Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1647733 original size:12 final size:11
Alignment explanation
Indices: 1647687--1647729 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
1647677 ACTGTGATAA
1647687 TATATTTATAT
1 TATATTTATAT
1647698 TA-ATTTATAGT
1 TATATTTATA-T
*
1647709 TATGTTTCATAT
1 TATATTT-ATAT
1647721 TATATTTAT
1 TATATTTAT
1647730 TATTTCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.26
11 7 0.26
12 10 0.37
13 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1656063 original size:24 final size:24
Alignment explanation
Indices: 1656010--1656064 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1656000 CCATGTTAGG
* * *
1656010 AATCAGAACATATTTCAGATCAGA
1 AATCAGAACAAAATTCAAATCAGA
**
1656034 TGTCAGAACAAAATTCAAATCAGA
1 AATCAGAACAAAATTCAAATCAGA
1656058 AATCAGA
1 AATCAGA
1656065 TAAAATATTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (24 bp):
AATCAGAACAAAATTCAAATCAGA
Found at i:1660659 original size:14 final size:14
Alignment explanation
Indices: 1660640--1660669 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1660630 TTAACTTTTT
1660640 GGTCAAAAGTCAAC
1 GGTCAAAAGTCAAC
*
1660654 GGTCAACAGTCAAC
1 GGTCAAAAGTCAAC
1660668 GG
1 GG
1660670 GACGGGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (14 bp):
GGTCAAAAGTCAAC
Found at i:1663272 original size:13 final size:13
Alignment explanation
Indices: 1663256--1663285 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1663246 GGAAAAATAC
1663256 AAAAGAAATAAAT
1 AAAAGAAATAAAT
*
1663269 AAAATAAATAAAT
1 AAAAGAAATAAAT
1663282 AAAA
1 AAAA
1663286 AATGAAAAAT
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:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAGAAATAAAT
Found at i:1663483 original size:38 final size:38
Alignment explanation
Indices: 1663364--1663668 Score: 349
Period size: 38 Copynumber: 7.9 Consensus size: 38
1663354 TTCAAAAACA
* **
1663364 TTTTCAAAACTATATATTATA-A-ATATTTAAAAAAATG
1 TTTTAAAAACTATATATTATATATATATTT-TCAAAATG
*
1663401 TTTTGAAAAAACTATACATTATATATATATTTTC-AAA--
1 TTTT--AAAAACTATATATTATATATATATTTTCAAAATG
* *
1663438 -TTCAAAAACTATATAATATATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATATTTTCAAAATG
* *
1663475 TCTTAAAAACTATATATTATATATATATTTTTAAAATG
1 TTTTAAAAACTATATATTATATATATATTTTCAAAATG
1663513 TTTTAAAAACTAATATATATATATATATATATATATATTCAAAATG
1 TTTTAAAAAC-----TATATAT-TATATATATAT-T-TTCAAAATG
*
1663559 TTTT-AAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATATTTTCAAAATG
*
1663596 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATATTTTCAAAATG
1663634 TTTTAAAAAACTATATA--ATATATATATTTTCAAAA
1 TTTT-AAAAACTATATATTATATATATATTTTCAAAA
1663669 AAGGATTTTT
Statistics
Matches: 235, Mismatches: 15, Indels: 36
0.82 0.05 0.13
Matches are distributed among these distances:
34 26 0.11
35 3 0.01
36 2 0.01
37 34 0.14
38 80 0.34
39 40 0.17
40 8 0.03
41 6 0.03
43 7 0.03
44 11 0.05
45 6 0.03
46 12 0.05
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATATATATTTTCAAAATG
Found at i:1663532 original size:2 final size:2
Alignment explanation
Indices: 1663525--1663550 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1663515 TTAAAAACTA
1663525 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
1663551 TCAAAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1663590 original size:121 final size:120
Alignment explanation
Indices: 1663369--1663660 Score: 374
Period size: 121 Copynumber: 2.5 Consensus size: 120
1663359 AAACATTTTC
** *
1663369 AAAACTATATATTATA-A-ATATTTAAAAAAATGTTTTGAAAAAAC--TAT-ACAT-TATATATA
1 AAAACTATATATTATATATATATTT-TCAAAATGTTTT-AAAAAACTATATAATATATATATATA
**
1663428 TAT-T-TTC-AAA--TTCAAAAACTATATAATATATATATATTTTCAAAATGTCTTA
64 TATATATTCAAAATGTTTTAAAACTATATAATATATATATATTTTCAAAATGTCTTA
*
1663480 AAAACTATATATTATATATATATTTTTAAAATGTTTT-AAAAACTAATATATATATATATATATA
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAAACT-ATATA-ATATATATATATA
* * *
1663544 TATATATTCAAAATGTTTTAAAACTATATATTATATATATGTTTTCAAAATGTTTTA
64 TATATATTCAAAATGTTTTAAAACTATATAATATATATATATTTTCAAAATGTCTTA
*
1663601 AAAACTATATATTATATATATGTTTTCAAAATGTTTTAAAAAACTATATAATATATATAT
1 AAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAAACTATATAATATATATAT
1663661 TTTCAAAAAA
Statistics
Matches: 157, Mismatches: 10, Indels: 19
0.84 0.05 0.10
Matches are distributed among these distances:
110 6 0.04
111 16 0.10
112 11 0.07
113 9 0.06
115 3 0.02
116 11 0.07
117 1 0.01
118 3 0.02
119 3 0.02
120 10 0.06
121 77 0.49
122 7 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAAACTATATAATATATATATATATA
TATATTCAAAATGTTTTAAAACTATATAATATATATATATTTTCAAAATGTCTTA
Found at i:1665419 original size:24 final size:22
Alignment explanation
Indices: 1665365--1665420 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
1665355 CATTAGGGTT
*
1665365 AAAA-TAAAGTAAATAAATAAA
1 AAAATTAAATTAAATAAATAAA
*
1665386 ATAATT--ATTAAATAAATAAA
1 AAAATTAAATTAAATAAATAAA
1665406 AGAAATTTAAATTAA
1 A-AAA-TTAAATTAA
1665421 TTGAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 14 0.52
21 5 0.19
22 3 0.11
24 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATTAAATTAAATAAATAAA
Found at i:1670892 original size:26 final size:26
Alignment explanation
Indices: 1670863--1670913 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1670853 GGTGATTGCA
*
1670863 TTTCTCCCATTCTCTTGATGATTAGT
1 TTTCCCCCATTCTCTTGATGATTAGT
*
1670889 TTTCCCCCATTCTCTTGGTGATTAG
1 TTTCCCCCATTCTCTTGATGATTAG
1670914 ATAGAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (26 bp):
TTTCCCCCATTCTCTTGATGATTAGT
Found at i:1675724 original size:9 final size:8
Alignment explanation
Indices: 1675710--1675761 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
1675700 ATTAGGGTTA
1675710 AAATAAAGT
1 AAATAAA-T
1675719 AAATAAAT
1 AAATAAAT
*
1675727 AATTAAAAT
1 AAAT-AAAT
1675736 AAATAAAAT
1 AAAT-AAAT
1675745 AATATTAAAT
1 AA-A-TAAAT
1675755 AAATAAA
1 AAATAAA
1675762 AGAAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
10 7 0.18
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (8 bp):
AAATAAAT
Found at i:1675727 original size:4 final size:4
Alignment explanation
Indices: 1675710--1675761 Score: 50
Period size: 4 Copynumber: 11.8 Consensus size: 4
1675700 ATTAGGGTTA
*
1675710 AAAT AAAGT AAAT AAAT AATT AAAAT AAAT AAAAT AATATT AAAT AAAT
1 AAAT AAA-T AAAT AAAT AAAT -AAAT AAAT -AAAT AA-A-T AAAT AAAT
1675759 AAA
1 AAA
1675762 AGAAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
4 25 0.61
5 13 0.32
6 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:1675735 original size:22 final size:20
Alignment explanation
Indices: 1675707--1675762 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
1675697 AGCATTAGGG
1675707 TTAAAATAAAGT-AAATAAATAA
1 TTAAAATAAA-TAAAAT-AAT-A
1675729 TTAAAATAAATAAAATAATA
1 TTAAAATAAATAAAATAATA
1675749 TT-AAATAAATAAAA
1 TTAAAATAAATAAAA
1675763 GAAATTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.36
20 3 0.09
21 4 0.12
22 14 0.42
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAAATAAATAAAATAATA
Found at i:1675772 original size:20 final size:19
Alignment explanation
Indices: 1675710--1675774 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
1675700 ATTAGGGTTA
*
1675710 AAATAAAGTAAATAAATAATT
1 AAATAAA-TAAAAAAAT-ATT
*
1675731 AAAATAAATAAAATAATATT
1 -AAATAAATAAAAAAATATT
*
1675751 AAATAAATAAAAGAAATTTT
1 AAATAAATAAAA-AAATATT
1675771 AAAT
1 AAAT
1675775 TAATTGATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.32
20 12 0.32
21 7 0.18
22 7 0.18
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
AAATAAATAAAAAAATATT
Found at i:1680358 original size:14 final size:13
Alignment explanation
Indices: 1680345--1680378 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
1680335 ATTAAAAATA
1680345 AATAAATAATAAT
1 AATAAATAATAAT
1680358 AATAATATAATAAT
1 AATAA-ATAATAAT
1680372 AATAAAT
1 AATAAAT
1680379 TATTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:1682868 original size:32 final size:32
Alignment explanation
Indices: 1682825--1682923 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 32
1682815 TTTAATTAGG
1682825 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTA-TATTTTAATTAAGTTTTAGGATATTAT
* *
1682858 TTTTATATTTT-ATATATGTTTTAGGTATTTTAAT
1 TTTTATATTTTAAT-TAAGTTTTAGG-ATATT-AT
** * * *
1682892 TTAAATATTTTAATTAGGATTTAGAATATTAT
1 TTTTATATTTTAATTAAGTTTTAGGATATTAT
1682924 ATTATTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
31 2 0.04
32 18 0.33
33 13 0.24
34 19 0.35
35 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (32 bp):
TTTTATATTTTAATTAAGTTTTAGGATATTAT
Found at i:1683616 original size:19 final size:18
Alignment explanation
Indices: 1683565--1683613 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1683555 AATCTCTTTA
1683565 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
1683584 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
1683603 ATTTTTTATTT
1 ATTTTTTATTT
1683614 TAAAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1686593 original size:6 final size:5
Alignment explanation
Indices: 1686580--1686672 Score: 68
Period size: 5 Copynumber: 18.8 Consensus size: 5
1686570 ATATCTTTGT
* * * **
1686580 TTTTA TTTTCA TTTTA TTTTCG TTTTA TTTT- TATT- TTTTA GTGAA TTTTA
1 TTTTA TTTT-A TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
1686630 TTTCA TTCTA -TTTA TTTTA TTTTGA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTT
1686673 TTTCTGAACA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
4 10 0.15
5 48 0.71
6 10 0.15
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:1686611 original size:23 final size:23
Alignment explanation
Indices: 1686563--1686616 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1686553 AGGCAACCCA
*
1686563 TTTCATTATATCTTTGTTTTTAT
1 TTTCATTTTATCTTTGTTTTTAT
1686586 TTTCATTTTAT-TTTCG-TTTTAT
1 TTTCATTTTATCTTT-GTTTTTAT
*
1686608 TTTTATTTT
1 TTTCATTTT
1686617 TTAGTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTCATTTTATCTTTGTTTTTAT
Found at i:1686657 original size:15 final size:14
Alignment explanation
Indices: 1686626--1686675 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1686616 TTTAGTGAAT
* *
1686626 TTTATTTCATTCTA
1 TTTATTTTATTTTA
1686640 TTTATTTTATTTTGA
1 TTTATTTTATTTT-A
1686655 TTTATTTTATTTTA
1 TTTATTTTATTTTA
1686669 TTT-TTTT
1 TTTATTTT
1686676 CTGAACAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 4 0.12
14 15 0.45
15 14 0.42
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:1686673 original size:11 final size:11
Alignment explanation
Indices: 1686580--1686673 Score: 56
Period size: 11 Copynumber: 8.9 Consensus size: 11
1686570 ATATCTTTGT
*
1686580 TTTTATTTTCA
1 TTTTATTTTTA
**
1686591 TTTTATTTTCG
1 TTTTATTTTTA
1686602 TTTTATTTTTA
1 TTTTATTTTTA
**
1686613 TTTT-TTAGTGAA
1 TTTTATT--TTTA
*
1686625 TTTTA-TTTCA
1 TTTTATTTTTA
*
1686635 TTCTA--TTTA
1 TTTTATTTTTA
*
1686644 TTTTATTTTGA
1 TTTTATTTTTA
1686655 -TTTA-TTTTA
1 TTTTATTTTTA
1686664 TTTTATTTTT
1 TTTTATTTTT
1686674 TTCTGAACAG
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
9 11 0.17
10 16 0.25
11 30 0.47
12 7 0.11
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1688473 original size:32 final size:32
Alignment explanation
Indices: 1688430--1688491 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1688420 TTTAATTAGG
1688430 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
1688463 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
1688492 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:1694027 original size:22 final size:22
Alignment explanation
Indices: 1693993--1694069 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
1693983 GGTCTAACTA
1693993 TTGACCTTT-ACCAGTTAGACTG
1 TTGA-CTTTGACCAGTTAGACTG
*
1694015 TTGACTTTGACCAG-TATGACCG
1 TTGACTTTGACCAGTTA-GACTG
*
1694037 TTGACTTTGACCGGTCT-GA-TCG
1 TTGACTTTGACCAGT-TAGACT-G
1694059 TTGACTTTGAC
1 TTGACTTTGAC
1694070 TTTGACCGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 6 0.13
22 40 0.85
24 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (22 bp):
TTGACTTTGACCAGTTAGACTG
Found at i:1709859 original size:13 final size:13
Alignment explanation
Indices: 1709841--1709880 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1709831 GACTTTTTTT
*
1709841 GTCAAAATCAACA
1 GTCAAAGTCAACA
*
1709854 GTCAAAGTCAATA
1 GTCAAAGTCAACA
1709867 GTCAAAGTCAACA
1 GTCAAAGTCAACA
1709880 G
1 G
1709881 GTTAACTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:1709910 original size:14 final size:14
Alignment explanation
Indices: 1709893--1709932 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1709883 TAACTCGAAC
1709893 GAGTTGACTCAGAT
1 GAGTTGACTCAGAT
* *
1709907 GAGTAGACTCAGGT
1 GAGTTGACTCAGAT
*
1709921 AAGTTGACTCAG
1 GAGTTGACTCAG
1709933 CTCTGACCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (14 bp):
GAGTTGACTCAGAT
Found at i:1713661 original size:39 final size:39
Alignment explanation
Indices: 1713618--1713694 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1713608 CGCCAATGTG
1713618 ATCTTTATAAAGGAATCTCATATGCTCAAAATGGTTGAA
1 ATCTTTATAAAGGAATCTCATATGCTCAAAATGGTTGAA
* *
1713657 ATCTTTATAATGGTATCTCATATGCTCAAAATGGTTGA
1 ATCTTTATAAAGGAATCTCATATGCTCAAAATGGTTGA
1713695 GTGATGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (39 bp):
ATCTTTATAAAGGAATCTCATATGCTCAAAATGGTTGAA
Found at i:1717538 original size:7 final size:7
Alignment explanation
Indices: 1717526--1717552 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1717516 AAACAAATTC
1717526 ATATCAT
1 ATATCAT
1717533 ATATCAT
1 ATATCAT
1717540 ATATCAT
1 ATATCAT
1717547 ATATCA
1 ATATCA
1717553 GAACAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATCAT
Found at i:1717596 original size:24 final size:24
Alignment explanation
Indices: 1717549--1717605 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1717539 TATATCATAT
*
1717549 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATCCAGATAAGAA
*
1717573 ATCAGAACAGAATTC-GAATAAGAA
1 ATCAGAACAGAATCCAG-ATAAGAA
*
1717597 ATCATAACA
1 ATCAGAACA
1717606 TATTTCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.53, C:0.18, G:0.14, T:0.16
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATAAGAA
Found at i:1722676 original size:5 final size:6
Alignment explanation
Indices: 1722658--1722683 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1722648 GAATAATTAT
1722658 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
1722684 CAAGATGAAA
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):
AATAAA
Found at i:1723989 original size:21 final size:19
Alignment explanation
Indices: 1723962--1724015 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1723952 TAACAGGTTG
1723962 AAATTTGACAAAAC-ATGTA
1 AAATTTGACAAAACGAT-TA
* *
1723981 ACGAATTTGACTAACCGATTA
1 A--AATTTGACAAAACGATTA
1724002 AAATTTGACAAAAC
1 AAATTTGACAAAAC
1724016 CAGTTGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 12 0.43
21 14 0.50
22 2 0.07
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATTTGACAAAACGATTA
Found at i:1724549 original size:197 final size:199
Alignment explanation
Indices: 1724002--1724554 Score: 568
Period size: 197 Copynumber: 2.8 Consensus size: 199
1723992 TAACCGATTA
* ** ** * * * *
1724002 AAATTTGACAAAACCAGTTGAAATTTGCTAAAACCGGTAAAGAGCA-ATCAGAATTGTTAAAATT
1 AAATTTGATAAAACCAGTTTCAATTTGAAAAAACCAGTAAAGAG-ATACCAGAATGGTT-GAATT
* * * * *
1724066 TGTATCGATACATTTATAAGTATATGTACCAAAATATCGGTA-TTGTAGGAATTTAAAAGAAATG
64 GGTATCGATACTTTTATAAGTATATGTACCAAAGTATCGATACTT-TAAGAATTTAAAAGAAATG
* *
1724130 AAAAAAGGAAAATGTCTCGAAAGTATTGATACATTACACACATGTATCGATACATGACAAAATAA
128 AAAAAATGAAAATGTCTCGAAAGTATCGATACATTACACACATGTATCGATACATGACAAAATAA
1724195 CAGGTTG
193 CAGGTTG
* * * * *
1724202 AAGTTTGATAAAACCAGTTTCAATTTGACAAACCCAGTAAAGAGATACCATAATGGTTGACATTT
1 AAATTTGATAAAACCAGTTTCAATTTGAAAAAACCAGTAAAGAGATACCAGAATGGTTGA-ATTG
* * * * * *
1724267 TTATCGATACTTTTATAAATATATGCACCAAAGTATCGATACTTTATGAATTTAAAAGAATTGCA
65 GTATCGATACTTTTATAAGTATATGTACCAAAGTATCGATACTTTAAGAATTTAAAAGAAATGAA
* ** * ** * * * *
1724332 ATAAT---AGCGCCTATAAAGTATCGATACCTTAGACACTTGTATCGATACATGACAATATAACA
130 AAAATGAAAATGTCTCGAAAGTATCGATACATTACACACATGTATCGATACATGACAAAATAACA
*
1724394 TGTTG
195 GGTTG
* * *
1724399 AAATTTGA-ACAAACCAGTTTCAATTTGAAAAAATCGGTAAAGA-ACTATCAGATAT-GTTG-A-
1 AAATTTGATA-AAACCAGTTTCAATTTGAAAAAACCAGTAAAGAGA-TACCAGA-ATGGTTGAAT
* * * *
1724459 TGGTATCAATACTTTTATAAGTATATGTACCATAGTATCGATACTTTAAGAACTGAAAAGAAATG
63 TGGTATCGATACTTTTATAAGTATATGTACCAAAGTATCGATACTTTAAGAATTTAAAAGAAATG
1724524 AAAAAATGAAAATGTCTCGAAAGTATCGATA
128 AAAAAATGAAAATGTCTCGAAAGTATCGATA
1724555 TCGTACACAA
Statistics
Matches: 286, Mismatches: 58, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
194 60 0.21
195 1 0.00
196 2 0.01
197 112 0.39
198 2 0.01
199 2 0.01
200 105 0.37
201 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (199 bp):
AAATTTGATAAAACCAGTTTCAATTTGAAAAAACCAGTAAAGAGATACCAGAATGGTTGAATTGG
TATCGATACTTTTATAAGTATATGTACCAAAGTATCGATACTTTAAGAATTTAAAAGAAATGAAA
AAATGAAAATGTCTCGAAAGTATCGATACATTACACACATGTATCGATACATGACAAAATAACAG
GTTG
Found at i:1728314 original size:18 final size:18
Alignment explanation
Indices: 1728293--1728343 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
1728283 GATGTAAGCC
*
1728293 AAATTTTATATGTGAATG
1 AAATTTTGTATGTGAATG
1728311 AAATTTTGTATGTGAATG
1 AAATTTTGTATGTGAATG
*
1728329 AAATTATGTATGTGA
1 AAATTTTGTATGTGA
1728344 TGACCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:1731212 original size:405 final size:394
Alignment explanation
Indices: 1730176--1731276 Score: 1501
Period size: 405 Copynumber: 2.8 Consensus size: 394
1730166 TTTTAAAGGT
* * ** *
1730176 TAAAATCCAAAAAAA-AAGTTGAATTATCTACAAATAGGTGAACACTCGATATCCATATCTTTTT
1 TAAAATCCAAAAAAATAAGTTGGATTATCTACAAGTAACTGAACACTCGATATTCATATC-TTTT
1730240 TTATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAACAGAAAGAAAAAAAATTAAGTGAACAC
65 TTATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAAC---AA-AAAAAAAATTAAGTGAACAC
* * ** *
1730305 AAATGTGTGTTGGTGTGTGGTCTAGTTGTTACCATGTTTGTCTAACACACTAAAGATTCCTAGTT
126 AAATGTGTGTT-GT-TGTGGTGTAGTTGTTATCACATTTGTCTTACACACTAAAGA-TCCTAGTT
1730370 CGATCCTGGGA-AACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTG
188 CGATCCT-GGACAACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTG
* * *
1730434 ACTTTTTCATTGTCTTCTTGATCATCGATATGCAAAAAGTGTC-T-TTGTCCTTAATATAAATTA
252 ACTTTCTCATTGTCTTCTTGATCATCGATATGCAACAAGTGTCTTCTTATCCTTAATATAAATTA
*
1730497 ATTAAATTCATGAAATAATAAGTTATAATATATAAATTTATATAAAAGTAGATTGAGACTTAATA
317 ATTAAATTCATGAAATAATAAGTTATAATATATAAATTTATATAAAAGTACATTGAGACTTAATA
1730562 TTTGTATATGTTA
382 TTTGTATATGTTA
*
1730575 TAAAA---ATAAAAATAAGTTGGATTATCTACAAGTAACTGAACACTCGATATTC--A--TTTTT
1 TAAAATCCAAAAAAATAAGTTGGATTATCTACAAGTAACTGAACACTCGATATTCATATCTTTTT
1730633 TATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAACAGAAAGAAAGAAATTAAGTGAACACAA
66 TATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAACA-AAA-AAA-AAATTAAGTGAACACAA
* *
1730698 ATGTGTGTTGTTATTGTGGTGTAGTTGTTATCACATTTGTCTTACACGCTAAAGATTCTCAGTTC
128 ATGTGTGTTG---TTGTGGTGTAGTTGTTATCACATTTGTCTTACACACTAAAGATCCT-AGTTC
* *
1730763 GATCCTGGGCAACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTGGC
189 GATCCTGGACAACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTGAC
*
1730828 TTTCTCATTGTCTTCTTGATCATCGATATGCAACAAGTGTCTTCGCCCTTAATACAAATTTGAAT
254 TTTCTCATTGTCTTCTTGATCATCGATATGCAACAAGTGTCTT----CTT-AT-C---CTT-AAT
* *
1730893 ATAAATTAATTAAATTCATGAAGTAATATGTTTATAATATATAAATTTATATAAAAGTACATTGA
309 ATAAATTAATTAAATTCATGAAATAATAAG-TTATAATATATAAATTTATATAAAAGTACATTGA
*
1730958 GAGTTAATATTTGTATATGTTA
373 GACTTAATATTTGTATATGTTA
*
1730980 TAAAATCCAAAAAAATTAA-TTGGATTATATACAAGTAACTGAACACTCGATATTCATATCTTTT
1 TAAAATCCAAAAAAA-TAAGTTGGATTATCTACAAGTAACTGAACACTCGATATTCATATCTTTT
* *
1731044 TTATAATGATTTCTTGAAAACAATTAAGTAAAGCTTAACAAAAAAAAAATTAAGTGAACACAAAT
65 TTATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAACAAAAAAAAAATTAAGTGAACACAAAT
* * * * *
1731109 GTGTGTTGTTGTGGTGT-GGTGTTATCACATTAGTTTTACACACTAAAGGTCCCTAGTTCTATCC
130 GTGTGTTGTTGTGGTGTAGTTGTTATCACATTTGTCTTACACACTAAAGAT-CCTAGTTCGATCC
* * *
1731173 TAGACAACAACATTGTTAAGTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTGACTTTCT
194 TGGACAACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTGACTTTCT
* * *
1731238 CATAT-TCTTCTTGATCATCGGTTTGCAGCAAGTGTCTTC
259 CAT-TGTCTTCTTGATCATCGATATGCAACAAGTGTCTTC
1731277 ATCTTTACCT
Statistics
Matches: 628, Mismatches: 42, Indels: 62
0.86 0.06 0.08
Matches are distributed among these distances:
389 3 0.00
390 5 0.01
391 31 0.05
392 182 0.29
393 2 0.00
395 1 0.00
396 6 0.01
397 34 0.05
398 2 0.00
399 6 0.01
400 1 0.00
401 1 0.00
403 2 0.00
404 31 0.05
405 189 0.30
406 12 0.02
408 41 0.07
409 30 0.05
410 4 0.01
411 3 0.00
412 42 0.07
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (394 bp):
TAAAATCCAAAAAAATAAGTTGGATTATCTACAAGTAACTGAACACTCGATATTCATATCTTTTT
TATCATGATTTCTTGAAAAGAATTAAGTAAAGCTTAACAAAAAAAAAATTAAGTGAACACAAATG
TGTGTTGTTGTGGTGTAGTTGTTATCACATTTGTCTTACACACTAAAGATCCTAGTTCGATCCTG
GACAACAATATTGTTAATTTTCATTTTAGAATGAAAGTATTCCCCAACCCTACTTGACTTTCTCA
TTGTCTTCTTGATCATCGATATGCAACAAGTGTCTTCTTATCCTTAATATAAATTAATTAAATTC
ATGAAATAATAAGTTATAATATATAAATTTATATAAAAGTACATTGAGACTTAATATTTGTATAT
GTTA
Found at i:1736347 original size:21 final size:20
Alignment explanation
Indices: 1736323--1736396 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
1736313 GTTTCCAGAT
1736323 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAAC-TCGACTA
*
1736344 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAAC-TCGACTA
*
1736365 TCGCAACGCGAACTTGAACTA
1 TCGCAACGCGAACTCG-ACTA
*
1736386 TCGCAATGCGA
1 TCGCAACGCGA
1736397 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAACTCGACTA
Found at i:1736416 original size:19 final size:19
Alignment explanation
Indices: 1736400--1736589 Score: 164
Period size: 21 Copynumber: 9.3 Consensus size: 19
1736390 AATGCGATTT
*
1736400 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
1736419 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1736442 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
1736461 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
1736482 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1736501 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
1736524 TCCAAGTTCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAG
* *
1736543 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
* *
1736566 TCCAAATTCATTGCGATAG
1 TCCAAGTTCGTTGCGATAG
1736585 TCCAA
1 TCCAA
1736590 AATCGCAACG
Statistics
Matches: 140, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
19 50 0.36
21 64 0.46
23 26 0.19
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:1736434 original size:21 final size:21
Alignment explanation
Indices: 1736408--1736561 Score: 176
Period size: 21 Copynumber: 7.4 Consensus size: 21
1736398 TTTCCAAATT
1736408 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1736429 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
1736450 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
1736471 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
1736490 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1736511 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1736532 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
1736553 CGTTGCGAT
1 CGTTGCGAT
1736562 TTATTCCAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
19 36 0.32
21 58 0.52
23 18 0.16
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1736449 original size:42 final size:42
Alignment explanation
Indices: 1736392--1736589 Score: 305
Period size: 42 Copynumber: 4.8 Consensus size: 42
1736382 ACTATCGCAA
1736392 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1736432 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1736474 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1736514 TGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
1736556 TGCGATTTATTCCAAATTCATTGCGATAGTCCAA
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1736590 AATCGCAACG
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
40 42 0.29
41 2 0.01
42 101 0.70
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1736534 original size:82 final size:83
Alignment explanation
Indices: 1736392--1736589 Score: 301
Period size: 82 Copynumber: 2.4 Consensus size: 83
1736382 ACTATCGCAA
*
1736392 TGCGATT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 TGCGATTAGTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1736456 GATAGTCCAAGTTCGCGT
66 GATAGTCCAAGTTCGCGT
* * * *
1736474 TGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGT
1 TGCGATTAGTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
*
1736538 GATAGTCGAAGTTCGCGT
66 GATAGTCCAAGTTCGCGT
* *
1736556 TGCGATTTATTCCAAATTCATTGCGATAGTCCAA
1 TGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAA
1736590 AATCGCAACG
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 79 0.77
84 23 0.22
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (83 bp):
TGCGATTAGTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
GATAGTCCAAGTTCGCGT
Found at i:1736684 original size:6 final size:6
Alignment explanation
Indices: 1736673--1736704 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1736663 GACACGTATT
1736673 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1736705 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1737516 original size:42 final size:42
Alignment explanation
Indices: 1737451--1737590 Score: 244
Period size: 42 Copynumber: 3.3 Consensus size: 42
1737441 CGTTGCGATT
1737451 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1737493 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1737535 TTGGACTATCACAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1737577 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1737591 TGCGAATATG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:1737587 original size:21 final size:20
Alignment explanation
Indices: 1737451--1737596 Score: 109
Period size: 21 Copynumber: 7.0 Consensus size: 20
1737441 CGTTGCGATT
*
1737451 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
1737470 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
1737493 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
1737512 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
1737535 TTGGACTATCACAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
*
1737554 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
1737577 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
1737597 TATGTAAATC
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 25 0.25
21 45 0.45
23 29 0.29
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:1737637 original size:21 final size:21
Alignment explanation
Indices: 1737611--1737657 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1737601 TAAATCGCAA
*
1737611 TGCGATAGTCGAAGTTTGCGT
1 TGCGATAGTCGAAGTTCGCGT
*
1737632 TGCGATAGTTGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1737653 TGCGA
1 TGCGA
1737658 ATCTGGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:1740665 original size:21 final size:21
Alignment explanation
Indices: 1740626--1740665 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1740616 TCAGTTCGAG
*
1740626 TTGACCTGATATCTTAATAAA
1 TTGACATGATATCTTAATAAA
1740647 TTGACATGA-ATCTTGAATA
1 TTGACATGATATCTT-AATA
1740666 TCATGAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
TTGACATGATATCTTAATAAA
Found at i:1746169 original size:27 final size:27
Alignment explanation
Indices: 1746120--1746171 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1746110 CGAGTCAACC
*
1746120 CGTTGACTTTGACAGTTGGCTTTGATT
1 CGTTGACTTTGACAGTTGACTTTGATT
*
1746147 CGTTGGCTTTGACCA-TTGACTTTGA
1 CGTTGACTTTGA-CAGTTGACTTTGA
1746172 CCAAAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (27 bp):
CGTTGACTTTGACAGTTGACTTTGATT
Found at i:1755053 original size:21 final size:21
Alignment explanation
Indices: 1755018--1755065 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1755008 ATTATTTCTA
1755018 TTAA-TTGCCTTTAATTTA-T
1 TTAATTTGCCTTTAATTTAGT
*
1755037 TTGATTTGCCTTTTAATTTAGT
1 TTAATTTGCC-TTTAATTTAGT
1755059 TTAATTT
1 TTAATTT
1755066 TATTACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 5 0.21
21 9 0.38
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (21 bp):
TTAATTTGCCTTTAATTTAGT
Found at i:1757533 original size:20 final size:21
Alignment explanation
Indices: 1757508--1757555 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
1757498 AATTCATTTG
1757508 TTGCATTTACATTTTGCAT-T
1 TTGCATTTACATTTTGCATAT
*
1757528 TTGCA-TTCCATTTTGCATAT
1 TTGCATTTACATTTTGCATAT
1757548 TTGCATTT
1 TTGCATTT
1757556 GCATGAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 11 0.44
21 2 0.08
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (21 bp):
TTGCATTTACATTTTGCATAT
Found at i:1758117 original size:17 final size:17
Alignment explanation
Indices: 1758091--1758124 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1758081 ATCTTTAAAA
*
1758091 AATGATAAGATTGAACC
1 AATGACAAGATTGAACC
1758108 AATGACAAGATTGAACC
1 AATGACAAGATTGAACC
1758125 CCATCAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (17 bp):
AATGACAAGATTGAACC
Found at i:1758516 original size:2 final size:2
Alignment explanation
Indices: 1758509--1758573 Score: 98
Period size: 2 Copynumber: 33.5 Consensus size: 2
1758499 TATACCCAGA
*
1758509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1758550 AT AT AT AT AT AT -T AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1758574 CAATAAAGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1760022 original size:38 final size:37
Alignment explanation
Indices: 1759971--1760165 Score: 169
Period size: 37 Copynumber: 5.5 Consensus size: 37
1759961 CAAAATATCA
*
1759971 TCTCACTAGAGACATTGTTTTCTTAAAAACAAATTTTG
1 TCTCACTTGAGACATT-TTTTCTTAAAAACAAATTTTG
*
1760009 TCTCACTTGAGACATTTTTCTCTT-AAAACAAATTTCG
1 TCTCACTTGAGACATTTTT-TCTTAAAAACAAATTTTG
* *** * *
1760046 TCTCACTTGAGACA-TTTTCCTTCGGAACACA-TAT-
1 TCTCACTTGAGACATTTTTTCTTAAAAACAAATTTTG
** *
1760080 T-TCA----A-AGTTTTTTTCTTAAAACCAAATTTTG
1 TCTCACTTGAGACATTTTTTCTTAAAAACAAATTTTG
*
1760111 TCTCATTTGAGACATTTTTCTCTTAAAAA-AAATTTTG
1 TCTCACTTGAGACATTTTT-TCTTAAAAACAAATTTTG
*
1760148 TCTTACTTGAGACATTTT
1 TCTCACTTGAGACATTTT
1760166 CCTTCGGAAC
Statistics
Matches: 123, Mismatches: 22, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.01
29 12 0.10
30 2 0.02
31 1 0.01
32 3 0.02
33 3 0.02
34 1 0.01
35 4 0.03
36 10 0.08
37 59 0.48
38 27 0.22
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (37 bp):
TCTCACTTGAGACATTTTTTCTTAAAAACAAATTTTG
Found at i:1760049 original size:37 final size:36
Alignment explanation
Indices: 1759971--1760269 Score: 159
Period size: 37 Copynumber: 8.5 Consensus size: 36
1759961 CAAAATATCA
*
1759971 TCTCACTAGAGACATTGTTT-TCTTAAAAACAAATTTTG
1 TCTCACTTGAGACATT-TTTCTCTT-AAAACAAA-TTTG
1760009 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCG
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTT-G
** * *
1760046 TCTCACTTGAGACA-TTTTC-CTTCGGAACACATAT-
1 TCTCACTTGAGACATTTTTCTCTT-AAAACAAATTTG
* *
1760080 T-TCA----A-A-GTTTTTTTCTTAAAACCAAATTTTG
1 TCTCACTTGAGACATTTTTCTCTTAAAA-CAAA-TTTG
* *
1760111 TCTCATTTGAGACATTTTTCTCTTAAAAAAAATTTTG
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAA-TTTG
* * ** *
1760148 TCTTACTTGAGACATTTTCCTTCGGAACACAAA--T-
1 TCTCACTTGAGACATTTTTC-TCTTAAAACAAATTTG
* ** *
1760182 T-TCA---AAGTTATTTTTCT-TAAAAACCAAATTTG
1 TCTCACTTGAGACATTTTTCTCTTAAAA-CAAATTTG
* *
1760214 TCTCACTTGAGACATTTTTTCTCTCAAAACGAATTTCG
1 TCTCACTTGAGACA-TTTTTCTCTTAAAACAAATTT-G
* *
1760252 ACTCACTTGAGATATTTT
1 TCTCACTTGAGACATTTT
1760270 CCTTTGGAAC
Statistics
Matches: 198, Mismatches: 36, Indels: 55
0.69 0.12 0.19
Matches are distributed among these distances:
28 10 0.05
29 12 0.06
30 10 0.05
31 2 0.01
32 4 0.02
33 8 0.04
34 2 0.01
35 4 0.02
36 19 0.10
37 69 0.35
38 58 0.29
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTG
Found at i:1760164 original size:102 final size:103
Alignment explanation
Indices: 1759988--1760368 Score: 502
Period size: 102 Copynumber: 3.7 Consensus size: 103
1759978 AGAGACATTG
*
1759988 TTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
1 TTTTCTTAAAACCAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
*
1760053 TGAGACATTTTCCTTCGGAACACATATTTCAAAGTT-T
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTAT
* * * *
1760090 TTTTCTTAAAACCAAATTTTGTCTCATTTGAGACATTTTTCTCTTAAAAAAAATTTTGTCTTACT
1 TTTTCTTAAAACCAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
1760155 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTAT
66 TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTAT
* * *
1760193 TTTTCTTAAAAACCAAA-TTTGTCTCACTTGAGACATTTTTTCTCTCAAAACGAATTTCGACTCA
1 TTTTCTT-AAAACCAAATTTTGTCTCACTTGAGACA-TTTTTCTCTTAAAACAAATTTCGTCTCA
* *
1760257 CTTGAGATATTTTCCTTTGGAACACAAATTTCAAAGTTGA-
64 CTTGAGACATTTTCCTTCGGAACACAAATTTCAAAGTT-AT
* * * * * * * * ** *
1760297 TTTACAT-GAACCAATTTTTTTCTCGCTTGAGACA-ATTTCTCTCAAAACAAACATCGTCTCGCT
1 TTTTCTTAAAACCAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
1760360 TGAGACATT
66 TGAGACATT
1760369 CTCCCAAATT
Statistics
Matches: 246, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
101 31 0.13
102 101 0.41
103 41 0.17
104 72 0.29
105 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (103 bp):
TTTTCTTAAAACCAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTCTCACT
TGAGACATTTTCCTTCGGAACACAAATTTCAAAGTTAT
Found at i:1760579 original size:63 final size:60
Alignment explanation
Indices: 1760425--1760582 Score: 174
Period size: 63 Copynumber: 2.5 Consensus size: 60
1760415 ATAGTTTTCC
* *
1760425 AAAAAAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTT
1 AAAACAAATTTGTCTCT-TTGAGACAGTTTCTCTTGAAACAAAATCTTTG---ATGTTTCACTT
* * *
1760489 GAAACAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTG-TGTTTCACTT
1 AAAACAAA-TTTGTCT-CTTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTTGATGTTTCACTT
1760552 AAAACAAGATTTGTCTCGTTTGAGACAGTTT
1 AAAACAA-ATTTGTCTC-TTTGAGACAGTTT
1760583 TTACTCGAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 33 0.41
64 7 0.09
65 24 0.30
66 3 0.04
67 12 0.15
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (60 bp):
AAAACAAATTTGTCTCTTTGAGACAGTTTCTCTTGAAACAAAATCTTTGATGTTTCACTT
Found at i:1760676 original size:77 final size:77
Alignment explanation
Indices: 1760549--1760884 Score: 400
Period size: 77 Copynumber: 4.4 Consensus size: 77
1760539 TTGTGTTTCA
* * *
1760549 CTTAAAACAAGATTTGTCTCGTTTGAGACAGTTTTTACTCG-AAAGAATACATTTCATTTCACTC
1 CTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAACAATACATTTCATTTCACTC
1760613 AAGATTGTTTTTT
66 AAGATTG-TTTTT
* *
1760626 CTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTGCTCGAAAA-AATACATTTCATTTAACTC
1 CTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAACAATACATTTCATTTCACTC
1760690 AAGATTGTTTTT
66 AAGATTGTTTTT
** * * * *
1760702 CTTAAAAC-AGACTTTGTCTCGCTTGAGAC-ATTTTTTTTCTTAAAACAAGACATTTCGTTTCTC
1 CTTAAAACAAGA-TTTGTCTCGCTTGAGACAATTTTTACTC-GAAAACAATACATTTCATTTCAC
1760765 TACAA-ATTGTTTTT
64 T-CAAGATTGTTTTT
* * *
1760779 CTTAAAA-TAGACTTTGTCTCGGTTGAGACATTTTTTTACTC-AAAACAATA-ATATTCATTTCA
1 CTTAAAACAAGA-TTTGTCTCGCTTGAGACA-ATTTTTACTCGAAAACAATACAT-TTCATTTCA
1760841 CTCAAGATTGTTTTT
63 CTCAAGATTGTTTTT
* *
1760856 CTTAAAACCAAAATTTATCTCGCTTGAGA
1 CTTAAAA-CAAGATTTGTCTCGCTTGAGA
1760885 TAGTTTCCCT
Statistics
Matches: 225, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
75 11 0.05
76 39 0.17
77 146 0.65
78 20 0.09
79 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (77 bp):
CTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAACAATACATTTCATTTCACTC
AAGATTGTTTTT
Found at i:1760739 original size:38 final size:38
Alignment explanation
Indices: 1760697--1760825 Score: 136
Period size: 38 Copynumber: 3.4 Consensus size: 38
1760687 CTCAAGATTG
1760697 TTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACATTT
1 TTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACATTT
* * * * *
1760735 TTTTTCTTAAAACAAGACATTTCGTTTCTC-T-ACAAATTG
1 TTTTTCTTAAAAC-AGAC-TTT-GTCTCGCTTGAGACATTT
* *
1760774 TTTTTCTTAAAATAGACTTTGTCTCGGTTGAGACATTT
1 TTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACATTT
* *
1760812 TTTTACTCAAAACA
1 TTTTTCTTAAAACA
1760826 ATAATATTCA
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
36 4 0.06
37 4 0.06
38 33 0.46
39 21 0.30
40 4 0.06
41 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (38 bp):
TTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACATTT
Found at i:1761048 original size:38 final size:38
Alignment explanation
Indices: 1760983--1761055 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
1760973 TTTCGATGTT
*
1760983 TTCAAATGAATTTCAAAGAAGAGAAGCCTTATTTTAGG
1 TTCAAATGAATTTCAAAGAAGAGAAGCCTAATTTTAGG
*
1761021 TTCAAATGAATTTCAAAGAA-ATTAAGCCTAATTTT
1 TTCAAATGAATTTCAAAGAAGA-GAAGCCTAATTTT
1761056 TAGGGATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (38 bp):
TTCAAATGAATTTCAAAGAAGAGAAGCCTAATTTTAGG
Found at i:1761107 original size:52 final size:53
Alignment explanation
Indices: 1761021--1761122 Score: 127
Period size: 52 Copynumber: 1.9 Consensus size: 53
1761011 TTATTTTAGG
* *
1761021 TTCAAATGAATTTCAAAGAAATTAAGCCTAATTTT-TAGGGATTTCTTGATATT
1 TTCAAATGAATTTCAAAGAAATTAAACCTAATTTTCAAGGG-TTTCTTGATATT
* * * *
1761074 TTCAAATGAGTTTCTAA-AAATTAAACTTGATTTTCAAGGGTTTCTTGAT
1 TTCAAATGAATTTCAAAGAAATTAAACCTAATTTTCAAGGGTTTCTTGAT
1761123 GATGATTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 23 0.55
53 19 0.45
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (53 bp):
TTCAAATGAATTTCAAAGAAATTAAACCTAATTTTCAAGGGTTTCTTGATATT
Found at i:1761328 original size:41 final size:41
Alignment explanation
Indices: 1761216--1761328 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
1761206 AACGTTTCTT
* **
1761216 GATGAGTAAGCCCTTCGGGCCAT-CAGTAAGTCTTTCAAGCGT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCAAGCAA
* * * *
1761258 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCAAGCAA
1761300 GATGATAAGTCCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
1761329 ACCTTCAGGC
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 21 0.36
42 36 0.62
43 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCAAGCAA
Found at i:1761646 original size:144 final size:144
Alignment explanation
Indices: 1761305--1761776 Score: 641
Period size: 144 Copynumber: 3.3 Consensus size: 144
1761295 AGCAAGATGA
* *
1761305 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCAACATTTCCTTTGCTCGATT
* * * * *
1761370 CACAACACTTTGAATCAACAACGCCCCACCAGAGGGGTAACATTTCTTATTGCTCGATTCAC-AC
66 CACAACACTTCGAATCAATAATGCCCCACCAGAGGGTTAACATTTCCTATTGCTCGATTCACAAC
* *
1761434 TCTTCGAATCAGCT
131 ACTTCAAATCAGCT
*
1761448 TAAGTCCTTTC-GGCCATCCATAAGACCTTCGGGCATGATGTTTTCAATATTTCCTTTGCTTC-A
1 TAAGTCC-TTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCAACATTTCCTTTGC-TCGA
* *
1761511 TTCACAACACTTCGAATCAATAATGCCCCACCAGAGTGATTAACATTTCCT-TTGCTCAATTCAC
64 TTCACAACACTTCGAATCAATAATGCCCCACCAGAG-GGTTAACATTTCCTATTGCTCGATTCAC
1761575 AACACTTCAAATCAGCT
128 AACACTTCAAATCAGCT
* * *
1761592 TAAGTCTTTCGGGCCATCCATAAGACCATCGGGTATGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCAACATTTCCTTTGCTCGATT
*
1761657 CACAACACTTCGAAT-AATCAATGCCCCACTAGAGGGGTTAACATTTCCTATTGCTCGATTCACA
66 CACAACACTTCGAATCAAT-AATGCCCCACCAGA-GGGTTAACATTTCCTATTGCTCGATTCACA
* * *
1761721 ATACATCAAATCAGCA
129 ACACTTCAAATCAGCT
* * * *
1761737 TAAGTCCTTCGGGCTAT-CAGTAAGTCTTTCGAGCATGATG
1 TAAGTCCTTCGGGCCATCCA-TAAGACCTTCGGGCATGATG
1761777 CTTAAATCCT
Statistics
Matches: 290, Mismatches: 29, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
143 106 0.37
144 127 0.44
145 57 0.20
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (144 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCAACATTTCCTTTGCTCGATT
CACAACACTTCGAATCAATAATGCCCCACCAGAGGGTTAACATTTCCTATTGCTCGATTCACAAC
ACTTCAAATCAGCT
Found at i:1762787 original size:139 final size:139
Alignment explanation
Indices: 1762588--1762928 Score: 434
Period size: 139 Copynumber: 2.5 Consensus size: 139
1762578 CATTGCTAGT
* * *
1762588 AGAA-AAGTTCATAATGAGAATAACTTATTCAACCTTAGCTCGATTCATCACATATCGAGTTGAA
1 AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCATAACTCGATTCATCACATATCGAGTTGAA
* * * * *
1762652 TCAGCAACATCTCACTCAAGGGATCAACATTTCTAGTAG-AGAGTTCATAATGAGAATAACTCAT
66 TCAGAAACATCTCACTCAAGAGATCAACATGTCCAG-AGAAGAGTTCATAATGAGAAAAACTCAT
1762716 CCGATAAGGG
130 CCGATAAGGG
* * * *
1762726 AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCATAATTCGGTTCGTCACATATGGAGTTGAA
1 AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCATAACTCGATTCATCACATATCGAGTTGAA
* ** * *
1762791 TCATAAACATCTCACTTGAGAGATCAACGTGTCCAGGGAAGAGTTCATAATGAGAAAAACTCATC
66 TCAGAAACATCTCACTCAAGAGATCAACATGTCCAGAGAAGAGTTCATAATGAGAAAAACTCATC
1762856 CGATAAGGG
131 CGATAAGGG
* * * * * * *
1762865 AGAAGAAGTTCATAAAGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCACATATGGAGTTG
1 AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCATAACTCGATT-CATCACATATCGAGTTG
1762929 GAACAATACC
Statistics
Matches: 175, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
138 5 0.03
139 154 0.88
140 16 0.09
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (139 bp):
AGAAGAAGTTCATAATGAGAATAACTTGTTCAACCATAACTCGATTCATCACATATCGAGTTGAA
TCAGAAACATCTCACTCAAGAGATCAACATGTCCAGAGAAGAGTTCATAATGAGAAAAACTCATC
CGATAAGGG
Found at i:1763916 original size:2 final size:2
Alignment explanation
Indices: 1763909--1763935 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1763899 GAATAATGAA
1763909 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1763936 TAAGAAAAAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1768465 original size:19 final size:19
Alignment explanation
Indices: 1768441--1768501 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
1768431 CAAGTCAACC
* *
1768441 TGACCCGACCCATTCACTT
1 TGACCCGACCCGTTGACTT
*
1768460 TGACCCGACCTGTTGACTT
1 TGACCCGACCCGTTGACTT
*
1768479 TGACCCGACTCGTTGACTT
1 TGACCCGACCCGTTGACTT
1768498 TGAC
1 TGAC
1768502 TTTGACCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.18, C:0.34, G:0.18, T:0.30
Consensus pattern (19 bp):
TGACCCGACCCGTTGACTT
Found at i:1770366 original size:18 final size:18
Alignment explanation
Indices: 1770343--1770403 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1770333 AAGAATCATG
*
1770343 ATATAAGAATCATAATTA
1 ATATAAAAATCATAATTA
*
1770361 ATATAATAAATCTATTTATTA
1 ATATAA-AAATC-A-TAATTA
* **
1770382 ATTTAATTATCATAATTA
1 ATATAAAAATCATAATTA
1770400 ATAT
1 ATAT
1770404 TTTATTATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 14 0.42
19 5 0.15
20 4 0.12
21 10 0.30
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATAAAAATCATAATTA
Found at i:1770548 original size:16 final size:16
Alignment explanation
Indices: 1770501--1770556 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
1770491 TTTCATCAAT
1770501 GGTAATATATAAG-TCA
1 GGTAA-ATATAAGATCA
*
1770517 GGTAAATGTTAA-ATCA
1 GGTAAAT-ATAAGATCA
*
1770533 GGTAAATATCAGATCA
1 GGTAAATATAAGATCA
*
1770549 GGTTAATA
1 GGTAAATA
1770557 ACAAGTCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (16 bp):
GGTAAATATAAGATCA
Found at i:1770618 original size:32 final size:32
Alignment explanation
Indices: 1770546--1770623 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1770536 AAATATCAGA
* * *
1770546 TCAGGTT-AATAACAAGTCGGTTCATTTACATG
1 TCAGGTTGAA-AACAAGTCAGTTCATTAACAAG
*
1770578 TCATGTTGAAAACAAGTCAAGTTCA-TAACAAG
1 TCAGGTTGAAAACAAGTC-AGTTCATTAACAAG
1770610 TCAGGTTGAAAACA
1 TCAGGTTGAAAACA
1770624 GATCGGGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 32 0.82
33 7 0.18
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (32 bp):
TCAGGTTGAAAACAAGTCAGTTCATTAACAAG
Found at i:1770623 original size:16 final size:16
Alignment explanation
Indices: 1770577--1770623 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1770567 TCATTTACAT
*
1770577 GTCATGTTGAAAACAA
1 GTCAAGTTGAAAACAA
* *
1770593 GTCAAGTTCATAACAA
1 GTCAAGTTGAAAACAA
*
1770609 GTCAGGTTGAAAACA
1 GTCAAGTTGAAAACA
1770624 GATCGGGTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (16 bp):
GTCAAGTTGAAAACAA
Found at i:1770896 original size:47 final size:49
Alignment explanation
Indices: 1770801--1770904 Score: 140
Period size: 47 Copynumber: 2.2 Consensus size: 49
1770791 ACTAGTTCAT
* * * * *
1770801 ACTCGAGTCAGGTTTTGGATCGCCATAGCTCAGGTCAAAAACAATTTTG
1 ACTCGAGTCAGGTTTCGAATCGCCACAGCGCAAGTCAAAAACAATTTTG
*
1770850 ACTCGAGTCA-GTTTCGAATC-CCACAGCGCAAGTCAAAAACAGTTTTG
1 ACTCGAGTCAGGTTTCGAATCGCCACAGCGCAAGTCAAAAACAATTTTG
1770897 ACTCGAGT
1 ACTCGAGT
1770905 TGGTTTCAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 31 0.63
48 8 0.16
49 10 0.20
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (49 bp):
ACTCGAGTCAGGTTTCGAATCGCCACAGCGCAAGTCAAAAACAATTTTG
Found at i:1771491 original size:16 final size:16
Alignment explanation
Indices: 1771468--1771528 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
1771458 TAATAAATAA
1771468 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1771484 ATGAACATAAGCGAAC
1 ACGAACATAAACGAAC
*
1771500 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1771516 ACGAACATAAACG
1 ACGAACATAAACG
1771529 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.54, C:0.21, G:0.15, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1772640 original size:14 final size:14
Alignment explanation
Indices: 1772621--1772676 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1772611 AATGAACATA
1772621 AACGAACATAATCG
1 AACGAACATAATCG
1772635 AACGAACAT-A---
1 AACGAACATAATCG
1772645 AACGAACATAATCG
1 AACGAACATAATCG
* *
1772659 AATGAACATAACCG
1 AACGAACATAATCG
1772673 AACG
1 AACG
1772677 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:1772641 original size:24 final size:24
Alignment explanation
Indices: 1772614--1772675 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1772604 ACAAATGAAT
1772614 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAATCGAAC
*
1772638 GAACATAAACGAACATAATCGAAT
1 GAACATAAACGAACATAATCGAAC
*
1772662 GAACATAACCGAAC
1 GAACATAAACGAAC
1772676 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
GAACATAAACGAACATAATCGAAC
Found at i:1773238 original size:18 final size:18
Alignment explanation
Indices: 1773212--1773246 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1773202 TTTCACAATT
*
1773212 TATTTTTAAAATTATATA
1 TATTCTTAAAATTATATA
1773230 TATTCTTAAAATTATAT
1 TATTCTTAAAATTATAT
1773247 TTAAACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTCTTAAAATTATATA
Found at i:1773255 original size:18 final size:18
Alignment explanation
Indices: 1773217--1773255 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1773207 CAATTTATTT
**
1773217 TTAAAATTATATATATTC
1 TTAAAATTATATATAAAC
*
1773235 TTAAAATTATATTTAAAC
1 TTAAAATTATATATAAAC
1773253 TTA
1 TTA
1773256 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATTATATATAAAC
Found at i:1777947 original size:27 final size:28
Alignment explanation
Indices: 1777891--1777947 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1777881 CGCGTTGCAT
*
1777891 TTCGCGTTGCGATAGTTGGAAAATCGCG
1 TTCGCATTGCGATAGTTGGAAAATCGCG
1777919 TTCGCATTGCGATAGTT-GAAAATCGCG
1 TTCGCATTGCGATAGTTGGAAAATCGCG
1777946 TT
1 TT
1777948 GCGATTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (28 bp):
TTCGCATTGCGATAGTTGGAAAATCGCG
Found at i:1778132 original size:5 final size:6
Alignment explanation
Indices: 1778093--1778129 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1778083 GACACGTATT
1778093 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1778130 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1778653 original size:6 final size:6
Alignment explanation
Indices: 1778627--1778712 Score: 151
Period size: 6 Copynumber: 14.8 Consensus size: 6
1778617 TCCGTCTCGT
1778627 GTGGT- GTGGT- GTGGT- GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1778672 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
1778713 AATACGTGTC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.19
6 65 0.81
ACGTcount: A:0.00, C:0.13, G:0.52, T:0.35
Consensus pattern (6 bp):
GTGGTC
Found at i:1785951 original size:18 final size:19
Alignment explanation
Indices: 1785903--1785951 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1785893 TTCACAATAC
1785903 ATAAGCATTTCAT-ACCATA
1 ATAA-CATTTCATAACCATA
*
1785922 ATAACA-TACATAACCATA
1 ATAACATTTCATAACCATA
1785940 A-AACATTTCATA
1 ATAACATTTCATA
1785952 TAACGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.31
18 14 0.54
19 4 0.15
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAACATTTCATAACCATA
Found at i:1786293 original size:21 final size:21
Alignment explanation
Indices: 1786269--1786356 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
1786259 GGCCCTAAGA
*
1786269 ACCATATATATGTTCCAAATG
1 ACCATATATATGTTCCAAAGG
* *
1786290 ACCAAATATAT-TTCTCGAAGG
1 ACCATATATATGTTC-CAAAGG
*
1786311 ACCGTATATATGTTCCAAAGG
1 ACCATATATATGTTCCAAAGG
* * * * *
1786332 ATCACATATAAGTCCCGAAGG
1 ACCATATATATGTTCCAAAGG
1786353 ACCA
1 ACCA
1786357 CATAGAACCC
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 3 0.06
21 46 0.88
22 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
ACCATATATATGTTCCAAAGG
Found at i:1786341 original size:42 final size:42
Alignment explanation
Indices: 1786273--1786355 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1786263 CTAAGAACCA
* ** *
1786273 TATATATGTTCCAAATGACCAAATATATTTCTCGAAGGACCG
1 TATATATGTTCCAAAGGACCAAATATAAGTCCCGAAGGACCG
* *
1786315 TATATATGTTCCAAAGGATCACATATAAGTCCCGAAGGACC
1 TATATATGTTCCAAAGGACCAAATATAAGTCCCGAAGGACC
1786356 ACATAGAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (42 bp):
TATATATGTTCCAAAGGACCAAATATAAGTCCCGAAGGACCG
Found at i:1790193 original size:18 final size:19
Alignment explanation
Indices: 1790145--1790193 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
1790135 TTCACAATAT
*
1790145 ATAAGCATTTCAT-ACCATA
1 ATAA-CATTTCATAACCACA
*
1790164 ATAACA-TACATAACCACA
1 ATAACATTTCATAACCACA
1790182 A-AACATTTCATA
1 ATAACATTTCATA
1790194 TAACGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAACATTTCATAACCACA
Found at i:1790509 original size:23 final size:23
Alignment explanation
Indices: 1790475--1790542 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1790465 AGTGCCACAT
*
1790475 AATTATCCCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
** * *
1790498 GTTTGTCCCGAAAGACCATATAG
1 AATTGTCCCGAAGGACCACATAG
* *
1790521 AATTGTCCCTAAGAACCACATA
1 AATTGTCCCGAAGGACCACATA
1790543 TATGTTCCAA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:1790559 original size:21 final size:21
Alignment explanation
Indices: 1790480--1790626 Score: 98
Period size: 21 Copynumber: 6.8 Consensus size: 21
1790470 CACATAATTA
* *
1790480 TCCCGAAGGACCACATAGGTTTG
1 TCCCAAAGGACCACATA--TATG
* *
1790503 TCCCGAAA-GACCATATAGAATTG
1 TCCC-AAAGGACCACATA-TA-TG
* *
1790526 TCCCTAAGAACCACATATATG
1 TCCCAAAGGACCACATATATG
* * *
1790547 TTCCAAATGACCAAATATATG
1 TCCCAAAGGACCACATATATG
* ***
1790568 TCCCGAAGGACTGTATATATG
1 TCCCAAAGGACCACATATATG
* *
1790589 TTCCAAAGGATCACATATATG
1 TCCCAAAGGACCACATATATG
*
1790610 TCCCGAAGGACCACATA
1 TCCCAAAGGACCACATA
1790627 GAACTCTCGA
Statistics
Matches: 93, Mismatches: 28, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
21 62 0.67
22 4 0.04
23 25 0.27
24 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
TCCCAAAGGACCACATATATG
Found at i:1790586 original size:42 final size:42
Alignment explanation
Indices: 1790540--1790620 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1790530 TAAGAACCAC
*
1790540 ATATATGTTCCAAATGACCAAATATATGTCCCGAAGGACTGT
1 ATATATGTTCCAAAGGACCAAATATATGTCCCGAAGGACTGT
* *
1790582 ATATATGTTCCAAAGGATCACATATATGTCCCGAAGGAC
1 ATATATGTTCCAAAGGACCAAATATATGTCCCGAAGGAC
1790621 CACATAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (42 bp):
ATATATGTTCCAAAGGACCAAATATATGTCCCGAAGGACTGT
Found at i:1797161 original size:21 final size:21
Alignment explanation
Indices: 1797137--1797189 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1797127 AGAATAGAGG
1797137 GTATCGGTACTTCTAAAGGGA
1 GTATCGGTACTTCTAAAGGGA
1797158 GTATCGGTACTTCTAAAGGGA
1 GTATCGGTACTTCTAAAGGGA
1797179 GTATCGGTACT
1 GTATCGGTACT
1797190 ACATTTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTACTTCTAAAGGGA
Found at i:1797264 original size:20 final size:21
Alignment explanation
Indices: 1797234--1797273 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1797224 AGCCGTTGGG
1797234 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
1797255 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
1797274 CTATACAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:1809976 original size:21 final size:19
Alignment explanation
Indices: 1809952--1809990 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1809942 GACACGATCA
1809952 TTATCTAATTGGAGATTAAAT
1 TTATCTAATT-GA-ATTAAAT
*
1809973 TTATTTAATTGAATTAAA
1 TTATCTAATTGAATTAAA
1809991 ATAAAGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (19 bp):
TTATCTAATTGAATTAAAT
Found at i:1811548 original size:32 final size:32
Alignment explanation
Indices: 1811512--1811582 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
1811502 TACATAACAT
* *
1811512 ATATCACGTCACTACTCTGGATTATGTGGTAC
1 ATATCACGTCACCACTCTGGATTATGTGGCAC
* *
1811544 ATATCACGTCACCACTTTGGGTTATGTGGCAC
1 ATATCACGTCACCACTCTGGATTATGTGGCAC
1811576 ATATCAC
1 ATATCAC
1811583 ATTAGCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (32 bp):
ATATCACGTCACCACTCTGGATTATGTGGCAC
Found at i:1813290 original size:13 final size:13
Alignment explanation
Indices: 1813272--1813314 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
1813262 TTTAAAAGTA
1813272 TTGCATCATATTC
1 TTGCATCATATTC
1813285 TTGCATCATATTC
1 TTGCATCATATTC
1813298 TTGCATCATATTC
1 TTGCATCATATTC
1813311 TTGC
1 TTGC
1813315 TTGACTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (13 bp):
TTGCATCATATTC
Found at i:1815985 original size:20 final size:21
Alignment explanation
Indices: 1815939--1815988 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1815929 TGGTTCAAAG
1815939 GATCGATCCCACTAAGAAAAA
1 GATCGATCCCACTAAGAAAAA
** *
1815960 GTATCGATCCC-CTTGGAAAAT
1 G-ATCGATCCCACTAAGAAAAA
1815981 GATCGATC
1 GATCGATC
1815989 ACTTGGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 9 0.36
22 9 0.36
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
GATCGATCCCACTAAGAAAAA
Found at i:1817750 original size:13 final size:13
Alignment explanation
Indices: 1817732--1817756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1817722 TTATGAATTT
1817732 AAAATTTTTAAAG
1 AAAATTTTTAAAG
1817745 AAAATTTTTAAA
1 AAAATTTTTAAA
1817757 CCAATTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAAATTTTTAAAG
Found at i:1819901 original size:23 final size:23
Alignment explanation
Indices: 1819874--1819923 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1819864 ATTTGCTTTG
1819874 TATTA-AAAACTATATCTTATTAT
1 TATTATAAAACTATAT-TTATTAT
* **
1819897 TATTATATATGTATATTTATTAT
1 TATTATAAAACTATATTTATTAT
1819920 TATT
1 TATT
1819924 TTCTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTATAAAACTATATTTATTAT
Found at i:1819945 original size:22 final size:21
Alignment explanation
Indices: 1819884--1819950 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
1819874 TATTAAAAAC
* *
1819884 TATATCTTATTATTATTATATATG
1 TATAT-TTATTATTATT-TCT-TT
1819908 TATATTTATTATTATTTTCTTT
1 TATATTTATTATTA-TTTCTTT
1819930 TATATTTATT-TCTATTTCTTT
1 TATATTTATTAT-TATTTCTTT
1819951 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.21
22 13 0.33
23 11 0.28
24 7 0.18
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.67
Consensus pattern (21 bp):
TATATTTATTATTATTTCTTT
Found at i:1823408 original size:23 final size:23
Alignment explanation
Indices: 1823363--1823425 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1823353 ATACCTTGCA
*
1823363 TTTTATA-TTT-CT-TGTTTATT
1 TTTTATATTTTCCTATGTTTAGT
1823383 TTTTATATTTTTCC-ATGTTTAGT
1 TTTTATA-TTTTCCTATGTTTAGT
1823406 TTTTATATTTTCCTATGTTT
1 TTTTATATTTTCCTATGTTT
1823426 TTACATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 7 0.19
22 9 0.24
23 21 0.57
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (23 bp):
TTTTATATTTTCCTATGTTTAGT
Found at i:1830083 original size:20 final size:21
Alignment explanation
Indices: 1830016--1830085 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
1830006 ATATATGGAG
**
1830016 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATAATTTAA
* *
1830037 -TAATCTCGAATATTTAATTTCAA
1 TTAAT-T-AAATATATAATTT-AA
1830060 TTAATTAAATATAT-ATTTAA
1 TTAATTAAATATATAATTTAA
1830080 TTAATT
1 TTAATT
1830086 TGAAATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 12 0.31
21 5 0.13
22 15 0.38
23 3 0.08
24 4 0.10
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (21 bp):
TTAATTAAATATATAATTTAA
Found at i:1830205 original size:90 final size:90
Alignment explanation
Indices: 1830047--1830222 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 90
1830037 TAATCTCGAA
* *
1830047 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1830112 TAGGGTAACTTGGACATAAAATGAT
66 TAGGGTAACTTGGACATAAAATGAT
1830137 TATTAAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATGAAAA-CCCTAATATGA
1 TATTAAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGA
*
1830201 TTAGGGTAACTTGGATATAAAA
65 TTAGGGTAACTTGGACATAAAA
1830223 GGGTGTGTTA
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 78 0.95
91 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTGGACATAAAATGAT
Found at i:1830758 original size:2 final size:2
Alignment explanation
Indices: 1830751--1830814 Score: 119
Period size: 2 Copynumber: 31.5 Consensus size: 2
1830741 ACAACGTATG
1830751 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
1830793 TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA T-A TA T
1830815 GTTTGTTTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1835138 original size:14 final size:14
Alignment explanation
Indices: 1835119--1835145 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1835109 AATCAGAACT
1835119 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
1835133 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1835146 TAGGCGACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:1836962 original size:15 final size:15
Alignment explanation
Indices: 1836936--1836980 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
1836926 ATGTCGTTAC
1836936 ATTATAT-AATGTAT
1 ATTATATAAATGTAT
1836950 -TTATATAACATGTTAT
1 ATTATATAA-ATG-TAT
1836966 ATTATATAAATGTAT
1 ATTATATAAATGTAT
1836981 CTATTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.22
14 1 0.04
15 6 0.22
16 6 0.22
17 8 0.30
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (15 bp):
ATTATATAAATGTAT
Found at i:1836986 original size:17 final size:17
Alignment explanation
Indices: 1836931--1836978 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1836921 CTTTAATGTC
*
1836931 GTTACATTATAT-A-AT
1 GTTATATTATATAACAT
1836946 G-TAT-TTATATAACAT
1 GTTATATTATATAACAT
1836961 GTTATATTATATAA-AT
1 GTTATATTATATAACAT
1836977 GT
1 GT
1836979 ATCTATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.21
14 3 0.11
15 4 0.14
16 7 0.25
17 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (17 bp):
GTTATATTATATAACAT
Found at i:1838138 original size:2 final size:2
Alignment explanation
Indices: 1838131--1838163 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1838121 TTACCCATTA
*
1838131 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1838164 AGTTACCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1838515 original size:22 final size:23
Alignment explanation
Indices: 1838473--1838515 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
1838463 ATTTTATTTT
*
1838473 TACCTTATTTTATTTATTTTCAG
1 TACCTTATTTTATATATTTTCAG
1838496 TACCTT-TTTTA-ATATGTTTC
1 TACCTTATTTTATATAT-TTTC
1838516 TTGACCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (23 bp):
TACCTTATTTTATATATTTTCAG
Found at i:1845172 original size:16 final size:16
Alignment explanation
Indices: 1845151--1845182 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1845141 ATCAAAATAC
1845151 GAGACAAAAAGTGAGG
1 GAGACAAAAAGTGAGG
*
1845167 GAGACAAAAGGTGAGG
1 GAGACAAAAAGTGAGG
1845183 ATACGATCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.41, T:0.06
Consensus pattern (16 bp):
GAGACAAAAAGTGAGG
Found at i:1845884 original size:18 final size:18
Alignment explanation
Indices: 1845862--1845898 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1845852 AAATTAAATT
1845862 TATATTATAAATAATATTAA
1 TATA-TATAAA-AATATTAA
1845882 TATATATAAAAATATTA
1 TATATATAAAAATATTA
1845899 TTTATAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATATAAAAATATTAA
Found at i:1845904 original size:15 final size:16
Alignment explanation
Indices: 1845857--1845904 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
1845847 TTTTAAAATT
1845857 AAAT-TTATATTATAA
1 AAATATTATATTATAA
1845872 ATAATATTAATATATATAA
1 A-AATATT-ATAT-TATAA
1845891 AAATATTAT-TTATA
1 AAATATTATATTATA
1845905 GTGTTAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 4 0.14
18 10 0.34
19 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTATATTATAA
Found at i:1846655 original size:30 final size:29
Alignment explanation
Indices: 1846583--1846651 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
1846573 GGGATTATGA
*
1846583 TTTAGG-ATTTAGGATTTTTTTGGGGGAT
1 TTTAGGAATTTAGGATTTTTTTGGGGAAT
* **
1846611 TTCTGGGAATTTAGGATTTTTTTTTGGAAT
1 TT-TAGGAATTTAGGATTTTTTTGGGGAAT
1846641 TTTAGGAATTT
1 TTTAGGAATTT
1846652 TAGGGGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 11 0.32
30 21 0.62
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.52
Consensus pattern (29 bp):
TTTAGGAATTTAGGATTTTTTTGGGGAAT
Found at i:1846726 original size:11 final size:11
Alignment explanation
Indices: 1846682--1846757 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
1846672 TTTTTAATTG
*
1846682 TAAATCATATA
1 TAAATAATATA
*
1846693 TTAATATATATA
1 TAAATA-ATATA
*
1846705 TATATTAATATA
1 TA-AATAATATA
*
1846717 TAAATAATATT
1 TAAATAATATA
**
1846728 TTTAT-A-ATA
1 TAAATAATATA
1846737 TAAAT-ATATTA
1 TAAATAATA-TA
1846748 TAAATAATAT
1 TAAATAATAT
1846758 TTTTATATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 22 0.45
12 16 0.33
13 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATAATATA
Found at i:1846754 original size:20 final size:20
Alignment explanation
Indices: 1846694--1846757 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1846684 AATCATATAT
*
1846694 TAATATATATATA-TATTAA
1 TAATATAAATATATTATTAA
*
1846713 T-ATATAAATAATATT-TTTA
1 TAATATAAAT-ATATTATTAA
*
1846732 TAATATAAATATATTATAAA
1 TAATATAAATATATTATTAA
1846752 TAATAT
1 TAATAT
1846758 TTTTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.19
19 13 0.35
20 17 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATAAATATATTATTAA
Found at i:1847070 original size:15 final size:15
Alignment explanation
Indices: 1847050--1847115 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
1847040 TATATTAATG
1847050 TATATATAAAATTTT
1 TATATATAAAATTTT
* *
1847065 TATATATTATATTTT
1 TATATATAAAATTTT
*
1847080 TATA-ATATTAATATTT
1 TATATATA-AAAT-TTT
* *
1847096 TATAAATAATATTTT
1 TATATATAAAATTTT
1847111 TATAT
1 TATAT
1847116 GTTAATTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 2 0.05
15 26 0.65
16 9 0.22
17 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATATAAAATTTT
Found at i:1847087 original size:16 final size:16
Alignment explanation
Indices: 1847060--1847114 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 16
1847050 TATATATAAA
1847060 ATTTTTAT-ATATTAT
1 ATTTTTATAATATTAT
1847075 ATTTTTATAATATTA-
1 ATTTTTATAATATTAT
*
1847090 ATATTTTATAA-ATAAT
1 AT-TTTTATAATATTAT
1847106 ATTTTTATA
1 ATTTTTATA
1847115 TGTTAATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 20 0.56
16 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTTATAATATTAT
Found at i:1847107 original size:14 final size:14
Alignment explanation
Indices: 1847062--1847110 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1847052 TATATAAAAT
* *
1847062 TTTTATATATTATA
1 TTTTATAAATAATA
1847076 TTTTTATAATATTAATA
1 -TTTTATAA-A-TAATA
1847093 TTTTATAAATAATA
1 TTTTATAAATAATA
1847107 TTTT
1 TTTT
1847111 TATATGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.30
15 8 0.27
16 9 0.30
17 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTATAAATAATA
Found at i:1847200 original size:350 final size:346
Alignment explanation
Indices: 1846428--1847437 Score: 1283
Period size: 350 Copynumber: 2.9 Consensus size: 346
1846418 TAATCGATCG
** *
1846428 TCAAACATTGAATGTGAAATGTTCCATACGAACCATGAATGACGACCGATCGACTAATGAATGTC
1 TCAAACACCGAATGTGAAATGTTCCATACGAACCATGAATGACGACCGATCGACGAATGAATGTC
*
1846493 GAGTGACGTACACAATGAGAAGAGAAGACTTCAGTGTGTCGACAACGGTGTGCAATCAACGATGA
66 GAGTGACGTACACAATGAGAAGAGGAGACTTCAGTGTGTCGACAACGGTGTGCAATCAACGATGA
* * * *
1846558 TGGTGGGTTAATTAAGGGATTATGATTTAGGATTTAGGATTTTTTTGGGGGATTTCTGGGAATTT
131 TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGA-TTTTTT-GGGGATTTATGGGAATTT
* * * *
1846623 AGGATTTTTTTTTGGAATTTTAGGAATTTTAGGGG--GTTTAGAAAATTATTTTTTAATTGTAAA
194 A--A-TATTTTTT-GAATTTTAGGAATTTTAGGGGTTCTTTAGAAAATAATTTTTTAATTATAAA
*
1846686 TCATATAT-TAATATATATATATATTAATATATAAATAATATTTTTATAATATAAATATATTATA
255 TCATATATATAATATATATATATATAAATATATAAATAATATTTTTATAATATAAATATATTATA
*
1846750 AATAATATTTTTATATATTAATTATCG
320 AATAATATTTTTATATATTAATTATCA
* * * *
1846777 TCAAACACCGAATATGAAATGTTCCATACGAACCATGAAGGACGACCGATCGATGATTGAATGTC
1 TCAAACACCGAATGTGAAATGTTCCATACGAACCATGAATGACGACCGATCGACGAATGAATGTC
** * * *
1846842 GAGTGACGTTTACAATGAGAAGAGGAGACTTCAGTGTGTCGATAACGATATGCAATCAACGATGA
66 GAGTGACGTACACAATGAGAAGAGGAGACTTCAGTGTGTCGACAACGGTGTGCAATCAACGATGA
1846907 TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGATTTTTTGGGGATTTATGGGAATTTAA
131 TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGATTTTTTGGGGATTTATGGGAATTTAA
*
1846972 TATTTTTTAGAATTTTAGGAATTTTAGGGGTTCTTTAGAAAATCAATTTTTTAATTATAATTCAT
196 TATTTTTT-GAATTTTAGGAATTTTAGGGGTTCTTTAGAAAAT-AATTTTTTAATTATAAATCAT
* * * * * * *
1847037 ATATATATTA-ATGTATATATAAAATTTTTATATATTATATTTTTATAATATTAATATTTTATAA
259 ATATATAATATATATATATAT-AAA--TATATAAATAATATTTTTATAATATAAATATATTATAA
*
1847101 ATAATATTTTTATATGTTAATTATCA
321 ATAATATTTTTATATATTAATTATCA
* * * * * *
1847127 TCAAACACCGAATGTGAAATGTTCCATATGAATCATGAATGACAATCGATCGAGGAATGAAAGTC
1 TCAAACACCGAATGTGAAATGTTCCATACGAACCATGAATGACGACCGATCGACGAATGAATGTC
* * * * * * *
1847192 GAGTGACGTGCATAGTGAGAAGAGGAGACTTCAATGTGTTGACAATGGTGTGCAATCAATGATGA
66 GAGTGACGTACACAATGAGAAGAGGAGACTTCAGTGTGTCGACAACGGTGTGCAATCAACGATGA
** *
1847257 TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGATTTTTTTAGGATATATGGGAATTTAA
131 TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGATTTTTTGGGGATTTATGGGAATTTAA
* *
1847322 GA---TTT---TTTTA-GAATTTTAGGGGTTTTTTAGAAAATTAA-TTTTTAATTATAAATCATA
196 TATTTTTTGAATTTTAGGAATTTTAGGGGTTCTTTAGAAAA-TAATTTTTTAATTATAAATCATA
* * ** *
1847379 TATA-AACATATAAATAATATTTTATATATATATTAAT-TTTTTATAATATAAATAATATT
260 TATATAATATATATAT-ATA-TAAATATATA-AATAATATTTTTATAATATAAAT-ATATT
1847438 TTAGTTTTAA
Statistics
Matches: 577, Mismatches: 71, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
340 22 0.04
341 33 0.06
342 29 0.05
343 7 0.01
344 28 0.05
345 1 0.00
346 10 0.02
347 52 0.09
348 12 0.02
349 153 0.27
350 230 0.40
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (346 bp):
TCAAACACCGAATGTGAAATGTTCCATACGAACCATGAATGACGACCGATCGACGAATGAATGTC
GAGTGACGTACACAATGAGAAGAGGAGACTTCAGTGTGTCGACAACGGTGTGCAATCAACGATGA
TGGTGGGTGAATTTAGGGATTATGGTTTAGGATTTAGGATTTTTTGGGGATTTATGGGAATTTAA
TATTTTTTGAATTTTAGGAATTTTAGGGGTTCTTTAGAAAATAATTTTTTAATTATAAATCATAT
ATATAATATATATATATATAAATATATAAATAATATTTTTATAATATAAATATATTATAAATAAT
ATTTTTATATATTAATTATCA
Found at i:1847415 original size:19 final size:19
Alignment explanation
Indices: 1847386--1847440 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1847376 ATATATAAAC
1847386 ATATAAATAATATTTTAT-
1 ATATAAATAATATTTTATA
* *
1847404 ATATATATTAATTTTTTATA
1 ATATA-AATAATATTTTATA
1847424 ATATAAATAATATTTTA
1 ATATAAATAATATTTTA
1847441 GTTTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATAAATAATATTTTATA
Found at i:1849357 original size:76 final size:77
Alignment explanation
Indices: 1849221--1849377 Score: 192
Period size: 76 Copynumber: 2.1 Consensus size: 77
1849211 AATCCTAATC
* * * * *
1849221 TTCTCTCAATCCTCTCACCTTTTTCGACAAGTTTTAGGATTCTGGAACGATTCTTTTCTTTGGA-
1 TTCTCTCAATCCTCTCACCTTTTTCAACAAGTTTTAGGATTCTAGAACCATTCCTGTCTTTGGAG
*
1849285 TTTTATAACAAT
66 TTTAATAACAAT
* * * *
1849297 TTCTCTCAATCCTCTCACTTTTTTCAACAA-TTTCTAGGATTTTATAACCATTCCTGTCTTTTGA
1 TTCTCTCAATCCTCTCACCTTTTTCAACAAGTTT-TAGGATTCTAGAACCATTCCTGTCTTTGGA
*
1849361 GTTTAATAACAGT
65 GTTTAATAACAAT
1849374 TTCT
1 TTCT
1849378 TATCAAGCGT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
75 3 0.04
76 51 0.75
77 14 0.21
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (77 bp):
TTCTCTCAATCCTCTCACCTTTTTCAACAAGTTTTAGGATTCTAGAACCATTCCTGTCTTTGGAG
TTTAATAACAAT
Found at i:1850173 original size:36 final size:36
Alignment explanation
Indices: 1850127--1850195 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1850117 AAAATAATCC
*
1850127 ACGTCATCACTTTGTTAATGAGAAAATAGTGGACAA
1 ACGTCATCACTTTGTTAATAAGAAAATAGTGGACAA
*
1850163 ACGTCGTCACTTTGTTAATAAGAAAATAGTGGA
1 ACGTCATCACTTTGTTAATAAGAAAATAGTGGA
1850196 GTGATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
ACGTCATCACTTTGTTAATAAGAAAATAGTGGACAA
Found at i:1851425 original size:17 final size:17
Alignment explanation
Indices: 1851403--1851435 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1851393 TCTGTAACTG
1851403 TTTTTTATG-ATGCCAAA
1 TTTTTTA-GCATGCCAAA
1851420 TTTTTTAGCATGCCAA
1 TTTTTTAGCATGCCAA
1851436 TGAAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTTTTAGCATGCCAAA
Found at i:1851712 original size:21 final size:22
Alignment explanation
Indices: 1851681--1851724 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1851671 ACTGAACCAA
1851681 AAAATATAGATGATAAAGAAAC
1 AAAATATAGATGATAAAGAAAC
**
1851703 AAAA-ATAGATGATGGAGAAAC
1 AAAATATAGATGATAAAGAAAC
1851724 A
1 A
1851725 TAGATATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.61, C:0.05, G:0.18, T:0.16
Consensus pattern (22 bp):
AAAATATAGATGATAAAGAAAC
Found at i:1869375 original size:14 final size:14
Alignment explanation
Indices: 1869338--1869376 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1869328 AGTTTAACCC
*
1869338 GACCCATTAACTTT
1 GACCCATTGACTTT
1869352 GACCCATTGACTTT
1 GACCCATTGACTTT
*
1869366 GACCCGTTGAC
1 GACCCATTGAC
1869377 CGTTACTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (14 bp):
GACCCATTGACTTT
Found at i:1871671 original size:15 final size:14
Alignment explanation
Indices: 1871641--1871682 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1871631 TACCAGTTCT
1871641 CAACATTTTTTATA
1 CAACATTTTTTATA
*
1871655 CAACATTTTTTGCTA
1 CAACATTTTTT-ATA
1871670 CAACATTTATTTA
1 CAACATTT-TTTA
1871683 CCATGTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.46
15 10 0.42
16 3 0.12
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (14 bp):
CAACATTTTTTATA
Found at i:1873741 original size:16 final size:17
Alignment explanation
Indices: 1873710--1873750 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1873700 ACATTTTAGA
* *
1873710 AAAGTCAACTTTTGGTT
1 AAAGTCAACTTATGGTC
1873727 AAAGTCAAC-TATGGTC
1 AAAGTCAACTTATGGTC
1873743 AAAGTCAA
1 AAAGTCAA
1873751 TAGGTCAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (17 bp):
AAAGTCAACTTATGGTC
Found at i:1879072 original size:15 final size:16
Alignment explanation
Indices: 1879050--1879086 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
1879040 TTTGTTTATT
1879050 TGTTTTAATAAACATA
1 TGTTTTAATAAACATA
1879066 T-TTTTAATAAACATA
1 TGTTTTAATAAACATA
1879081 TGTTTT
1 TGTTTT
1879087 TACAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (16 bp):
TGTTTTAATAAACATA
Found at i:1879952 original size:20 final size:20
Alignment explanation
Indices: 1879922--1879974 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1879912 AAGCTAATTA
1879922 AGCCA-CGTTGACCGAGTTG
1 AGCCACCGTTGACCGAGTTG
** *
1879941 AGCCGTCGTTGACTGAGTTG
1 AGCCACCGTTGACCGAGTTG
1879961 AGCCACCGTTGACC
1 AGCCACCGTTGACC
1879975 AACCGTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (20 bp):
AGCCACCGTTGACCGAGTTG
Found at i:1883719 original size:17 final size:18
Alignment explanation
Indices: 1883685--1883721 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1883675 ACAGATGATC
1883685 TACCATTTTACGAAAATAA
1 TACCATTTTAC-AAAATAA
1883704 TACCATTTTA-AAAATAA
1 TACCATTTTACAAAATAA
1883721 T
1 T
1883722 TACAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (18 bp):
TACCATTTTACAAAATAA
Found at i:1883737 original size:29 final size:29
Alignment explanation
Indices: 1883692--1883938 Score: 311
Period size: 29 Copynumber: 8.6 Consensus size: 29
1883682 ATCTACCATT
*
1883692 TTACGAAAATAAT-ACCATTTTAAAAATAA
1 TTACAAAAAT-ATCACCATTTTAAAAATAA
1883721 TTACAAAAATATCACCATTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* * *
1883750 TTACAAAAATAGC-GCTTTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* * *
1883778 TTACGAAAATAACATCATTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
*
1883807 TTACAAAAATATCACCTTTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* *
1883836 TTACTAAAATAACACCATTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* *
1883865 TTACGAAAATATCA-CATTTTTAAAAGTAA
1 TTACAAAAATATCACCA-TTTTAAAAATAA
* *
1883894 TTACTAAAATATGACCATTTTAAAAATAA
1 TTACAAAAATATCACCATTTTAAAAATAA
* *
1883923 TTACTAAAATAACACC
1 TTACAAAAATATCACC
1883939 CAGTCAACGG
Statistics
Matches: 191, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
28 28 0.15
29 161 0.84
30 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACAAAAATATCACCATTTTAAAAATAA
Done.