 TTTTTAAAAACTATATAATATATAAA
1 TTTTTAAAAACTATATAATATATAAA
* * *
2439012 TGTTTTCAAAACTATATATTATATATA
1 T-TTTTAAAAACTATATAATATATAAA
2439039 TTTT
1 TTTT
2439043 AAATATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTAAAAACTATATAATATATAAA
Found at i:2439017 original size:63 final size:64
Alignment explanation
Indices: 2438946--2439075 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 64
2438936 TAAGTTTTCA
*
2438946 AAATGTTTT-AAGAACTATATATTATATA-AGTTTTCAAAT-T-TTTTTAAAAA-CTATATAATA
1 AAATGTTTTCAA-AACTATATATTATATATA-TTTT-AAATATATTTTCAAAAATC-ATATAATA
2439006 TAT
62 TAT
2439009 AAATGTTTTCAAAACTATATATTATATATATTTTAAATATATTTTCAAAAATCATATAATATAT
1 AAATGTTTTCAAAACTATATATTATATATATTTTAAATATATTTTCAAAAATCATATAATATAT
2439073 AAA
1 AAA
2439076 CTTTTGAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
62 4 0.07
63 30 0.49
64 26 0.43
65 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (64 bp):
AAATGTTTTCAAAACTATATATTATATATATTTTAAATATATTTTCAAAAATCATATAATATAT
Found at i:2439039 original size:74 final size:71
Alignment explanation
Indices: 2438741--2439022 Score: 251
Period size: 75 Copynumber: 3.9 Consensus size: 71
2438731 AAGTTTTCAA
*
2438741 AACTATATATTATATAGTTTTCAAAATGTTTT--AAAA--ATAT--TATATAAGTTTTCAAAAAA
1 AACTATATATTATATAATTTTC-AAATGTTTTAAAAAACTATATAATATATAAGTTTTC--AAAA
*
2438800 TGTTTTTAA-
63 T-ATTTTAAG
* **
2438809 AACTATATATTATATAATTTTTCCAAAAATGATTTT--AAAACTATATATTATATATTTTTTCAA
1 AACTATATATTATATAA-TTTT-C--AAATG-TTTTAAAAAACTATATAATATATAAGTTTTC-A
*
2438872 AAATGTTTTTAA-
60 AAAT-ATTTTAAG
*
2438884 AACTATATATTATATAATTTTTCAAAAATGTTTTAAAAAACTATATACTATATAAGTTTTCAAAA
1 AACTATATATTATATAA-TTTTC--AAATGTTTTAAAAAACTATATAATATATAAGTTTTCAAAA
*
2438949 TGTTTTAAG
63 TATTTTAAG
* *
2438958 AACTATATATTATATAAGTTTTCAAATTTTTTTAAAAACTATATAATATATAAATGTTTTCAAAA
1 AACTATATATTATATAA-TTTTCAAATGTTTTAAAAAACTATATAATATAT-AA-GTTTTCAAAA
2439023 CTATATATTA
Statistics
Matches: 190, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
68 16 0.08
69 4 0.02
70 1 0.01
71 6 0.03
72 33 0.17
73 12 0.06
74 49 0.26
75 58 0.31
76 11 0.06
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (71 bp):
AACTATATATTATATAATTTTCAAATGTTTTAAAAAACTATATAATATATAAGTTTTCAAAATAT
TTTAAG
Found at i:2439106 original size:40 final size:37
Alignment explanation
Indices: 2439014--2439112 Score: 103
Period size: 37 Copynumber: 2.6 Consensus size: 37
2439004 TATATAAATG
* *
2439014 TTTTC-AAAACTATATATTATATATATTTTAAATATA
1 TTTTCAAAAATTATATATTATATAAATTTTAAATATA
* *
2439050 TTTTCAAAAATCATATAATATATAAACTTTTGAAA-ATCA
1 TTTTCAAAAATTATATATTATATAAA-TTTT-AAATAT-A
*
2439089 TTTTCTGAAAATTATATATTATAT
1 TTTTC-AAAAATTATATATTATAT
2439113 TTTGTCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
36 5 0.10
37 16 0.31
38 6 0.12
39 9 0.18
40 15 0.29
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
TTTTCAAAAATTATATATTATATAAATTTTAAATATA
Found at i:2439162 original size:2 final size:2
Alignment explanation
Indices: 2439145--2439236 Score: 143
Period size: 2 Copynumber: 47.0 Consensus size: 2
2439135 ACTATATTAC
* * *
2439145 TA TA TA CA TA TT TA TA TA TA TA TA TA TA TA -A AA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2439185 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
2439227 TA TA TA TA TA
1 TA TA TA TA TA
2439237 ATAAAATTAT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
1 2 0.02
2 81 0.98
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2441079 original size:64 final size:64
Alignment explanation
Indices: 2440977--2441106 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
2440967 CTCTCACAAT
* * *
2440977 TGTGGAAACCCTAGGTGCTTCATGAGTTGGATCATTCGATTGGGTTAGATCCAACGGCCCCAAG
1 TGTGGAAACCCTAGGTGCTTCATGAGTTGGACCATTCGATTGGGTCAGATCCAACAGCCCCAAG
* *
2441041 TGTGGAAACCCTAGGTGCTTCATGATTTGGACCGTTCGATTGGGTCAGATCCAACAGCCCCAAG
1 TGTGGAAACCCTAGGTGCTTCATGAGTTGGACCATTCGATTGGGTCAGATCCAACAGCCCCAAG
2441105 TG
1 TG
2441107 ATGCAATTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (64 bp):
TGTGGAAACCCTAGGTGCTTCATGAGTTGGACCATTCGATTGGGTCAGATCCAACAGCCCCAAG
Done.