Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007808.1 Hibiscus syriacus cultivar Beakdansim tig00110129_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: 1698870
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1608528 original size:7 final size:7
Alignment explanation
Indices: 1608476--1608537 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
1608466 TAAAAAAAAA
*
1608476 AAAACAG
1 AAAAGAG
*
1608483 AAAACAG
1 AAAAGAG
1608490 AAAAGA-
1 AAAAGAG
*
1608496 AAACAGAA
1 AAA-AGAG
*
1608504 AAAAGAA
1 AAAAGAG
1608511 AAAAGAAAG
1 AAAAG--AG
1608520 AAAAGAG
1 AAAAGAG
1608527 AAAAGAG
1 AAAAGAG
1608534 AAAA
1 AAAA
1608538 AAAGAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
6 3 0.06
7 37 0.76
8 3 0.06
9 6 0.12
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:1608570 original size:28 final size:26
Alignment explanation
Indices: 1608491--1608591 Score: 95
Period size: 25 Copynumber: 4.0 Consensus size: 26
1608481 AGAAAACAGA
* *
1608491 AAAGAAAACAGAAAAAAG-AAAAAAG
1 AAAGAAAAGAGAAAAGAGAAAAAAAG
1608516 AAAGAAAAGAGAAAAGAGAAAAAAAG
1 AAAGAAAAGAGAAAAGAGAAAAAAAG
**
1608542 AAAGAATTAAGAGAAAATGA-AAATGAAG
1 AAAGAA--AAGAGAAAA-GAGAAAAAAAG
*
1608570 -AAG-AAA-AGAAAATAGAAAAAAA
1 AAAGAAAAGAGAAAAGAGAAAAAAA
1608592 TAAAAATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
22 1 0.02
23 11 0.17
24 2 0.03
25 16 0.25
26 14 0.22
27 3 0.05
28 15 0.23
29 2 0.03
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (26 bp):
AAAGAAAAGAGAAAAGAGAAAAAAAG
Found at i:1608578 original size:25 final size:23
Alignment explanation
Indices: 1608481--1608590 Score: 80
Period size: 26 Copynumber: 4.3 Consensus size: 23
1608471 AAAAAAAAAC
* *
1608481 AGAAAACAGAAAAGAAAACAGAAAAA
1 AGAAAAAAG-AAAG-AAA-AGAGAAA
1608507 AGAAAAAAGAAAGAAAAGAGAAAA
1 AGAAAAAAGAAAGAAAAGAG-AAA
1608531 GAGAAAAAAAGAAAGAATTAAGAGAAA
1 -AG-AAAAAAGAAAGAA--AAGAGAAA
1608558 ATGAAAATGAAG-AAGAAAAGA-AAA
1 A-GAAAA--AAGAAAGAAAAGAGAAA
1608582 TAGAAAAAA
1 -AGAAAAAA
1608591 ATAAAAATAA
Statistics
Matches: 73, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
22 2 0.03
23 3 0.04
24 14 0.19
25 11 0.15
26 26 0.36
27 9 0.12
28 8 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (23 bp):
AGAAAAAAGAAAGAAAAGAGAAA
Found at i:1608586 original size:12 final size:11
Alignment explanation
Indices: 1608467--1608588 Score: 70
Period size: 12 Copynumber: 10.4 Consensus size: 11
1608457 CATAAGAGCT
*
1608467 AAAA-AAAAAA
1 AAAAGAAAAAG
1608477 AAACAGAAAACAG
1 AAA-AGAAAA-AG
1608490 AAAAGAAAACAG
1 AAAAGAAAA-AG
1608502 AAAAAAGAAAAA-
1 --AAAAGAAAAAG
1608514 AGAAAGAAAAGAG
1 A-AAAGAAAA-AG
*
1608527 AAAAGAGAAA-
1 AAAAGAAAAAG
*
1608537 AAAAGAAAGAATT
1 AAAAGAAA-AA-G
* *
1608550 AAGAGAAAATG
1 AAAAGAAAAAG
*
1608561 AAAATGAAGAAG
1 AAAA-GAAAAAG
1608573 AAAAGAAAATAG
1 AAAAGAAAA-AG
1608585 AAAA
1 AAAA
1608589 AAATAAAAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
10 11 0.12
11 19 0.21
12 37 0.42
13 13 0.15
14 9 0.10
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:1608598 original size:6 final size:6
Alignment explanation
Indices: 1608587--1608612 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1608577 GAAAATAGAA
1608587 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1608613 TAAAATGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1608602 original size:21 final size:21
Alignment explanation
Indices: 1608573--1608617 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1608563 AATGAAGAAG
1608573 AAAAG-AAAATAGAAAAAAATA
1 AAAAGAAAAATA-AAAAAAATA
* *
1608594 AAAATAAAAATAAAAATAATA
1 AAAAGAAAAATAAAAAAAATA
1608615 AAA
1 AAA
1608618 TGAGAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (21 bp):
AAAAGAAAAATAAAAAAAATA
Found at i:1612297 original size:40 final size:40
Alignment explanation
Indices: 1612242--1612335 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
1612232 TGCAGGTTTA
*
1612242 TAATACACTTCGGTGTATATGATGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
*
1612282 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
1612322 TAATACACTTCGGT
1 TAATACACTTCGGT
1612336 ACTATTCATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
Found at i:1613100 original size:36 final size:35
Alignment explanation
Indices: 1612989--1613100 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
1612979 ATAGAAGACG
*
1612989 AAATTTGTTTTAAGAAAAAAATCTTAAGTAAGATAA
1 AAATTTGTTTTAAGAAAAAAATCTCAAGTAAGAT-A
** * * *
1613025 AAATCCGTTTTGAGAAAAACAATCTCAAGTGAGACA
1 AAATTTGTTTTAAGAAAAA-AATCTCAAGTAAGATA
*
1613061 AAATTTGTTTTAACAAAAATAATCTCAAGTAAGATA
1 AAATTTGTTTTAAGAAAAA-AATCTCAAGTAAGATA
1613097 AAAT
1 AAAT
1613101 CTTGAGTGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
36 50 0.81
37 12 0.19
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (35 bp):
AAATTTGTTTTAAGAAAAAAATCTCAAGTAAGATA
Found at i:1613232 original size:17 final size:17
Alignment explanation
Indices: 1613190--1613225 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1613180 TGATAGAATC
* *
1613190 GAGCGAAATTTACTATT
1 GAGCAAAATGTACTATT
1613207 GAGCAAAATGTACTATT
1 GAGCAAAATGTACTATT
1613224 GA
1 GA
1613226 TCCAAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (17 bp):
GAGCAAAATGTACTATT
Found at i:1613273 original size:44 final size:43
Alignment explanation
Indices: 1613222--1613378 Score: 163
Period size: 44 Copynumber: 3.6 Consensus size: 43
1613212 AAATGTACTA
* * *
1613222 TTGATCCAAATCTTTATGTGATGGAATCAAGCAAAATAGTGATG
1 TTGATCCAACTCCTTATGTGATGGAATCAAGC-AAATGGTGATG
* ** ** *
1613266 TTGATCCAACTACTTATACGATAAAATCAGGCGAAATGGTGATG
1 TTGATCCAACTCCTTATGTGATGGAATCAAGC-AAATGGTGATG
* *
1613310 TTGATCTAACTCCTTATGTGATGGAATCGAATG-AAATGGTGATA
1 TTGATCCAACTCCTTATGTGATGGAATC-AA-GCAAATGGTGATG
*
1613354 ATGATCCAACTCCTTATGTGATGGA
1 TTGATCCAACTCCTTATGTGATGGA
1613379 CGAGAAAAGG
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
44 89 0.98
45 1 0.01
46 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (43 bp):
TTGATCCAACTCCTTATGTGATGGAATCAAGCAAATGGTGATG
Found at i:1613907 original size:155 final size:157
Alignment explanation
Indices: 1613319--1613943 Score: 690
Period size: 159 Copynumber: 4.0 Consensus size: 157
1613309 GTTGATCTAA
* * *
1613319 CTCCTTATGTGATGGAATCGAA-TGAAATGGTGATAATGATCCAACTCCTTATGTGATGGACGAG
1 CTCCTTATGTGATGGAATC-AAGCGAAATGGTGGTGATGATCC-ACTCCTTATGTGATGGACGA-
* * *
1613383 A-AAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCAT-GGACGAGTTCTTCTTAT
63 ACAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCAT
* * *
1613446 TATGAACTCTCAACTGAACATATTGATTCAC
128 TATGAACTCTCCATTGAA-ATGTTGATTCAC
* * * * * * * *
1613477 CTCTTTGTGTGAGGGAATCAAGAGAAATAGTGGTGCTAATCCAACTCCTTATGTGATGGGCGAAC
1 CTCCTTATGTGATGGAATCAAGCGAAATGGTGGTGATGATCC-ACTCCTTATGTGATGGACGAAC
* * * * *
1613542 AAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATCTGATGAGTTCTTCTCATTA
65 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTA
* * *
1613607 TGAATTCTCCACTAGAAATGTCGATTCAC
130 TGAACTCTCCA-TTGAAATGTTGATTCAC
* * * *
1613636 CTCCTTTTGTGGTGGAATCAAGCGAAACGGTGGTGTTGATCCAACTCCTTATGTGATGGAC-AAG
1 CTCCTTATGTGATGGAATCAAGCGAAATGGTGGTGATGATCC-ACTCCTTATGTGATGGACGAA-
* *
1613700 CAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGACGAGTTATTCTCATT
64 CAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATT
*
1613765 ATGAACTCTCCATTGAAAGTGTTGATCCAC
129 ATGAACTCTCCATTGAAA-TGTTGATTCAC
** * * * *
1613795 CTCCTTATACGATGAAATCAAGCGAAATGGT-GAGATGAT-C-CTTCTTATATGATGGACGAACA
1 CTCCTTATGTGATGGAATCAAGCGAAATGGTGGTGATGATCCACTCCTTATGTGATGGACGAACA
** * ** *
1613857 AATATTAAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTTTCGGACGAGTTTTTCTCATTAT
66 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTAT
1613922 GAAC-CATTCCATTGGAAATGTT
131 GAACTC--TCCATT-GAAATGTT
1613944 TGGTCTACCT
Statistics
Matches: 398, Mismatches: 59, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
154 1 0.00
155 79 0.20
156 12 0.03
157 8 0.02
158 105 0.26
159 190 0.48
160 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (157 bp):
CTCCTTATGTGATGGAATCAAGCGAAATGGTGGTGATGATCCACTCCTTATGTGATGGACGAACA
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTAT
GAACTCTCCATTGAAATGTTGATTCAC
Found at i:1619163 original size:51 final size:51
Alignment explanation
Indices: 1619087--1619189 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1619077 GGGATTTGCA
1619087 TATCATCCGATGAGAATTCTATCCTATCTATTTATTCTCTATACAGGAGTG
1 TATCATCCGATGAGAATTCTATCCTATCTATTTATTCTCTATACAGGAGTG
*
1619138 TATCATCTGATGAGAATTCTATCCTATCTATTTATTCTCTATACAGGAGTG
1 TATCATCCGATGAGAATTCTATCCTATCTATTTATTCTCTATACAGGAGTG
1619189 T
1 T
1619190 TCCCTTCTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (51 bp):
TATCATCCGATGAGAATTCTATCCTATCTATTTATTCTCTATACAGGAGTG
Found at i:1625609 original size:18 final size:18
Alignment explanation
Indices: 1625543--1625601 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1625533 AATGACCCTG
*
1625543 AGATCGTTGATGATACTC
1 AGATCGTTGATGATCCTC
1625561 AGATCGTTGATGATCCTC
1 AGATCGTTGATGATCCTC
*
1625579 ATATCGTTGATGATCCTC
1 AGATCGTTGATGATCCTC
1625597 AGATC
1 AGATC
1625602 ATTAATGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (18 bp):
AGATCGTTGATGATCCTC
Found at i:1627697 original size:13 final size:14
Alignment explanation
Indices: 1627668--1627702 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
1627658 CTTTCACATG
1627668 TTGACTTTGACCCA
1 TTGACTTTGACCCA
1627682 TTGACTTTGA-CCA
1 TTGACTTTGACCCA
1627695 TTGACTTT
1 TTGACTTT
1627703 AAATTTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (14 bp):
TTGACTTTGACCCA
Found at i:1627957 original size:29 final size:29
Alignment explanation
Indices: 1627915--1627980 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
1627905 CGTTGAATTC
*
1627915 AAGTTTGAGAGTGATCGAATGGATTTTAA
1 AAGTTCGAGAGTGATCGAATGGATTTTAA
1627944 AAGTTCGAGAGTGATCGAATGGATTTTAA
1 AAGTTCGAGAGTGATCGAATGGATTTTAA
*
1627973 ATGTTCGA
1 AAGTTCGA
1627981 CCGGTGGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (29 bp):
AAGTTCGAGAGTGATCGAATGGATTTTAA
Found at i:1631280 original size:41 final size:40
Alignment explanation
Indices: 1631235--1631368 Score: 126
Period size: 41 Copynumber: 3.3 Consensus size: 40
1631225 GATTCTGACT
* * *
1631235 ATCGCATTGCGATTTTCCAAATTCGCAATGCGAATACGTAA
1 ATCGCAATGCGA-TTTACAAAATCGCAATGCGAATACGTAA
** ** * *
1631276 ATCGCAACACGAATTTGGAAAATCGCAATGCGATTACATAA
1 ATCGCAATGCG-ATTTACAAAATCGCAATGCGAATACGTAA
* *
1631317 ATCGCAATGCGA-ATACATAAATCGCAACGCGAATACGTAA
1 ATCGCAATGCGATTTACA-AAATCGCAATGCGAATACGTAA
*
1631357 ATCGCAACGCGA
1 ATCGCAATGCGA
1631369 ATCTGACTAT
Statistics
Matches: 74, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 40 0.54
42 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (40 bp):
ATCGCAATGCGATTTACAAAATCGCAATGCGAATACGTAA
Found at i:1631282 original size:20 final size:20
Alignment explanation
Indices: 1631257--1631370 Score: 129
Period size: 20 Copynumber: 5.7 Consensus size: 20
1631247 TTTTCCAAAT
*
1631257 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* ** *
1631277 TCGCAACACGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
* * *
1631298 TCGCAATGCGATTACATAAA
1 TCGCAACGCGAATACGTAAA
* *
1631318 TCGCAATGCGAATACATAAA
1 TCGCAACGCGAATACGTAAA
1631338 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
1631358 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1631371 CTGACTATCG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:1631380 original size:20 final size:20
Alignment explanation
Indices: 1631357--1631423 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1631347 GAATACGTAA
* *
1631357 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
1631377 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1631397 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1631417 ATCGCAA
1 ATCGCAA
1631424 TACTGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:1631381 original size:40 final size:39
Alignment explanation
Indices: 1631257--1631385 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 39
1631247 TTTTCCAAAT
* * *
1631257 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAATCT-G-AAA
* * * *
1631298 TCGCAATGCGATTACATAAATCGCAATGCGAATACAT-AAA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAAT-C-TGAAA
*
1631338 TCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACTA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAATCTGA-AA
1631378 TCGCAACG
1 TCGCAACG
1631386 AGATTCTGAC
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 41 0.55
41 29 0.39
43 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (39 bp):
TCGCAACGCGAATACGTAAATCGCAACGCGAATCTGAAA
Found at i:1634776 original size:20 final size:21
Alignment explanation
Indices: 1634751--1634858 Score: 93
Period size: 20 Copynumber: 5.4 Consensus size: 21
1634741 CAACGCGGAA
*
1634751 ATCGCAACGC-GAATATGGCT
1 ATCGCAACGCAGAATATGACT
*
1634771 ATCGCAACACAGAA-ATGACT
1 ATCGCAACGCAGAATATGACT
*
1634791 ATCGCAACGCGGAAT-TGACT
1 ATCGCAACGCAGAATATGACT
* *
1634811 ATCACAACGC-GAAAATGACT
1 ATCGCAACGCAGAATATGACT
* * **
1634831 ATCTCAATGCA-AA-ATGAAA
1 ATCGCAACGCAGAATATGACT
1634850 ATCGCAACG
1 ATCGCAACG
1634859 AGTGAATCGC
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.19
20 55 0.76
21 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCAGAATATGACT
Found at i:1634813 original size:40 final size:40
Alignment explanation
Indices: 1634751--1634833 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
1634741 CAACGCGGAA
* *
1634751 ATCGCAACGCGAATATGGCTATCGCAACAC-AGAAATGACT
1 ATCGCAACGCGAATATGACTATCACAACACGA-AAATGACT
*
1634791 ATCGCAACGCGGAAT-TGACTATCACAACGCGAAAATGACT
1 ATCGCAACGC-GAATATGACTATCACAACACGAAAATGACT
1634831 ATC
1 ATC
1634834 TCAATGCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 33 0.87
41 5 0.13
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCACAACACGAAAATGACT
Found at i:1634971 original size:33 final size:34
Alignment explanation
Indices: 1634907--1634972 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
1634897 TTTAGTTTCA
1634907 CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
* * *
1634941 CGTTGCGATTTTTA-TTTCGCGTTGCGATTCTC
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCTC
1634973 ATTTTGCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
Found at i:1634976 original size:19 final size:19
Alignment explanation
Indices: 1634941--1634991 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
1634931 GCAATTCTCT
* *
1634941 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTCTCATTTCG
*
1634960 CGTTGCGATTCTCATTTTG
1 CGTTGCGATTCTCATTTCG
* *
1634979 CATTGCAATTCTC
1 CGTTGCGATTCTC
1634992 TCGTTGAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTCTCATTTCG
Found at i:1634994 original size:52 final size:54
Alignment explanation
Indices: 1634897--1634997 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 54
1634887 ACAACGCGAA
*
1634897 TTTAGTTTCACGTTGCGATTTTCATTTTCGCATTGCAATTCTCTCGTTGCGATT
1 TTTAGTTTCACGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTGCGATT
*
1634951 TTTA-TTTCGCGTTGCGATTCTCATTTT-GCATTGCAATTCTCTCGTTG
1 TTTAGTTTCACGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTG
1634998 AGATAGTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 20 0.44
53 21 0.47
54 4 0.09
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.49
Consensus pattern (54 bp):
TTTAGTTTCACGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTGCGATT
Found at i:1635010 original size:52 final size:53
Alignment explanation
Indices: 1634902--1635017 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 53
1634892 GCGAATTTAG
* * * ** *
1634902 TTTCACGTTGCGATTTTCATTTTCGCATTGCAATTCTCTCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTGAGATAGTCA
1634955 TTTCGCGTTGCGATTCTCATTTT-GCATTGCAATTCTCTCGTTGAGATAGTCA
1 TTTCGCGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTGAGATAGTCA
1635007 TTTCCGCGTTG
1 TTT-CGCGTTG
1635018 TGATAGTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 28 0.50
53 28 0.50
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTTCGCGTTGCGATTCTCATTTTCGCATTGCAATTCTCTCGTTGAGATAGTCA
Found at i:1635146 original size:14 final size:14
Alignment explanation
Indices: 1635127--1635163 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1635117 CATCAATTAA
1635127 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1635141 ACAAATCATCTTTT
1 ACAAATCAACATTT
1635155 ACAAATCAA
1 ACAAATCAA
1635164 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1636591 original size:21 final size:21
Alignment explanation
Indices: 1636542--1636644 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
1636532 TCTAGAATGT
* *
1636542 TGGGAGTGACCTCTTCAACGA
1 TGGGAGTGGCCTCTTGAACGA
** *
1636563 TGACAGTGGCCTCTTGAACGG
1 TGGGAGTGGCCTCTTGAACGA
* **
1636584 TGGGAGTGGACTCTTGAGGGA
1 TGGGAGTGGCCTCTTGAACGA
** *
1636605 TGATAGGGGCCTCTTGAACGA
1 TGGGAGTGGCCTCTTGAACGA
*
1636626 TAGGG-GAGGCCTCTTGAAC
1 T-GGGAGTGGCCTCTTGAAC
1636645 AATGATAGGT
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
21 60 0.98
22 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
TGGGAGTGGCCTCTTGAACGA
Found at i:1636650 original size:42 final size:42
Alignment explanation
Indices: 1636542--1636653 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
1636532 TCTAGAATGT
* * * * * *
1636542 TGGGAGTGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
* * **
1636584 TGGGAGTGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
1636626 TAGGG-GAGGCCTCTTGAACAATGATAGG
1 T-GGGAGAGGCCTCTTGAACGATGATAGG
1636654 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:1637155 original size:20 final size:20
Alignment explanation
Indices: 1637132--1637180 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1637122 GAAACTTAAA
1637132 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1637152 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1637172 ATCGCAACG
1 ATCGCAACG
1637181 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1637244 original size:34 final size:34
Alignment explanation
Indices: 1637203--1637358 Score: 136
Period size: 34 Copynumber: 4.4 Consensus size: 34
1637193 TGCGATTTTC
1637203 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1637237 AATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCA
* ** * * **
1637277 TTTTCGTGTTGCAATT-TTGTTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
* *
1637310 ATTTCGCATTACGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1637344 TTTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
1637359 AGTAAACTAT
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
33 22 0.24
34 37 0.40
35 2 0.02
36 4 0.04
38 6 0.06
40 22 0.24
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:1637288 original size:20 final size:20
Alignment explanation
Indices: 1637225--1637282 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1637215 GATTCTTTCG
**
1637225 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1637245 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1637265 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCG
1637283 TGTTGCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1637356 original size:53 final size:53
Alignment explanation
Indices: 1637187--1637358 Score: 147
Period size: 53 Copynumber: 3.2 Consensus size: 53
1637177 AACGAGAGAA
* * **
1637187 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
** ** *
1637240 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCAT--TTTCG-T-GTTGCAATTT
1 TCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTC-TCGTTGCGATAG-T-C-ATTT
** *
1637294 T-GTTGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTT
1 TCG-CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1637347 TCGCATTGCGAT
1 TCGCATTGCGAT
1637359 AGTAAACTAT
Statistics
Matches: 89, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
51 1 0.01
52 3 0.03
53 47 0.53
54 34 0.38
55 3 0.03
56 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
Found at i:1639290 original size:20 final size:20
Alignment explanation
Indices: 1639242--1639291 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1639232 GAAACTTTAA
*
1639242 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1639262 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1639282 ATCGCAACGC
1 ATCGCAACGC
1639292 AAGAATCGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1639713 original size:22 final size:22
Alignment explanation
Indices: 1639671--1639717 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1639661 CGGAGATGAA
1639671 GACTGATATCCTCGAAGATGGG
1 GACTGATATCCTCGAAGATGGG
* *
1639693 GACTGATTTCGTCGGAA-ATGGG
1 GACTGATATCCTC-GAAGATGGG
1639715 GAC
1 GAC
1639718 GGTTGTCGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (22 bp):
GACTGATATCCTCGAAGATGGG
Found at i:1639944 original size:20 final size:20
Alignment explanation
Indices: 1639921--1640087 Score: 226
Period size: 20 Copynumber: 8.3 Consensus size: 20
1639911 CAGATTTGCG
*
1639921 TTGCGATTAACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1639941 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
1639961 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
* *
1639981 TTACGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
1640001 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
1640021 TTGCGATTTACGTAATCTCA
1 TTGCGATTTACGTATTCGCA
* ** * *
1640041 TTGCGATTTTCCAAATTCACG
1 TTGCGA-TTTACGTATTCGCA
1640062 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1640082 TTGCGA
1 TTGCGA
1640088 ATTAGGAAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
20 112 0.89
21 14 0.11
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1640108 original size:21 final size:21
Alignment explanation
Indices: 1640084--1640129 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1640074 TATTCGCATT
1640084 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1640105 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1640126 GCGA
1 GCGA
1640130 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1640150 original size:41 final size:40
Alignment explanation
Indices: 1640105--1640192 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
1640095 AAATCGCAAC
*
1640105 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* * *
1640146 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
1640186 GCGAATT
1 GCGAATT
1640193 ATCGATCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 5 0.12
40 22 0.55
41 13 0.32
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:1640715 original size:26 final size:27
Alignment explanation
Indices: 1640681--1640742 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1640671 AATGTTACCC
* *
1640681 TTTTAAAAATAATTAC-AACTATCACA
1 TTTTTAAAATAATTACGAAATATCACA
*
1640707 TTTTTAAAATAATTACGAAATATCACT
1 TTTTTAAAATAATTACGAAATATCACA
1640734 TTTTTAAAA
1 TTTTTAAAA
1640743 ATATAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (27 bp):
TTTTTAAAATAATTACGAAATATCACA
Found at i:1640730 original size:27 final size:26
Alignment explanation
Indices: 1640681--1640830 Score: 98
Period size: 29 Copynumber: 5.7 Consensus size: 26
1640671 AATGTTACCC
* *
1640681 TTTTAAAAATAATTACAACTATCACA
1 TTTTTAAAATAATTACAAATATCACA
1640707 TTTTTAAAATAATTACGAAATATCAC-
1 TTTTTAAAATAATTAC-AAATATCACA
* *
1640733 TTTTTTAAA-AA-TATAAAT-T-ATCA
1 TTTTTAAAATAATTACAAATATCA-CA
*
1640756 -TTTTAAAA-AATTACAAAAATAGCACCA
1 TTTTTAAAATAATTAC--AAATATCA-CA
* *
1640783 TTTTCAAAATAATTACCAAAATACCACCA
1 TTTTTAAAATAATTA-C-AAATATCA-CA
* *
1640812 ATTTCAAAATAATTACAAA
1 TTTTTAAAATAATTACAAA
1640831 AATACCTCCT
Statistics
Matches: 102, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.01
22 11 0.11
23 6 0.06
24 2 0.02
25 6 0.06
26 23 0.23
27 14 0.14
28 8 0.08
29 30 0.29
30 1 0.01
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (26 bp):
TTTTTAAAATAATTACAAATATCACA
Found at i:1640803 original size:29 final size:29
Alignment explanation
Indices: 1640754--1640836 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
1640744 TATAAATTAT
*
1640754 CATTTT-AAAA-AATTACAAAAATAGCAC
1 CATTTTCAAAATAATTACAAAAATACCAC
*
1640781 CATTTTCAAAATAATTACCAAAATACCAC
1 CATTTTCAAAATAATTACAAAAATACCAC
*
1640810 CAATTTCAAAATAATTACAAAAATACC
1 CATTTTCAAAATAATTACAAAAATACC
1640837 TCCTGGTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.12
28 4 0.08
29 40 0.80
ACGTcount: A:0.53, C:0.19, G:0.01, T:0.27
Consensus pattern (29 bp):
CATTTTCAAAATAATTACAAAAATACCAC
Found at i:1648749 original size:23 final size:23
Alignment explanation
Indices: 1648678--1648751 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
1648668 CCATAGAACC
* **
1648678 ACATA-GTTTGTCCCGAAATACA
1 ACATAGGTTTGTCTCGAAGGACA
* *
1648700 ACATAGGTTTGTCTCCAAGGATA
1 ACATAGGTTTGTCTCGAAGGACA
*
1648723 ACATAGGTTTGTCTCGAAGGACC
1 ACATAGGTTTGTCTCGAAGGACA
1648746 ACATAG
1 ACATAG
1648752 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 5 0.12
23 38 0.88
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
ACATAGGTTTGTCTCGAAGGACA
Found at i:1656958 original size:3 final size:3
Alignment explanation
Indices: 1656950--1657039 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
1656940 ATATGCTTTG
1656950 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1656998 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1657040 GCCTCACTAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1661813 original size:9 final size:10
Alignment explanation
Indices: 1661797--1661833 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
1661787 TGATATGTTT
1661797 TGTATTATTA
1 TGTATTATTA
1661807 T-TATTATTA
1 TGTATTATTA
*
1661816 TGT-TTATTT
1 TGTATTATTA
1661825 TGTATTATT
1 TGTATTATT
1661834 GATTATGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TGTATTATTA
Found at i:1663070 original size:2 final size:2
Alignment explanation
Indices: 1663065--1663092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1663055 ACACACATAC
1663065 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
1663093 TGATAGATAC
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:1666556 original size:36 final size:36
Alignment explanation
Indices: 1666506--1666579 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1666496 TCGATGGAAT
*
1666506 ATTTATGAGAGAATTAAAATTTGTGAAAAAATTAGA
1 ATTTATGAGAGAATTAAAATCTGTGAAAAAATTAGA
* *
1666542 ATTTATGA-AGGAATTAGAATCTGTGAAAGAATTAGA
1 ATTTATGAGA-GAATTAAAATCTGTGAAAAAATTAGA
1666578 AT
1 AT
1666580 CTGTAGGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.47, C:0.01, G:0.19, T:0.32
Consensus pattern (36 bp):
ATTTATGAGAGAATTAAAATCTGTGAAAAAATTAGA
Found at i:1666580 original size:18 final size:18
Alignment explanation
Indices: 1666515--1666597 Score: 89
Period size: 18 Copynumber: 4.7 Consensus size: 18
1666505 TATTTATGAG
* *
1666515 AGAATTAAAATTTGTGAA
1 AGAATTAGAATCTGTGAA
* * *
1666533 AAAATTAGAATTTATGAA
1 AGAATTAGAATCTGTGAA
*
1666551 GGAATTAGAATCTGTGAA
1 AGAATTAGAATCTGTGAA
1666569 AGAATTAGAATCTGT--A
1 AGAATTAGAATCTGTGAA
*
1666585 GGAATTAGAATCT
1 AGAATTAGAATCT
1666598 AATTCCATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
16 13 0.23
18 43 0.77
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (18 bp):
AGAATTAGAATCTGTGAA
Found at i:1666593 original size:34 final size:35
Alignment explanation
Indices: 1666508--1666597 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 35
1666498 GATGGAATAT
* *
1666508 TTATG-AGAGAATTAAAATTTGTGAAAAAATTAGAA
1 TTATGAAG-GAATTAGAATCTGTGAAAAAATTAGAA
*
1666543 TTTATGAAGGAATTAGAATCTGTGAAAGAATTAGAA
1 -TTATGAAGGAATTAGAATCTGTGAAAAAATTAGAA
* *
1666579 -TCTGTAGGAATTAGAATCT
1 TTATGAAGGAATTAGAATCT
1666598 AATTCCATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 17 0.35
36 29 0.60
37 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32
Consensus pattern (35 bp):
TTATGAAGGAATTAGAATCTGTGAAAAAATTAGAA
Found at i:1667208 original size:27 final size:26
Alignment explanation
Indices: 1667177--1667239 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 26
1667167 AAACCCGAAC
1667177 CCGACCCGAATATCACACTTAAAAAA
1 CCGACCCGAATATCACACTTAAAAAA
1667203 CTCGACCCGAATATCACACTTAAAAAA
1 C-CGACCCGAATATCACACTTAAAAAA
1667230 CCTGACCCGA
1 CC-GACCCGA
1667240 CCCGAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.16
Consensus pattern (26 bp):
CCGACCCGAATATCACACTTAAAAAA
Found at i:1667211 original size:32 final size:30
Alignment explanation
Indices: 1667175--1667245 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 30
1667165 CTAAACCCGA
1667175 ACCCGACCCGAATATCACACTTAAAAAACT
1 ACCCGACCCGAATATCACACTTAAAAAACT
1667205 ---CGACCCGAATATCACACTTAAAAAACCT
1 ACCCGACCCGAATATCACACTTAAAAAA-CT
1667233 GACCCGACCCGAA
1 -ACCCGACCCGAA
1667246 CAAAATAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
27 25 0.69
28 2 0.06
32 9 0.25
ACGTcount: A:0.41, C:0.35, G:0.10, T:0.14
Consensus pattern (30 bp):
ACCCGACCCGAATATCACACTTAAAAAACT
Found at i:1667639 original size:221 final size:217
Alignment explanation
Indices: 1667202--1667672 Score: 688
Period size: 221 Copynumber: 2.2 Consensus size: 217
1667192 CACTTAAAAA
* *
1667202 ACTCGACCCGAATATCACACTTAAAAAACCTGACCCGACCCGAACAAAATAAAGTTTCATCCGAC
1 ACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAGTTTCATCCGAC
* * *
1667267 CGACCCGAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAAGTATTTTTATTTAA
66 CGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAAATATTCTTATTTAA
*
1667332 TAAAAACATTAACTTAATTCGACCCGACCCGAATTATATATATATTCGGGTCGGTCTAATTTTTT
131 TAAAAACAGTAACTTAATT---CCCGACCCGAATTATATATATATTCGGGTCGGTCTAATTTTTT
*
1667397 TCACCCTAAACCCGAACCCGACCCG
193 TCACCCTAAACCCAAACCCGACCCG
*
1667422 ACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACTCGAACAAAATAAAGTTTCATCCGAC
1 ACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAGTTTCATCCGA-
*
1667487 CCGACCCAAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAAATATTCTTATTTA
65 CCGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAAATATTCTTATTTA
* * * *
1667552 ATAAAAATAGTGACTTAA-T-CCGACCCGAATTATATATATTTTCGGGTCGGT-TCAGTTTTTTT
130 ATAAAAACAGTAACTTAATTCCCGACCCGAATTATATATATATTCGGGTCGGTCT-AATTTTTTT
* *
1667614 CACTCTAAACCCAAACTCGA--C-
194 CACCCTAAACCCAAACCCGACCCG
*
1667635 -C-CGACCCGAATATCACACTTAAAAAAACCTGACCCAAC
1 ACTCGACCCGAATATCACACTT-AAAAAACCCGACCCAAC
1667673 TCGACCCGAA
Statistics
Matches: 232, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
211 19 0.08
212 17 0.07
214 1 0.00
215 1 0.00
216 56 0.24
220 62 0.27
221 76 0.33
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (217 bp):
ACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAGTTTCATCCGAC
CGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAAATATTCTTATTTAA
TAAAAACAGTAACTTAATTCCCGACCCGAATTATATATATATTCGGGTCGGTCTAATTTTTTTCA
CCCTAAACCCAAACCCGACCCG
Found at i:1667697 original size:249 final size:254
Alignment explanation
Indices: 1667411--1667902 Score: 780
Period size: 249 Copynumber: 1.9 Consensus size: 254
1667401 CCTAAACCCG
* *
1667411 AACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACTCGAACAAAATAAAG
1 AACCCGACCCAACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAG
1667476 TTTCATCCGACCCGACCCAAATATATGAATTAGAAAT-CCGACCCGACCCGAAATAATAAAAAAA
66 TTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAA
* *
1667540 TATTCTTATTTAATAAAAATAGTGACTTAATCCG-A-C-CC-GAATTATATATATTTTCGGGTCG
131 TATTCTTATTTAATAAAAACAGTGACTTAATCCGAACCACCTAAATTATATATATTTTCGGGTCG
*
1667601 GTTCAG-TTTTTTTCACTCTAAACCCAAACTCGACCCGACCCGAATATCACACTTAAAAA
196 G-TCAGATTTTTTTCACCCTAAACCCAAACTCGACCCGACCCGAATATCACACTTAAAAA
*
1667660 AACCTGACCCAACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAG
1 AACCCGACCCAACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAG
*
1667725 TTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAA
66 TTTCATCCGACCCGACCCAAATATATGAATTAGAAAT----CCCGACCCGACCCGAAATAATAAA
* * * *
1667790 AAATTATTTTTATTTAATAAAACCAGTGACTTAATCCGAACCGACCTAAATTCTATATATTTTCG
127 AAAATATTCTTATTTAATAAAAACAGTGACTTAATCCGAACC-ACCTAAATTATATATATTTTCG
*
1667855 GGTCGGTCCGATTTTTTTCACCCTAAACCCAAACTCGACCCGACCCGA
191 GGTCGGTCAGATTTTTTTCACCCTAAACCCAAACTCGACCCGACCCGA
1667903 CCCTACCCGA
Statistics
Matches: 220, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
249 98 0.45
254 57 0.26
255 1 0.00
256 1 0.00
258 5 0.02
259 58 0.26
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (254 bp):
AACCCGACCCAACTCGACCCGAATATCACACTTAAAAAACCCGACCCAACCCGAACAAAATAAAG
TTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAA
TATTCTTATTTAATAAAAACAGTGACTTAATCCGAACCACCTAAATTATATATATTTTCGGGTCG
GTCAGATTTTTTTCACCCTAAACCCAAACTCGACCCGACCCGAATATCACACTTAAAAA
Found at i:1667706 original size:37 final size:38
Alignment explanation
Indices: 1667636--1667709 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
1667626 AAACTCGACC
*
1667636 CGACCCGAATATCACACTTAAAAAAACCTGACCCAACT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCAACT
1667674 CGACCCGAATATCACACTT-AAAAAACCCGACCCAAC
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCAAC
1667710 CCGAACAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.42, C:0.36, G:0.08, T:0.14
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCAACT
Found at i:1669121 original size:161 final size:163
Alignment explanation
Indices: 1668820--1669322 Score: 480
Period size: 181 Copynumber: 3.0 Consensus size: 163
1668810 TGATAAAACC
* * * * *
1668820 GGTAAAGCGCTACCTAATATGTTTAAAGTATTGATTCTATTGAAATAAGTATCGACACTTTTGGA
1 GGTAAAGCGCTACCGAATATGTTGAAAGTATCGATACTATTGAAATAAGTATCAACACTTTTGGA
1668885 ATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTACAAAAATATATCGATCCA
66 ATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTACAAAAATATATCGATCCA
*
1668950 TTACAATATAACAGGTAAAAATATGACAAAATT
131 TAACAATATAACAGGTAAAAATATGACAAAATT
* * *
1668983 GGTAAAGCGCTATCGGATATGTTGAAAGTGTCGATACT-TT-AATATAAGTATCAACACTTTTGG
1 GGTAAAGCGCTACCGAATATGTTGAAAGTATCGATACTATTGAA-ATAAGTATCAACACTTTTGG
* * * * * *
1669046 AATTTAAAAGATAAGCAGTAATA-CGCCTATAAAGTGTCGATACTTTATAAAAATGTTTTGATCC
65 AATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTACAAAAATATATCGATCC
*
1669110 ATAATAATATAACAGGTAAAAATATGACAAAACCGGTCT
130 ATAACAATATAACAGGTAAAAATATGACAAAA----T-T
* * * **
1669149 CGAAATGAAAAAACCGGTAAATCACTACC-ATATATGTT-AAAGTGTTAATACT-TT-AATATAA
1 -G----G--TAAA---G-----CGCTACCGA-ATATGTTGAAAGTATCGATACTATTGAA-ATAA
* * * * *
1669210 GTATCGACACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAATGTCGATACTTTAT
49 GTATCAACACTTTTGGAATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTAC
* * * *
1669275 AAAAATGTATCAATCCATAACAATATAACAAGTAAAAATATGATAAAA
114 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA
1669323 CCGGTCTCGA
Statistics
Matches: 285, Mismatches: 32, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
161 69 0.24
162 42 0.15
163 31 0.11
165 1 0.00
166 1 0.00
167 1 0.00
171 1 0.00
173 3 0.01
176 1 0.00
180 57 0.20
181 78 0.27
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (163 bp):
GGTAAAGCGCTACCGAATATGTTGAAAGTATCGATACTATTGAAATAAGTATCAACACTTTTGGA
ATTTAAAAGAGAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTACAAAAATATATCGATCCA
TAACAATATAACAGGTAAAAATATGACAAAATT
Found at i:1669366 original size:180 final size:181
Alignment explanation
Indices: 1668983--1669570 Score: 894
Period size: 181 Copynumber: 3.2 Consensus size: 181
1668973 TGACAAAATT
* * *
1668983 GGTAAAGCGCTATCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCAACACTTTTGGAA
1 GGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAA
* * *
1669048 TTTAAAAGATAAGCAGTAATA-CGCCTATAAAGTGTCGATACTTTATAAAAATGTTTTGATCCAT
66 TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG-TATAATCCAT
*
1669112 AATAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGAAAAAACC
130 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGAAAAAACC
* * * ** *
1669164 GGTAAATCACTACCATATATGTT-AAAGTGTTAATACTTTAATATAAGTATCGACACTTTTAGAA
1 GGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAA
*
1669228 TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAATGTCGATACTTTATAAAAATGTATCAATCCAT
66 TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTAT-AATCCAT
* * *
1669293 AACAATATAACAAGTAAAAATATGATAAAACCGGTCTCGAAATGATAAAACC
130 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGAAAAAACC
*
1669345 GGTAAAGCGCTA-CAGATATGTTGAAAGTGTCGATACTTTAATATATGTATCGACACTTTTGGAA
1 GGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAA
** * *
1669409 TTTAAAAGAGAAGCAGTAATAGTACATATAAAGTGTCTATACTTTATAAAAATGTATAGATCCAT
66 TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATA-ATCCAT
* *
1669474 AACAATATAACAGGTAAAAAATATAACAAAACCGGTCTCGAAATGACAAAACC
130 AACAATATAACAGGT-AAAAATATGACAAAACCGGTCTCGAAATGAAAAAACC
*
1669527 GGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
1 GGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATA
1669571 AGTACGCGTA
Statistics
Matches: 367, Mismatches: 34, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
180 69 0.19
181 222 0.60
182 46 0.13
183 30 0.08
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
GGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAA
TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATAATCCATA
ACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGAAAAAACC
Found at i:1676043 original size:18 final size:18
Alignment explanation
Indices: 1676020--1676110 Score: 57
Period size: 18 Copynumber: 5.2 Consensus size: 18
1676010 ACCGGTCACA
1676020 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
** * * *
1676038 ACCCGATTCGAACCATTT
1 ACCCGACCCGACCCGTTG
1676056 ACCCG-----ACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1676069 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
*
1676087 ACTCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
1676108 ACC
1 ACC
1676111 GTTGACCCGT
Statistics
Matches: 53, Mismatches: 12, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
13 10 0.19
18 33 0.62
21 10 0.19
ACGTcount: A:0.19, C:0.43, G:0.20, T:0.19
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1676061 original size:31 final size:31
Alignment explanation
Indices: 1676024--1676104 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
1676014 GTCACAACCC
**
1676024 GACCCGACCCGTTGACCCGATTCGAACCAT-TT
1 GACCCGACCCGTTGACCCGACCCG-ACC-TGTT
1676056 -ACCCGACCCGTTGACCCGACCCGACCTGTT
1 GACCCGACCCGTTGACCCGACCCGACCTGTT
*
1676086 GACTCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
1676105 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 1 0.02
30 5 0.11
31 38 0.86
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.19
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCTGTT
Found at i:1676114 original size:15 final size:15
Alignment explanation
Indices: 1676094--1676127 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1676084 TTGACTCGAC
1676094 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1676109 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1676124 CCGT
1 CCGT
1676128 CGTTGACCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.35, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1676133 original size:10 final size:8
Alignment explanation
Indices: 1676091--1676145 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1676081 CTGTTGACTC
1676091 GACCCGTT
1 GACCCGTT
1676099 GACCCGTT
1 GACCCGTT
1676107 GA-CCGTT
1 GACCCGTT
1676114 GACCCGTT
1 GACCCGTT
1676122 GACCGTCGTT
1 GACC--CGTT
1676132 GACCACTGTT
1 GACC-C-GTT
1676142 GACC
1 GACC
1676146 AAAACTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:1682998 original size:13 final size:13
Alignment explanation
Indices: 1682980--1683005 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1682970 TGACATATTC
1682980 TAAATATGTCAAA
1 TAAATATGTCAAA
1682993 TAAATATGTCAAA
1 TAAATATGTCAAA
1683006 AGTTGAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TAAATATGTCAAA
Found at i:1683819 original size:16 final size:15
Alignment explanation
Indices: 1683794--1683827 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1683784 CTGCAATTTC
*
1683794 TTAATATAATTAGTA
1 TTAATATAATTAATA
1683809 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
1683825 TTA
1 TTA
1683828 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:1684161 original size:3 final size:3
Alignment explanation
Indices: 1684155--1684179 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1684145 ATCGAAAATA
1684155 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1684180 TTTTTCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1687271 original size:20 final size:21
Alignment explanation
Indices: 1687246--1687286 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1687236 CAAAGAGAAA
1687246 AACATATAAATATT-TAATAC
1 AACATATAAATATTGTAATAC
**
1687266 AACATATCCATATTGTAATAC
1 AACATATAAATATTGTAATAC
1687287 CCTAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (21 bp):
AACATATAAATATTGTAATAC
Found at i:1688185 original size:95 final size:94
Alignment explanation
Indices: 1688057--1688281 Score: 265
Period size: 95 Copynumber: 2.4 Consensus size: 94
1688047 ATACCGATGA
* * * * * *
1688057 GGTATTATCGATAAT-ATGGTAAGGGTATTGATACTACGCAACATCAAATCTAAAATTGGTATCG
1 GGTAGTATCGAT-ATCATGGTAAGTGTATCGATACTACGCAACATCAAACCTAAAACTGATATCG
* *
1688121 ATACCGGAAGGGGATATCAGTACTATAGTAT
65 ATACCGGAAGGGG-TATCAATACCATAGTAT
* * *
1688152 GGTAGTATCGATATCATGGTAAGTGTATCGATACTAGGCAACTTCGAACCTAAAACTGATATCGA
1 GGTAGTATCGATATCATGGTAAGTGTATCGATACTACGCAACATCAAACCTAAAACTGATATCGA
*
1688217 TACCGTAAGGGGTATCAATACCATAGTAT
66 TACCGGAAGGGGTATCAATACCATAGTAT
* * * *
1688246 AGAAGTATCGGTACCATGGT-AGTAGTATCGATACTA
1 GGTAGTATCGATATCATGGTAAGT-GTATCGATACTA
1688282 TTGAACTGCG
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 45 0.40
95 64 0.57
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (94 bp):
GGTAGTATCGATATCATGGTAAGTGTATCGATACTACGCAACATCAAACCTAAAACTGATATCGA
TACCGGAAGGGGTATCAATACCATAGTAT
Found at i:1688773 original size:58 final size:59
Alignment explanation
Indices: 1688581--1688791 Score: 361
Period size: 59 Copynumber: 3.6 Consensus size: 59
1688571 TGTACAAAGT
*
1688581 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCTAAAATGA
* * *
1688640 TAAGAAATTCATATTAAGTGTATGAATTTCCATATTGGGCACTTTGTATGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCTAAAATGA
*
1688699 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGAGCAC-TTGTGTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCTAAAATGA
*
1688757 TAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1688792 GGGAAATATA
Statistics
Matches: 143, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 49 0.34
59 94 0.66
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (59 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCTAAAATGA
Found at i:1689246 original size:68 final size:68
Alignment explanation
Indices: 1689137--1689392 Score: 404
Period size: 68 Copynumber: 3.8 Consensus size: 68
1689127 AAAAGATTAA
* *
1689137 AGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAAGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1689202 TTG
66 TTG
* * *
1689205 AGGCCTAATTGTGCATTTGACAAAAAGGTTTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1689270 TTG
66 TTG
* * * *
1689273 AGGCCTAACTGTGCATTTGACAGAGAGGTATCAATTATGCCAGTTAGATGGAAGGCTAAGTGGCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1689338 TTG
66 TTG
* * *
1689341 AGGCCTAACTGTGCATTTGATAGAAATGTGTCAATTATGCTAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1689393 CAGTTAAATA
Statistics
Matches: 171, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 171 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:1689491 original size:81 final size:81
Alignment explanation
Indices: 1689350--1689798 Score: 562
Period size: 81 Copynumber: 5.5 Consensus size: 81
1689340 GAGGCCTAAC
* * * * * *
1689350 TGTGCATTTGATAGAAATGTGTCAATTATGCTAGTTAGATGAACAGTTAAATACCATTGAGTAAA
1 TGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAAA
* * *
1689415 ATAATAATAGTCTAGC
66 AGAATAATAGCCTAGT
* * *
1689431 TGTGCATTTGAAAGAAAGGTGTTAATTATGCCAGCTAGATAAACAGTTAAGTATCGTTGAGTAAA
1 TGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAAA
*
1689496 AGAATAATAGCCTCGT
66 AGAATAATAGCCTAGT
* * *
1689512 TGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAA
1 TGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAAA
1689577 AGAATAATAGCCTAGT
66 AGAATAATAGCCTAGT
* * * *
1689593 TTTGCATTGGACAA-AAAGGAGTCAATTATGCCAGTTAGATGAAC-GATTAAGTACCGTTGAGTA
1 TGTGCATTTGA-AAGAAAGGTGTCAATTATGCCAGTTAGATGAACAG-TTAAGTATCGTTGAGTA
*
1689656 AAAGAATAATAGGCTAGT
64 AAAGAATAATAGCCTAGT
* * * * ** *
1689674 TGTTCATTCGACAA-AAATGTGTCAATTATTCCAGTTAGATGAATGGTTAAGTATTGTTGAGTAA
1 TGTGCATTTGA-AAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAA
*
1689738 AAGAATAATGGCCTAGT
65 AAGAATAATAGCCTAGT
* * *
1689755 TGTGCATTTGACAGAAAGTTGTCAATTATGCCAGTTAGAGGAAC
1 TGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAC
1689799 GATTAAACAC
Statistics
Matches: 318, Mismatches: 46, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
80 2 0.01
81 313 0.98
82 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
TGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAAA
AGAATAATAGCCTAGT
Found at i:1689816 original size:243 final size:243
Alignment explanation
Indices: 1689370--1689822 Score: 626
Period size: 243 Copynumber: 1.9 Consensus size: 243
1689360 ATAGAAATGT
* * *
1689370 GTCAATTATGCTAGTTAGATGAACAGTTAAATACCATTGAGTAAAATAATAATAGTCTAGCTGTG
1 GTCAATTATGCCAGTTAGATGAACAGTTAAATACCATTGAGTAAAAGAATAATAGGCTAGCTGTG
* *
1689435 CATTTGAAAGAAAGGTGTTAATTATGCCAGCTAGATAAACAGTTAAGTATCGTTGAGTAAAAGAA
66 CATTCGAAAGAAAGGTGTCAATTATGCCAGCTAGATAAACAGTTAAGTATCGTTGAGTAAAAGAA
* * * **
1689500 TAATAGCCTCGTTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGATGAACGGTTAAGTA
131 TAATAGCCTAGTTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGAGGAACGATTAAACA
1689565 TCGTTGAGTAAAAGAATAATAGCCTAGTTTTGCATTGGACAAAAAGGA
196 TCGTTGAGTAAAAGAATAATAGCCTAGTTTTGCATTGGACAAAAAGGA
* * *
1689613 GTCAATTATGCCAGTTAGATGAAC-GATTAAGTACCGTTGAGTAAAAGAATAATAGGCTAGTTGT
1 GTCAATTATGCCAGTTAGATGAACAG-TTAAATACCATTGAGTAAAAGAATAATAGGCTAGCTGT
* * * * * ** *
1689677 TCATTCGACAA-AAATGTGTCAATTATTCCAGTTAGATGAATGGTTAAGTATTGTTGAGTAAAAG
65 GCATTCGA-AAGAAAGGTGTCAATTATGCCAGCTAGATAAACAGTTAAGTATCGTTGAGTAAAAG
* * *
1689741 AATAATGGCCTAGTTGTGCATTTGACAGAAA-GTTGTCAATTATGCCAGTTAGAGGAACGATTAA
129 AATAATAGCCTAGTTGTGCATTTGAAAGAAATG-TGTCAATTATACCAGTTAGAGGAACGATTAA
1689805 ACA-CTGTTGAGTAAAAGA
193 ACATC-GTTGAGTAAAAGA
1689823 TGAACGGTTA
Statistics
Matches: 182, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
242 3 0.02
243 177 0.97
244 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (243 bp):
GTCAATTATGCCAGTTAGATGAACAGTTAAATACCATTGAGTAAAAGAATAATAGGCTAGCTGTG
CATTCGAAAGAAAGGTGTCAATTATGCCAGCTAGATAAACAGTTAAGTATCGTTGAGTAAAAGAA
TAATAGCCTAGTTGTGCATTTGAAAGAAATGTGTCAATTATACCAGTTAGAGGAACGATTAAACA
TCGTTGAGTAAAAGAATAATAGCCTAGTTTTGCATTGGACAAAAAGGA
Found at i:1692866 original size:20 final size:16
Alignment explanation
Indices: 1692816--1692853 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1692806 TTATTGAAAA
1692816 GATTTAAAAATATGAG
1 GATTTAAAAATATGAG
1692832 GATTTAAAAATATGAG
1 GATTTAAAAATATGAG
1692848 GATTTA
1 GATTTA
1692854 TTCAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
GATTTAAAAATATGAG
Found at i:1694131 original size:59 final size:59
Alignment explanation
Indices: 1694050--1694213 Score: 253
Period size: 59 Copynumber: 2.8 Consensus size: 59
1694040 ATGGCACTAA
* *
1694050 GTGTGC-AAAGT--TAAGAAATTCATACTAAGTGTATGAGTTTCCGTATTGGGCACTTT
1 GTGTGCTAAAGTGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAACTTT
* *
1694106 GTGTGCTAAAGTGATAAGAAATTCATACTAAGTGTATGAATTTCTGTAATGGGAACTTT
1 GTGTGCTAAAGTGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAACTTT
* *
1694165 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
1 GTGTGCTAAAGTGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1694214 GGAAATATAT
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
56 6 0.06
57 5 0.05
59 86 0.89
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAGTGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAACTTT
Found at i:1694443 original size:14 final size:14
Alignment explanation
Indices: 1694426--1694456 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1694416 AATGAACAAG
*
1694426 AATAAGAAGTTAGT
1 AATAAGAAGTTAAT
1694440 AATAAGAAGTTAAT
1 AATAAGAAGTTAAT
1694454 AAT
1 AAT
1694457 TACCATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (14 bp):
AATAAGAAGTTAAT
Found at i:1694681 original size:68 final size:68
Alignment explanation
Indices: 1694565--1694905 Score: 522
Period size: 68 Copynumber: 5.0 Consensus size: 68
1694555 AAAAGATTAA
** * * *
1694565 AGGCCTAACTGTGCATTTGACAGAAAAATGTTAATAATACCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1694630 TTG
66 TTG
* * * *
1694633 AGGTCTGACTGTGCATTTGACAGAAAAGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1694698 TTG
66 TTG
* *
1694701 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1694766 TTG
66 TTG
* *
1694769 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTAT-ACAGTTAGATGAAAGGCTAATTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1694833 TTG
66 TTG
* * * *
1694836 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCG
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1694901 TTG
66 TTG
1694904 AG
1 AG
1694906 TAAAAGAATA
Statistics
Matches: 249, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
67 64 0.26
68 185 0.74
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Done.