Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 13 of 24
Found at i:1755230 original size:31 final size:33
Alignment explanation
Indices: 1755178--1755239 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1755168 TTCCCATAAG
*
1755178 ATGAAATTTTGGCTTTTTTAAA-ATTTACTACA
1 ATGAAATTTTGGCTTTTTTAAAGAATTACTACA
1755210 ATGAAATTTTGGC-TTTTTAAAGAATTACTA
1 ATGAAATTTTGGCTTTTTTAAAGAATTACTA
1755240 AATTGTAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (33 bp):
ATGAAATTTTGGCTTTTTTAAAGAATTACTACA
Found at i:1755400 original size:6 final size:6
Alignment explanation
Indices: 1755389--1755425 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1755379 TTAAATTTGT
* *
1755389 TTTATA TTTATA TTTACA TTTATA GTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
1755426 ATAATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:1757776 original size:21 final size:21
Alignment explanation
Indices: 1757752--1757791 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1757742 TATTATTATT
*
1757752 TAAAT-TTAATTATACAATATA
1 TAAATATTAA-TATAAAATATA
1757773 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1757792 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1758610 original size:16 final size:16
Alignment explanation
Indices: 1758571--1758617 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1758561 TGTATAAAAA
1758571 ATAAATTTTATATGTTAAT
1 ATAAATTTTA-A--TTAAT
*
1758590 GTAAATTTTAATTAAT
1 ATAAATTTTAATTAAT
1758606 ATAAATTTTAAT
1 ATAAATTTTAAT
1758618 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 16 0.62
18 1 0.04
19 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATAAATTTTAATTAAT
Found at i:1759853 original size:13 final size:13
Alignment explanation
Indices: 1759832--1759863 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1759822 TGATATTTTA
*
1759832 ATAAATTAATAAT
1 ATAATTTAATAAT
1759845 ATAATTTAATAAT
1 ATAATTTAATAAT
1759858 ATAATT
1 ATAATT
1759864 ATACTCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTAATAAT
Found at i:1760794 original size:14 final size:14
Alignment explanation
Indices: 1760777--1760826 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
1760767 AAATATATTA
1760777 ATATTTTAAAATTT
1 ATATTTTAAAATTT
*
1760791 ATATAATATAAATTATTT
1 ATAT--TTTAAA--ATTT
1760809 ATATTTTAAAATTT
1 ATATTTTAAAATTT
1760823 ATAT
1 ATAT
1760827 AAATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.40
16 10 0.33
18 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTTTAAAATTT
Found at i:1760816 original size:32 final size:34
Alignment explanation
Indices: 1760763--1760844 Score: 123
Period size: 32 Copynumber: 2.5 Consensus size: 34
1760753 TAATTAAATG
1760763 ATATAAATATATTAATATTTTAAAATTTATAT-A
1 ATATAAATATATTAATATTTTAAAATTTATATAA
*
1760796 ATATAAAT-TATTTATATTTTAAAATTTATATAA
1 ATATAAATATATTAATATTTTAAAATTTATATAA
* *
1760829 ATATAAAAATTTTAAT
1 ATATAAATATATTAAT
1760845 CACAATTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 22 0.51
33 16 0.37
34 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATATAAATATATTAATATTTTAAAATTTATATAA
Found at i:1760824 original size:18 final size:18
Alignment explanation
Indices: 1760767--1760824 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 18
1760757 TAAATGATAT
* *
1760767 AAATATATTAATATTTTA
1 AAATTTATTTATATTTTA
* *
1760785 AAATTTA--TATAATAT-
1 AAATTTATTTATATTTTA
1760800 AAA-TTATTTATATTTTA
1 AAATTTATTTATATTTTA
1760817 AAATTTAT
1 AAATTTAT
1760825 ATAAATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 11 0.37
17 3 0.10
18 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATTTATTTATATTTTA
Found at i:1760827 original size:16 final size:16
Alignment explanation
Indices: 1760777--1760827 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1760767 AAATATATTA
1760777 ATATTTTAAAATTTAT
1 ATATTTTAAAATTTAT
* * *
1760793 ATAATAT-AAATTATTT
1 ATATTTTAAAATT-TAT
1760809 ATATTTTAAAATTTAT
1 ATATTTTAAAATTTAT
1760825 ATA
1 ATA
1760828 AATATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 5 0.19
16 17 0.63
17 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTAAAATTTAT
Found at i:1760837 original size:18 final size:17
Alignment explanation
Indices: 1760784--1760840 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1760774 TTAATATTTT
1760784 AAAATTTATATAATATA
1 AAAATTTATATAATATA
* *
1760801 AATTATTTATAT--T-TT
1 AA-AATTTATATAATATA
1760816 AAAATTTATATAAATATA
1 AAAATTTATAT-AATATA
1760834 AAAATTT
1 AAAATTT
1760841 TAATCACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 1 0.03
17 3 0.10
18 16 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTATATAATATA
Found at i:1761464 original size:17 final size:19
Alignment explanation
Indices: 1761442--1761477 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1761432 TGTATTAGTT
1761442 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
1761459 ATATAAATTATTAAATATA
1 ATATAAATTATTAAATATA
1761478 TTAAAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:1762996 original size:3 final size:3
Alignment explanation
Indices: 1762988--1763018 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1762978 GCTATTCTAA
1762988 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1763019 ACTAACGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1763292 original size:53 final size:54
Alignment explanation
Indices: 1763212--1763314 Score: 165
Period size: 53 Copynumber: 1.9 Consensus size: 54
1763202 CTTGTTCACC
*
1763212 TTACATCTTGACTTCATATTCTGTGAC-AAGAAAATTTGTTAAGAAAAGTAACT
1 TTACATCTTGACTTCATATTCTGTGACAAAAAAAATTTGTTAAGAAAAGTAACT
*
1763265 TTACATCTTGACTTCATATTAC-GTGACAAAAAAAATTTGTTAATAAAAGT
1 TTACATCTTGACTTCATATT-CTGTGACAAAAAAAATTTGTTAAGAAAAGT
1763315 CTTTGGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 25 0.54
54 21 0.46
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (54 bp):
TTACATCTTGACTTCATATTCTGTGACAAAAAAAATTTGTTAAGAAAAGTAACT
Found at i:1764969 original size:17 final size:17
Alignment explanation
Indices: 1764949--1764987 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1764939 AATTTAAATT
1764949 TTAAAATTAATTAATAA
1 TTAAAATTAATTAATAA
* *
1764966 TTAAATTTATTTAATAA
1 TTAAAATTAATTAATAA
*
1764983 GTAAA
1 TTAAA
1764988 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAAATTAATTAATAA
Found at i:1765785 original size:18 final size:19
Alignment explanation
Indices: 1765748--1765787 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1765738 GTTTTTACTT
* *
1765748 AATTCATTTTTACATATTA
1 AATTAATTTTTAAATATTA
1765767 AATTAATTTTTAAAT-TTA
1 AATTAATTTTTAAATATTA
1765785 AAT
1 AAT
1765788 AAACAACTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTAATTTTTAAATATTA
Found at i:1767260 original size:13 final size:14
Alignment explanation
Indices: 1767243--1767295 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1767233 CACCCAATTC
1767243 ATTATTTTAATTT-
1 ATTATTTTAATTTA
* *
1767256 TTTATTTTTATTTA
1 ATTATTTTAATTTA
*
1767270 AATATTTTAATTTA
1 ATTATTTTAATTTA
1767284 ATATATATTTAA
1 AT-TAT-TTTAA
1767296 ACATAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 11 0.35
14 12 0.39
15 3 0.10
16 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTTTAATTTA
Found at i:1768087 original size:17 final size:18
Alignment explanation
Indices: 1768065--1768098 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1768055 TCGGGCTATC
1768065 TATCTAAG-TTAAAAGTT
1 TATCTAAGTTTAAAAGTT
1768082 TATCTAAGTTTAAAAGT
1 TATCTAAGTTTAAAAGT
1768099 ATATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
TATCTAAGTTTAAAAGTT
Found at i:1768141 original size:14 final size:15
Alignment explanation
Indices: 1768111--1768157 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
1768101 ATTTAATATT
*
1768111 TAAAAATATT-TGAA
1 TAAAAATATTAAGAA
1768125 TAAAAATATTAAG-A
1 TAAAAATATTAAGAA
* *
1768139 TAAAAAAATTAAAAA
1 TAAAAATATTAAGAA
1768154 TAAA
1 TAAA
1768158 TAATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 22 0.79
15 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (15 bp):
TAAAAATATTAAGAA
Found at i:1772814 original size:104 final size:104
Alignment explanation
Indices: 1772634--1772846 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 104
1772624 TAACCGTCAT
* * *
1772634 ATGCTGGAATGGGAACACCAGTAAGAAGTTACATGGTCTAACTCTACTTATGCTACATTTGTATG
1 ATGCTGGAATGGCAACACCACTAAGAAGTTACATGGTCTAACTCTACTTATGCTACATTTGCATG
*
1772699 GTTTCCACATGCAAGATTAATAAAAAATGCTTGATCCAG
66 GTTTCCACATGCAAGAATAATAAAAAATGCTTGATCCAG
* *
1772738 ATGCTGGAATGGCAACACCACTGAGAAGTTACATGGTCTAACTCTACTTATGCTACATTTGCATT
1 ATGCTGGAATGGCAACACCACTAAGAAGTTACATGGTCTAACTCTACTTATGCTACATTTGCATG
*
1772803 GTTTCCACATGCAAGAATAATAAAGAATGCTTGATCCAG
66 GTTTCCACATGCAAGAATAATAAAAAATGCTTGATCCAG
1772842 ATGCT
1 ATGCT
1772847 ATACACTCTA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (104 bp):
ATGCTGGAATGGCAACACCACTAAGAAGTTACATGGTCTAACTCTACTTATGCTACATTTGCATG
GTTTCCACATGCAAGAATAATAAAAAATGCTTGATCCAG
Found at i:1775221 original size:12 final size:12
Alignment explanation
Indices: 1775204--1775230 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1775194 GATTTTGATC
1775204 CGATTTCTTCCA
1 CGATTTCTTCCA
1775216 CGATTTCTTCCA
1 CGATTTCTTCCA
1775228 CGA
1 CGA
1775231 AGAGATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.37
Consensus pattern (12 bp):
CGATTTCTTCCA
Found at i:1776653 original size:13 final size:13
Alignment explanation
Indices: 1776635--1776660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1776625 TAAATAAAAC
1776635 TTTTTTTAAATTT
1 TTTTTTTAAATTT
1776648 TTTTTTTAAATTT
1 TTTTTTTAAATTT
1776661 AAAATTATTG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTAAATTT
Found at i:1776721 original size:2 final size:2
Alignment explanation
Indices: 1776714--1776762 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1776704 ACACTTGCTT
1776714 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
1776756 TA TA TA T
1 TA TA TA T
1776763 TCCCTTTGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1777309 original size:22 final size:24
Alignment explanation
Indices: 1777271--1777316 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1777261 AATATTTTAA
1777271 TTTTATTAAGTTATATAACTAAAT
1 TTTTATTAAGTTATATAACTAAAT
*
1777295 TTTTATT-A-TTATATAATTAAAT
1 TTTTATTAAGTTATATAACTAAAT
1777317 CAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTATTAAGTTATATAACTAAAT
Found at i:1777382 original size:13 final size:13
Alignment explanation
Indices: 1777366--1777400 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1777356 TTAATTATTT
*
1777366 TAATTTTATTAAA
1 TAATTTTAATAAA
1777379 TAATTTTAATAAA
1 TAATTTTAATAAA
*
1777392 AAATTTTAA
1 TAATTTTAA
1777401 CTTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTTTAATAAA
Found at i:1782879 original size:23 final size:23
Alignment explanation
Indices: 1782853--1782896 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1782843 ATCGTTCAAC
1782853 ATGACTCAAATCTAAGGGAAACA
1 ATGACTCAAATCTAAGGGAAACA
1782876 ATGACTCAAATCTAAGGGAAA
1 ATGACTCAAATCTAAGGGAAA
1782897 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
ATGACTCAAATCTAAGGGAAACA
Found at i:1795925 original size:2 final size:2
Alignment explanation
Indices: 1795918--1795953 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1795908 GTGCAGTCAC
1795918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1795954 CCATTATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1797302 original size:16 final size:16
Alignment explanation
Indices: 1797281--1797311 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1797271 TTGAGGTTAA
1797281 TTTGAATTAAAATAAG
1 TTTGAATTAAAATAAG
1797297 TTTGAATTAAAATAA
1 TTTGAATTAAAATAA
1797312 ATTTAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
TTTGAATTAAAATAAG
Found at i:1798826 original size:14 final size:14
Alignment explanation
Indices: 1798789--1798864 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1798779 TTAAATTTTT
1798789 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
* * *
1798803 TAACTATTTAAAAA
1 TTATTTTTTAAAAA
**
1798817 TTATTTTTT-AATC
1 TTATTTTTTAAAAA
1798830 TT-TTAATTTT--AAA
1 TTATT--TTTTAAAAA
1798843 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
*
1798857 ATATTTTT
1 TTATTTTT
1798865 CACTCACACA
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
12 6 0.13
13 7 0.15
14 33 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTTTTTAAAAA
Found at i:1799429 original size:21 final size:22
Alignment explanation
Indices: 1799368--1799435 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
1799358 GAGTGGAAGA
*
1799368 AAAAATAAAT-TAT-GTATTTT
1 AAAAATAAATAGATAGTATTTT
** * *
1799388 TTAAATAAATAGGT-GGATTTT
1 AAAAATAAATAGATAGTATTTT
*
1799409 AAAAATAAATAGATAGTTTTTT
1 AAAAATAAATAGATAGTATTTT
1799431 AAAAA
1 AAAAA
1799436 GTTATTAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 8 0.22
21 18 0.50
22 10 0.28
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (22 bp):
AAAAATAAATAGATAGTATTTT
Found at i:1800128 original size:19 final size:19
Alignment explanation
Indices: 1800104--1800186 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
1800094 TTTCAACGAT
1800104 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1800123 TTGTATCAATAC--AA---
1 TTGTATCGATACATAAGTG
1800137 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1800155 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1800174 TTGTATCGATACA
1 TTGTATCGATACA
1800187 ATGTATCGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
19 41 0.75
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1800146 original size:32 final size:32
Alignment explanation
Indices: 1800105--1800167 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1800095 TTCAACGATT
1800105 TGTATCGATACATAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
1800137 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCAATACA
1800168 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:1802336 original size:10 final size:9
Alignment explanation
Indices: 1802308--1802335 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1802298 GGCGTCCTCC
1802308 ACAAAAAAA
1 ACAAAAAAA
1802317 ACAAAAAAA
1 ACAAAAAAA
1802326 ACAAAAAAA
1 ACAAAAAAA
1802335 A
1 A
1802336 AGGGTCCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:1803748 original size:28 final size:28
Alignment explanation
Indices: 1803708--1803772 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1803698 AGACATTCCT
** *
1803708 CACCCTTCAAAAGCCCACAACTCTGTGG
1 CACCCTTTTAAAGCCCACAACTCCGTGG
*
1803736 CACCCTTTTAAAGCCCACAATTCCGTGG
1 CACCCTTTTAAAGCCCACAACTCCGTGG
*
1803764 CACTCTTTT
1 CACCCTTTT
1803773 TCCTTTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.37, G:0.12, T:0.26
Consensus pattern (28 bp):
CACCCTTTTAAAGCCCACAACTCCGTGG
Found at i:1803833 original size:36 final size:36
Alignment explanation
Indices: 1803738--1803893 Score: 191
Period size: 34 Copynumber: 4.5 Consensus size: 36
1803728 CTCTGTGGCA
1803738 CCCTTTTAAAGCCCACAA-TTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTT-CGTGGCACTCTTTTT
*
1803774 -CCTTTT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTT
* *
1803808 CCCTTTTAAAGTCCACAACTTCGTGGCAC-CTTGTT
1 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTT
* **
1803843 -CCTTTT-AAGTCCACAACTTCGTGGCA-TCTTTCA
1 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTT
1803876 CCCTTTTTAAAGCCCACA
1 CCC-TTTTAAAGCCCACA
1803894 CAAGTCGGTG
Statistics
Matches: 105, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
33 23 0.22
34 33 0.31
35 22 0.21
36 27 0.26
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.35
Consensus pattern (36 bp):
CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTT
Found at i:1803867 original size:69 final size:69
Alignment explanation
Indices: 1803736--1803893 Score: 221
Period size: 69 Copynumber: 2.3 Consensus size: 69
1803726 AACTCTGTGG
*
1803736 CACCCTTTTAAAGCCCACAATTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCAC
1 CACCCTTTTAAAGCCCACAATTCCGTGGCACTCTTGTTCCTTTTAAGCCCACAACTCCGTGGCA-
1803801 TCTTT
65 TCTTT
** * * *
1803806 TTCCCTTTTAAAGTCCACAACTT-CGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
1 CACCCTTTTAAAGCCCACAA-TTCCGTGGCACTCTTGTTCCTTTTAAGCCCACAACTCCGTGGCA
1803869 TCTTT
65 TCTTT
1803874 CACCCTTTTTAAAGCCCACA
1 CACCC-TTTTAAAGCCCACA
1803894 CAAGTCGGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
68 8 0.10
69 42 0.55
70 25 0.32
71 2 0.03
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (69 bp):
CACCCTTTTAAAGCCCACAATTCCGTGGCACTCTTGTTCCTTTTAAGCCCACAACTCCGTGGCAT
CTTT
Found at i:1803962 original size:63 final size:66
Alignment explanation
Indices: 1803883--1804070 Score: 312
Period size: 63 Copynumber: 2.9 Consensus size: 66
1803873 TCACCCTTTT
1803883 TAAAGCCCACACAAGTCGGTGGCAACCCTTC-CTAAAGCCCACACAAGTTGGTGGCAACC-CCCT
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCACCCT
1803946 C
66 C
* *
1803947 -AAAGCCCACACAAGTCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTTAGTGGCAACCACTCT
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCACCCT
1804010 C
66 C
* *
1804011 TAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTTGGTGGCAACC
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACC
1804071 TTCTAAGCCC
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
62 2 0.02
63 54 0.47
64 4 0.03
65 25 0.22
66 30 0.26
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (66 bp):
TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCACCCT
C
Found at i:1804015 original size:33 final size:32
Alignment explanation
Indices: 1803883--1804081 Score: 291
Period size: 33 Copynumber: 6.3 Consensus size: 32
1803873 TCACCCTTTT
*
1803883 TAAAGCCCACACAAGTCGGTGGCAACCCT-TCC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTCT-C
*
1803915 TAAAGCCCACACAAGTTGGTGGCAACCCCCTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTCTC
*
1803947 -AAAGCCCACACAAGTCGGTGGCAACCCTCTC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTCTC
*
1803978 TAAAGCCCACACAAGTTAGTGGCAACCACTCTC
1 TAAAGCCCACACAAGTTGGTGGCAACC-CTCTC
*
1804011 TAAAGCCCACACAAGTTGGTGGCAACCATTCTC
1 TAAAGCCCACACAAGTTGGTGGCAACC-CTCTC
1804044 TAAAGCCCACACAAGTTGGTGGCAA-CCT-TC
1 TAAAGCCCACACAAGTTGGTGGCAACCCTCTC
1804074 T-AAGCCCA
1 TAAAGCCCA
1804082 ATATAGCTGG
Statistics
Matches: 155, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
29 7 0.05
30 3 0.02
31 30 0.19
32 53 0.34
33 62 0.40
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (32 bp):
TAAAGCCCACACAAGTTGGTGGCAACCCTCTC
Found at i:1809110 original size:21 final size:20
Alignment explanation
Indices: 1809076--1809130 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1809066 GTTTGCCCAA
* *
1809076 CTTTTTACAAAAAGATTTAT
1 CTTTTTAAAAAAAGATTGAT
1809096 CTTTATTAAAAAAAGATTGAT
1 CTTT-TTAAAAAAAGATTGAT
*
1809117 TTTTTTCAAAAAAA
1 CTTTTT-AAAAAAA
1809131 CTCGAATACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
CTTTTTAAAAAAAGATTGAT
Found at i:1809772 original size:14 final size:11
Alignment explanation
Indices: 1809730--1809801 Score: 74
Period size: 11 Copynumber: 6.3 Consensus size: 11
1809720 ATACAGCATA
1809730 AAAAATTAAT-T
1 AAAAA-TAATAT
1809741 AAAAATAATAT
1 AAAAATAATAT
1809752 AAAAATAATAT
1 AAAAATAATAT
* *
1809763 AAACATAATAAA
1 AAAAATAAT-AT
1809775 AAAAATGAACTAT
1 AAAAAT-AA-TAT
*
1809788 AAAAATAAAAT
1 AAAAATAATAT
1809799 AAA
1 AAA
1809802 TTATAAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 4 0.08
11 30 0.58
12 8 0.15
13 9 0.17
14 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:1809806 original size:18 final size:17
Alignment explanation
Indices: 1809742--1809809 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
1809732 AAATTAATTA
1809742 AAAAT-AATATAAAAAT
1 AAAATAAATATAAAAAT
* * *
1809758 AATATAAACATAATAAAA
1 AAAATAAATATAA-AAAT
*
1809776 AAAATGAACTATAAAAAT
1 AAAAT-AAATATAAAAAT
1809794 AAAATAAATTATAAAA
1 AAAATAAA-TATAAAA
1809810 TTTAAAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
16 4 0.10
17 8 0.20
18 22 0.55
19 6 0.15
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (17 bp):
AAAATAAATATAAAAAT
Found at i:1809942 original size:15 final size:15
Alignment explanation
Indices: 1809911--1809952 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1809901 TCTCCCGGTC
*
1809911 CTTTTCTTTCTT-TCT
1 CTTTTCTTT-TTCCCT
*
1809926 CTTTTTTTTTTCCCT
1 CTTTTCTTTTTCCCT
1809941 CTTTTCTTTTTC
1 CTTTTCTTTTTC
1809953 TTCATGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTCTTTTTCCCT
Found at i:1810881 original size:21 final size:21
Alignment explanation
Indices: 1810857--1810897 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1810847 AATTATTATA
* *
1810857 TATTTTATATAATTTTAAAAT
1 TATTTTATAAAAATTTAAAAT
*
1810878 TATTTTTTAAAAATTTAAAA
1 TATTTTATAAAAATTTAAAA
1810898 AATTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTTATAAAAATTTAAAAT
Found at i:1812757 original size:6 final size:6
Alignment explanation
Indices: 1812746--1812813 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
1812736 AATATTTTTA
* * *
1812746 ATATTT ATATTT -TATTT TTATTT AAATTT -TA-AT ATATTT AATAATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT -AT-ATTT
*
1812793 ATA-TT ATTTTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATAT
1812814 AATTAATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.02
5 12 0.24
6 28 0.57
7 4 0.08
8 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:1812793 original size:17 final size:16
Alignment explanation
Indices: 1812764--1812822 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
1812754 ATTTTATTTT
*
1812764 TATTTAA-ATTTTAATA
1 TATTTAATAATTT-ATA
1812780 TATTTAATAATTTATA
1 TATTTAATAATTTATA
*
1812796 TTATTT-TTATATTTATA
1 -TATTTAATA-ATTTATA
*
1812813 TAATTAATAA
1 TATTTAATAA
1812823 AAATATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 17 0.49
17 18 0.51
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTAATAATTTATA
Found at i:1813836 original size:18 final size:18
Alignment explanation
Indices: 1813813--1813863 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1813803 CCTTTTCAAA
*
1813813 TTATATTTAT-AATTATTT
1 TTATATTTATAAAATA-TT
1813831 TTATATTT-TAAAATATT
1 TTATATTTATAAAATATT
1813848 TTATATTTTATAAAAT
1 TTATA-TTTATAAAAT
1813864 TTAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 15 0.52
19 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATAAAATATT
Found at i:1813851 original size:17 final size:17
Alignment explanation
Indices: 1813829--1813933 Score: 85
Period size: 17 Copynumber: 6.3 Consensus size: 17
1813819 TTATAATTAT
1813829 TTTTATATTTTA-AAATA
1 TTTTATATTTTATAAA-A
1813846 TTTTATATTTTATAAAA
1 TTTTATATTTTATAAAA
* * *
1813863 TTTAATATATTA-ATAA
1 TTTTATATTTTATAAAA
* *
1813879 -TTTATATTATATTAAA
1 TTTTATATTTTATAAAA
*
1813895 TTTTATATTTTTGATATAA
1 TTTTATA-TTTT-ATAAAA
*
1813914 --TTATATTTTATTAAA
1 TTTTATATTTTATAAAA
1813929 TTTTA
1 TTTTA
1813934 ATAAATTTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
15 12 0.18
16 9 0.13
17 37 0.54
18 6 0.09
19 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTTATATTTTATAAAA
Found at i:1813896 original size:32 final size:34
Alignment explanation
Indices: 1813842--1813936 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 34
1813832 TATATTTTAA
* *
1813842 AATATTTTATATTTTATAAAATTTAATA-TATT-
1 AATAATTTATATTTTATTAAATTTAATATTATTG
* * *
1813874 AATAATTTATATTATATTAAATTTTATATTTTTG
1 AATAATTTATATTTTATTAAATTTAATATTATTG
1813908 ATATAA-TTATATTTTATTAAATTTTAATA
1 A-ATAATTTATATTTTATTAAA-TTTAATA
1813937 AATTTTAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 24 0.46
33 3 0.06
34 15 0.29
35 10 0.19
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (34 bp):
AATAATTTATATTTTATTAAATTTAATATTATTG
Found at i:1813979 original size:17 final size:17
Alignment explanation
Indices: 1813959--1813995 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1813949 AAATTTAAAT
1813959 TTATTAAAAAATATTAA
1 TTATTAAAAAATATTAA
* *
1813976 TTATTTAATAATATTAA
1 TTATTAAAAAATATTAA
1813993 TTA
1 TTA
1813996 AAATTACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAAAAATATTAA
Found at i:1814308 original size:20 final size:20
Alignment explanation
Indices: 1814283--1814323 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1814273 AAAATATGTT
1814283 TTAAATCA-AATTGATTTTAA
1 TTAAATCATAATT-ATTTTAA
*
1814303 TTAAATTATAATTATTTTAA
1 TTAAATCATAATTATTTTAA
1814323 T
1 T
1814324 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAATCATAATTATTTTAA
Found at i:1814331 original size:16 final size:16
Alignment explanation
Indices: 1814303--1814338 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1814293 TTGATTTTAA
1814303 TTAAATTATAATTATT
1 TTAAATTATAATTATT
1814319 TTAATATTA-AATTATT
1 TTAA-ATTATAATTATT
1814335 TTAA
1 TTAA
1814339 GTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAATTATAATTATT
Found at i:1814380 original size:6 final size:6
Alignment explanation
Indices: 1814371--1814399 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1814361 AATATTTAAA
1814371 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1814400 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:1815204 original size:2 final size:2
Alignment explanation
Indices: 1815197--1815231 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1815187 ATATCTCTTA
1815197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1815232 ATTGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1816442 original size:23 final size:24
Alignment explanation
Indices: 1816416--1816476 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
1816406 ATAAAAGATT
*
1816416 ATTTTTATATTAATATTT-A-TATA
1 ATTTTTATATTAA-ATTTAATTAAA
1816439 A-TTTTATAATTAAATTTAATTAAA
1 ATTTTTAT-ATTAAATTTAATTAAA
1816463 ATTTTT-TATTAAAT
1 ATTTTTATATTAAAT
1816477 AATAATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 10 0.30
23 14 0.42
24 5 0.15
25 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTATATTAAATTTAATTAAA
Found at i:1816482 original size:24 final size:24
Alignment explanation
Indices: 1816438--1816483 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1816428 ATATTTATAT
*
1816438 AATTTTATAATTAAATTTAATTAA
1 AATTTTATAATTAAATATAATTAA
*
1816462 AATTTT-TTATTAAATAATAATT
1 AATTTTATAATTAAAT-ATAATT
1816484 CAAACCGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTTTATAATTAAATATAATTAA
Found at i:1817787 original size:77 final size:77
Alignment explanation
Indices: 1817678--1817868 Score: 267
Period size: 77 Copynumber: 2.5 Consensus size: 77
1817668 AGAAAATTCT
* * * * * *
1817678 AATAAGTCCTAAAAGATTCGATTTAGGAATGAAAACATTAGTATGACTTTGAAAGATTG-GTTAT
1 AATAA-TCCCAAAAGATTCGATTTAGGTATGAAAACATTAGTATGACCTTAAAAGATCGACTT-T
*
1817742 AGAAAGAAGCATAA
64 AAAAAGAAGCATAA
* *
1817756 AATAATCTCAAAAGATTCGATTTAGGTATGAAAACATTAGTATGACCTTAAAAGCTCGACTTTAA
1 AATAATCCCAAAAGATTCGATTTAGGTATGAAAACATTAGTATGACCTTAAAAGATCGACTTTAA
*
1817821 AAAGAAGTATAA
66 AAAGAAGCATAA
1817833 AATAATCCCAAAAGATTCGATTTAGGTATGAAAACA
1 AATAATCCCAAAAGATTCGATTTAGGTATGAAAACA
1817869 CAAACATGAC
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
77 94 0.93
78 7 0.07
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (77 bp):
AATAATCCCAAAAGATTCGATTTAGGTATGAAAACATTAGTATGACCTTAAAAGATCGACTTTAA
AAAGAAGCATAA
Found at i:1819770 original size:17 final size:18
Alignment explanation
Indices: 1819738--1819777 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1819728 TTTAAACTTA
*
1819738 AAAAATAACTTGAAAAAT
1 AAAAATAACTTAAAAAAT
1819756 AAAAATAA-TTAAAAAAT
1 AAAAATAACTTAAAAAAT
1819773 AAAAA
1 AAAAA
1819778 AACGAAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAAATAACTTAAAAAAT
Found at i:1819778 original size:18 final size:19
Alignment explanation
Indices: 1819736--1819778 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1819726 AATTTAAACT
*
1819736 TAAAAAATAACTTGAAAAA
1 TAAAAAATAACTTAAAAAA
1819755 T-AAAAATAA-TTAAAAAA
1 TAAAAAATAACTTAAAAAA
1819772 TAAAAAA
1 TAAAAAA
1819779 ACGAAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAAAATAACTTAAAAAA
Found at i:1819853 original size:2 final size:2
Alignment explanation
Indices: 1819846--1819876 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1819836 TTTTCTCTTT
1819846 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1819877 TTTCTCGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1820416 original size:14 final size:14
Alignment explanation
Indices: 1820371--1820420 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1820361 TAATTTTTAA
*
1820371 ATAAAATTAAGTAT
1 ATAAAATTAAATAT
*
1820385 TTATAAATATAAAT-T
1 ATA-AAAT-TAAATAT
1820400 ATAAAATTAAATAT
1 ATAAAATTAAATAT
1820414 ATAAAAT
1 ATAAAAT
1820421 ATTATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.17
14 14 0.47
15 7 0.23
16 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATAAAATTAAATAT
Found at i:1820440 original size:23 final size:23
Alignment explanation
Indices: 1820387--1820441 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1820377 TTAAGTATTT
*
1820387 ATAAATATAAATTATAAAATTAA
1 ATAAATAAAAATTATAAAATTAA
* *
1820410 ATATATAAAATATTATTAAA-TAA
1 ATAAATAAAA-ATTATAAAATTAA
1820433 ATAAATAAA
1 ATAAATAAA
1820442 TAAATTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAATAAAAATTATAAAATTAA
Found at i:1820943 original size:14 final size:14
Alignment explanation
Indices: 1820924--1820962 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
1820914 TCATTTTTAA
1820924 AATTTTTTAAAAAT
1 AATTTTTTAAAAAT
1820938 AATTTTTTTTAAAAAT
1 AA--TTTTTTAAAAAT
*
1820954 AATTATTTA
1 AATTTTTTA
1820963 TTATCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTTTAAAAAT
Found at i:1820947 original size:16 final size:16
Alignment explanation
Indices: 1820926--1820957 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1820916 ATTTTTAAAA
1820926 TTTTTTAAAAATAATT
1 TTTTTTAAAAATAATT
1820942 TTTTTTAAAAATAATT
1 TTTTTTAAAAATAATT
1820958 ATTTATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTTAAAAATAATT
Found at i:1821594 original size:21 final size:21
Alignment explanation
Indices: 1821568--1821622 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1821558 TTTTACTTAG
1821568 ATGTATCGATACATGCCTTTC
1 ATGTATCGATACATGCCTTTC
1821589 ATGTATCGATACATGCCTTTC
1 ATGTATCGATACATGCCTTTC
1821610 ATGTATCGATACA
1 ATGTATCGATACA
1821623 AAGTCCCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACATGCCTTTC
Found at i:1821702 original size:20 final size:21
Alignment explanation
Indices: 1821660--1821710 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
1821650 TTCTACAATT
*
1821660 TGTATCGATATAATAATTGAA
1 TGTATCGATATAATAAGTGAA
1821681 TGTATCGATATAA-AAGTGAA
1 TGTATCGATATAATAAGTGAA
1821701 TGTATCGATA
1 TGTATCGATA
1821711 CATGTATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTATCGATATAATAAGTGAA
Found at i:1824286 original size:51 final size:51
Alignment explanation
Indices: 1824210--1824322 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
1824200 AATCAAAAGT
* *
1824210 GGATATTCCAACCCCGTTTTTACTTCCAAAATATTGAAT-TTTTCATCACGG
1 GGATACTCCAACCCCGTTTTTACTTCCAAAACATTGAATATTTT-ATCACGG
* * *
1824261 GGATACTCCAACTCTGTTTTTACTTCCAAAACATTGAATATTTTATCTCGG
1 GGATACTCCAACCCCGTTTTTACTTCCAAAACATTGAATATTTTATCACGG
1824312 GGATACTCCAA
1 GGATACTCCAA
1824323 TCCCATCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (51 bp):
GGATACTCCAACCCCGTTTTTACTTCCAAAACATTGAATATTTTATCACGG
Found at i:1824352 original size:79 final size:79
Alignment explanation
Indices: 1824262--1824761 Score: 269
Period size: 79 Copynumber: 6.3 Consensus size: 79
1824252 TCATCACGGG
* *
1824262 GATACTCCAACTCTGTTTTTACTTCCAAAACATTGAATATTTT-ATCTCGGGGATACTCCAATCC
1 GATACTTCAACTCTGTTTTTACTTTCAAAACATTGAATATTTTCATCTCGGGGATACTCCAA-CC
*
1824326 CATCATTTTCGAGGA
65 CACCATTTTCGAGGA
* * * * **
1824341 GATACTTCAACTCTGTTTTTACTTTTAAAATATTGAATTTTTTCATCTATGGGGATACTTGAACT
1 GATACTTCAACTCTGTTTTTACTTTCAAAACATTGAATATTTTCATCT-CGGGGATACTCCAAC-
*
1824406 CCACCATTTTCCGA-AA
64 CCACCATTTT-CGAGGA
* * ** * * * *
1824422 GGATACTCCAACCCCATTTTTACTTTCAAAATATTTAAT-TTCTTCATCTACGGGGATATTTCAA
1 -GATACTTCAACTCTGTTTTTACTTTCAAAACATTGAATATT-TTCATCT-CGGGGATACTCCAA
*
1824486 CCTCACCATTTTC-AGTGG
63 CC-CACCATTTTCGAG-GA
* * * * ** *
1824504 GATAC-TCAAACTCCGTTCTTATTTTTCAAATAC--TGAATATTTT-ATTTTTGGAATACTCCAA
1 GATACTTC-AACTCTGTTTTTA-CTTTCAAA-ACATTGAATATTTTCATCTCGGGGATACTCCAA
* * * *
1824565 CCCTATC-GTCTCTGAGGG
63 CCC-ACCATTTTC-GAGGA
* *
1824583 GATAC-TCTAAC-CT-TAGTTTTAC-TTCTAAAACATT-AAAATTTTCATCTCAGGGATACTCCA
1 GATACTTC-AACTCTGT--TTTTACTTTC-AAAACATTGAATATTTTCATCTCGGGGATACTCCA
*
1824643 ACCTCACCATTTTCGAGTA
62 ACC-CACCATTTTCGAGGA
* ** * ** * * *
1824662 GATACTTCAACCCCATTGTTACTTTCAAAACA-CCAA-ACTTTACATCTCTGAGGATACTCCAGC
1 GATACTTCAACTCTGTTTTTACTTTCAAAACATTGAATA-TTTTCATCTC-GGGGATACTCCA-A
*
1824725 CCCACCATTTTCGA-AA
63 CCCACCATTTTCGAGGA
* *
1824741 GGATACTTTAACTCTGATTTT
1 -GATACTTCAACTCTGTTTTT
1824762 CACCAAAAAT
Statistics
Matches: 323, Mismatches: 65, Indels: 65
0.71 0.14 0.14
Matches are distributed among these distances:
77 6 0.02
78 16 0.05
79 120 0.37
80 58 0.18
81 49 0.15
82 73 0.23
83 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (79 bp):
GATACTTCAACTCTGTTTTTACTTTCAAAACATTGAATATTTTCATCTCGGGGATACTCCAACCC
ACCATTTTCGAGGA
Found at i:1824531 original size:82 final size:81
Alignment explanation
Indices: 1824261--1824541 Score: 213
Period size: 82 Copynumber: 3.5 Consensus size: 81
1824251 TTCATCACGG
* * * * *
1824261 GGATACTCCAACTCTGTTTTTACTTCCAAAACATTGAATATT-TT-ATCT-CGGGGATACTCCAA
1 GGATACT-CAACTCCGTTTTTATTTTCAAAATATTGAAT-TTCTTCATCTACGGGGATACTTCAA
* *
1824323 -TCCCATCATTTTC-G-AG
64 CT-CCACCATTTTCAGAAA
* * * *
1824339 GAGATACTTCAACTCTGTTTTTACTTTT-AAAATATTGAATTTTTTCATCTATGGGGATACTTGA
1 G-GATAC-TCAACTCCGTTTTTA-TTTTCAAAATATTGAATTTCTTCATCTACGGGGATACTTCA
*
1824403 ACTCCACCATTTTCCGAAA
63 ACTCCACCATTTTCAGAAA
* * * * *
1824422 GGATACTCCAACCCCATTTTTACTTTCAAAATATTTAATTTCTTCATCTACGGGGATATTTCAAC
1 GGATACT-CAACTCCGTTTTTATTTTCAAAATATTGAATTTCTTCATCTACGGGGATACTTCAAC
**
1824487 -CTCACCATTTTCAG-TG
65 TC-CACCATTTTCAGAAA
* *
1824503 GGATACTCAAACTCCGTTCTTATTTTTC-AAATACTGAAT
1 GGATACTC-AACTCCGTTTTTA-TTTTCAAAATATTGAAT
1824542 ATTTTATTTT
Statistics
Matches: 163, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
78 3 0.02
79 32 0.20
80 8 0.05
81 52 0.32
82 66 0.40
83 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.38
Consensus pattern (81 bp):
GGATACTCAACTCCGTTTTTATTTTCAAAATATTGAATTTCTTCATCTACGGGGATACTTCAACT
CCACCATTTTCAGAAA
Found at i:1825528 original size:12 final size:12
Alignment explanation
Indices: 1825511--1825538 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1825501 TTCATATTTT
1825511 AAATCTAACCTA
1 AAATCTAACCTA
1825523 AAATCTAACCTA
1 AAATCTAACCTA
1825535 AAAT
1 AAAT
1825539 GAGTGGTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATCTAACCTA
Found at i:1825953 original size:37 final size:38
Alignment explanation
Indices: 1825902--1825976 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1825892 TTTATATTTA
1825902 AATTTAAATAAAAAT-AATTTTTTATTAAT-TAAATAAT
1 AATTTAAATAAAAATAAATTTTTTA-TAATCTAAATAAT
*
1825939 AATTTAAATCAAAATAAAATTTTTTATAATCTAAATAA
1 AATTTAAATAAAAAT-AAATTTTTTATAATCTAAATAA
1825977 ATCTAACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
37 14 0.41
38 4 0.12
39 16 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (38 bp):
AATTTAAATAAAAATAAATTTTTTATAATCTAAATAAT
Found at i:1825974 original size:21 final size:21
Alignment explanation
Indices: 1825917--1825977 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1825907 AAATAAAAAT
1825917 AATTTTTTATTAAT-TAAATAA
1 AATTTTTTA-TAATCTAAATAA
*
1825938 TAA---TTTA-AATCAAAATAA
1 -AATTTTTTATAATCTAAATAA
1825956 AATTTTTTATAATCTAAATAA
1 AATTTTTTATAATCTAAATAA
1825977 A
1 A
1825978 TCTAACTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 4 0.12
20 4 0.12
21 11 0.34
22 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTTTTATAATCTAAATAA
Found at i:1826083 original size:25 final size:24
Alignment explanation
Indices: 1826026--1826093 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
1826016 TATTTAAATT
1826026 TAAATA-TAATTATATAAAA-TATA
1 TAAATATTAA-TATATAAAATTATA
*
1826049 TAAATATTAATATATAAAATTTTA
1 TAAATATTAATATATAAAATTATA
*
1826073 TAATATTTTAA-ATAATAAAAT
1 TAA-ATATTAATAT-ATAAAAT
1826094 AACCTTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 15 0.38
24 11 0.28
25 13 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATATTAATATATAAAATTATA
Found at i:1828691 original size:15 final size:15
Alignment explanation
Indices: 1828671--1828710 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1828661 ACGTATTTGA
1828671 AGTTCTTTTTGTCTC
1 AGTTCTTTTTGTCTC
*
1828686 AGTTCTTCTTG--TC
1 AGTTCTTTTTGTCTC
1828699 AGTT-TTTTTGTC
1 AGTTCTTTTTGTC
1828711 CGTGGTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.24
13 6 0.29
15 10 0.48
ACGTcount: A:0.07, C:0.17, G:0.15, T:0.60
Consensus pattern (15 bp):
AGTTCTTTTTGTCTC
Found at i:1830560 original size:42 final size:42
Alignment explanation
Indices: 1830479--1830560 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1830469 GCTATGCATC
* *
1830479 GTAACGAGTGGGTGGAAAACGCTGACCGCTGGGTTGCCGGAT
1 GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTCGCCGGAT
* * *
1830521 GTAATGAGTGGGTGGAAAATGCTGATCGCTGGCTCGCCGG
1 GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTCGCCGG
1830561 GTTTCTTGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.40, T:0.21
Consensus pattern (42 bp):
GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTCGCCGGAT
Found at i:1830853 original size:3 final size:3
Alignment explanation
Indices: 1830845--1830870 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1830835 GGAATACTAT
1830845 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
1830871 ACATTATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:1832244 original size:44 final size:43
Alignment explanation
Indices: 1832194--1832278 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
1832184 TTATTATATG
* *
1832194 ATTATAATATAA-CTATTAATA-TTATTGTTATTTTTATTTTATTT
1 ATTATAATATAATC-AATAATATTTA-TGTT-TTATTATTTTATTT
1832238 ATTATAATATAATCAATAATATTTATGTTTTATTATTTTAT
1 ATTATAATATAATCAATAATATTTATGTTTTATTATTTTAT
1832279 ATTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
43 11 0.30
44 22 0.59
45 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (43 bp):
ATTATAATATAATCAATAATATTTATGTTTTATTATTTTATTT
Found at i:1833186 original size:45 final size:45
Alignment explanation
Indices: 1833130--1833224 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
1833120 ATAAGTATGT
* *
1833130 TAAATTTATATTA-TTTAAAT-T-ATTAA-AATATAAAAATTT-ATA
1 TAAATATATAATATTTTAAATATAATTAATAA-AT-AAAATTTAATA
1833172 TAAATATATAATATTTTAAATATAATTAATAAATAAAATTTAATA
1 TAAATATATAATATTTTAAATATAATTAATAAATAAAATTTAATA
1833217 TAAATATA
1 TAAATATA
1833225 ATATAAATAC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
42 11 0.24
43 7 0.15
44 8 0.17
45 18 0.39
46 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (45 bp):
TAAATATATAATATTTTAAATATAATTAATAAATAAAATTTAATA
Found at i:1833202 original size:25 final size:26
Alignment explanation
Indices: 1833169--1833233 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
1833159 ATAAAAATTT
*
1833169 ATATAAATATATAATATTTTAA-ATATA
1 ATAT-AATATATAATAATTTAATATA-A
*
1833196 AT-TAATAAATAA-AATTTAATATAA
1 ATATAATATATAATAATTTAATATAA
1833220 ATATAATATA-AATA
1 ATATAATATATAATA
1833234 CATAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 11 0.34
25 18 0.56
26 1 0.03
27 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATAATATATAATAATTTAATATAA
Found at i:1833221 original size:11 final size:11
Alignment explanation
Indices: 1833188--1833233 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1833178 TATAATATTT
1833188 TAAATATAAT-
1 TAAATATAATA
1833198 T-AATA-AATA
1 TAAATATAATA
*
1833207 -AAATTTAATA
1 TAAATATAATA
1833217 TAAATATAATA
1 TAAATATAATA
1833228 TAAATA
1 TAAATA
1833234 CATAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 3 0.10
9 7 0.23
10 5 0.17
11 15 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1833939 original size:21 final size:22
Alignment explanation
Indices: 1833914--1833965 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
1833904 ATAATTATTT
*
1833914 TATTTAAATATTTT-TTATTAA
1 TATTTAAATATTTTATAATTAA
*
1833935 TATTTATATATTTTATAATTAA
1 TATTTAAATATTTTATAATTAA
1833957 -ATTTAAATA
1 TATTTAAATA
1833966 AAATATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTAAATATTTTATAATTAA
Found at i:1835376 original size:40 final size:39
Alignment explanation
Indices: 1835309--1835385 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
1835299 CTTATATTAA
* *
1835309 TATAAAAATAAATTAATTTTATATAATTTTTAAATTTTT
1 TATAAAAATAAATTAATTTAATATAATTATTAAATTTTT
* * * *
1835348 TATAAGAAATATATTTATTTAATTTAATTATTATATTT
1 TATAA-AAATAAATTAATTTAATATAATTATTAAATTT
1835386 AATTATATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
39 5 0.16
40 26 0.84
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TATAAAAATAAATTAATTTAATATAATTATTAAATTTTT
Found at i:1835453 original size:16 final size:17
Alignment explanation
Indices: 1835416--1835454 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1835406 AAATTTTTAT
*
1835416 ATAAATAAATATATAAA
1 ATAATTAAATATATAAA
1835433 ATAATTAAATAT-TAAA
1 ATAATTAAATATATAAA
*
1835449 TTAATT
1 ATAATT
1835455 TTAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTAAATATATAAA
Found at i:1836104 original size:14 final size:13
Alignment explanation
Indices: 1836073--1836113 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1836063 TAAATAAATT
1836073 TAATATATTT-TT-
1 TAATAT-TTTATTA
1836085 TAATATTTATATTA
1 TAATATTT-TATTA
1836099 TAATATTTTATTA
1 TAATATTTTATTA
1836112 TA
1 TA
1836114 TACAATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 7 0.27
13 9 0.35
14 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TAATATTTTATTA
Found at i:1836115 original size:15 final size:14
Alignment explanation
Indices: 1836085--1836113 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1836075 ATATATTTTT
1836085 TAATATTTATATTA
1 TAATATTTATATTA
1836099 TAATATTT-TATTA
1 TAATATTTATATTA
1836112 TA
1 TA
1836114 TACAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:1838135 original size:80 final size:81
Alignment explanation
Indices: 1837972--1838127 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 81
1837962 ACCTGGTCGA
* *
1837972 ATTTGATGAGTTTAATTTATATTAAAATAAATTTAAATAAAAATTATAATAATTTAAATTAATTT
1 ATTTAATGAATTTAATTTATATTAAAATAAATTTAAATAAAAATTATAATAATTTAAATTAATTT
1838037 AATTTAAATTAAAAAT
66 AATTTAAATTAAAAAT
* * * * * *
1838053 ATTTAATGAATTTGATTT-TATTAAATTGAATTTGAATAAAAATTTTAATAATTTAGATTAATTT
1 ATTTAATGAATTTAATTTATATTAAAATAAATTTAAATAAAAATTATAATAATTTAAATTAATTT
1838117 AATTTAAATTA
66 AATTTAAATTA
1838128 GTAATATTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 52 0.78
81 15 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (81 bp):
ATTTAATGAATTTAATTTATATTAAAATAAATTTAAATAAAAATTATAATAATTTAAATTAATTT
AATTTAAATTAAAAAT
Found at i:1839139 original size:21 final size:21
Alignment explanation
Indices: 1839107--1839146 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1839097 CGCTATGTCA
1839107 AAATATTTAAAATATAAATAT
1 AAATATTTAAAATATAAATAT
1839128 AAAT-TTTAAAAATATAAAT
1 AAATATTT-AAAATATAAAT
1839147 TTTTTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATTTAAAATATAAATAT
Found at i:1840616 original size:20 final size:21
Alignment explanation
Indices: 1840591--1840637 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1840581 AAAATTTGAA
* *
1840591 AATTTAAT-TTTAAAATTATT
1 AATTTAATAATTAAAATAATT
1840611 AATTTAATAATTAAAATAATT
1 AATTTAATAATTAAAATAATT
1840632 -ATTTAA
1 AATTTAA
1840638 AATATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTAATAATTAAAATAATT
Found at i:1841955 original size:19 final size:19
Alignment explanation
Indices: 1841933--1841970 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1841923 TGTCTACTAA
1841933 TGACGATTGTGATCTGGAT
1 TGACGATTGTGATCTGGAT
1841952 TGACGATTGTGATCTGGAT
1 TGACGATTGTGATCTGGAT
1841971 GACAATGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (19 bp):
TGACGATTGTGATCTGGAT
Found at i:1844285 original size:31 final size:30
Alignment explanation
Indices: 1844236--1844294 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
1844226 TAATTATTTA
*
1844236 TAATAATAAAAATAAATATTTTATTTAAATT
1 TAATAATAAAAATAAATATTAT-TTTAAATT
* * *
1844267 TAATTATAAATATTAATATTATTTTAAA
1 TAATAATAAAAATAAATATTATTTTAAA
1844295 CAGTAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATAATAAAAATAAATATTATTTTAAATT
Found at i:1844410 original size:16 final size:17
Alignment explanation
Indices: 1844389--1844423 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1844379 AAATAAAAAC
1844389 TTAAAAA-ATAAGAATT
1 TTAAAAACATAAGAATT
1844405 TTAAAAACATAAGAATT
1 TTAAAAACATAAGAATT
1844422 TT
1 TT
1844424 TTTCCTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (17 bp):
TTAAAAACATAAGAATT
Found at i:1846671 original size:19 final size:20
Alignment explanation
Indices: 1846647--1846699 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1846637 AAAGAAGTAA
* *
1846647 TTTATATATT-TATATTATG
1 TTTATATATTATAAATCATG
1846666 TTTATATATTATAAATCATG
1 TTTATATATTATAAATCATG
*
1846686 TTTAAAGTATTATA
1 TTTATA-TATTATA
1846700 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.34
20 12 0.41
21 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTATATATTATAAATCATG
Found at i:1846761 original size:10 final size:11
Alignment explanation
Indices: 1846748--1846839 Score: 56
Period size: 11 Copynumber: 9.0 Consensus size: 11
1846738 TAAATTTTAA
1846748 TATATT-TATT
1 TATATTATATT
*
1846758 TATATTATTTT
1 TATATTATATT
1846769 TATA-TA-ATT
1 TATATTATATT
*
1846778 T-T-TTATA-C
1 TATATTATATT
* *
1846786 CATATCATATT
1 TATATTATATT
1846797 T-TATATATATT
1 TATAT-TATATT
*
1846808 T-TATTTTATT
1 TATATTATATT
* *
1846818 TATGTTATTTT
1 TATATTATATT
1846829 TATATTATATT
1 TATATTATATT
1846840 AAAAATTATC
Statistics
Matches: 60, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 21 0.35
11 31 0.52
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (11 bp):
TATATTATATT
Found at i:1846767 original size:23 final size:23
Alignment explanation
Indices: 1846741--1846784 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1846731 TATTATATAA
1846741 ATTTTAATAT-ATTTATTTATATT
1 ATTTTAATATAATTT-TTTATATT
*
1846764 ATTTTTATATAATTTTTTATA
1 ATTTTAATATAATTTTTTATA
1846785 CCATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTAATATAATTTTTTATATT
Found at i:1846812 original size:16 final size:16
Alignment explanation
Indices: 1846793--1846839 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1846783 TACCATATCA
1846793 TATTTTATATATATTT
1 TATTTTATATATATTT
*
1846809 TATTTTAT-T-TATGT
1 TATTTTATATATATTT
1846823 TATTTTTATATTATATT
1 TA-TTTTATA-TATATT
1846840 AAAAATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 8 0.32
17 1 0.04
18 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TATTTTATATATATTT
Found at i:1846953 original size:21 final size:21
Alignment explanation
Indices: 1846923--1846970 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1846913 GGATGAATAC
*
1846923 CATATCAGGCATTTATG-TCTT
1 CATATTAGGCATTTATGCT-TT
1846944 CATATTAGGCATTTATGCTTT
1 CATATTAGGCATTTATGCTTT
1846965 CATATT
1 CATATT
1846971 TTATGCCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (21 bp):
CATATTAGGCATTTATGCTTT
Found at i:1851258 original size:15 final size:15
Alignment explanation
Indices: 1851237--1851294 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
1851227 AATTCTAATA
*
1851237 ATTTAAAATTTTTAT
1 ATTTAAAATATTTAT
*
1851252 TTTTAAAATATTTAT
1 ATTTAAAATATTTAT
*
1851267 ATTTAATAAATATTTAA
1 ATTT-A-AAATATTTAT
1851284 ATTT-AAATATT
1 ATTTAAAATATT
1851295 AATAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.19
15 16 0.43
16 1 0.03
17 13 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAAAATATTTAT
Found at i:1851277 original size:17 final size:17
Alignment explanation
Indices: 1851257--1851289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1851247 TTTATTTTTA
*
1851257 AAATATTTATATTTAAT
1 AAATATTTAAATTTAAT
1851274 AAATATTTAAATTTAA
1 AAATATTTAAATTTAA
1851290 ATATTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATTTAAATTTAAT
Found at i:1851302 original size:28 final size:25
Alignment explanation
Indices: 1851271--1851329 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 25
1851261 ATTTATATTT
*
1851271 AATAAATATTTAAATTTAAATATTAATA
1 AATAAATATTTAAATATAAA-A--AATA
*
1851299 AATAAATTTTTAAATATAAAAAATA
1 AATAAATATTTAAATATAAAAAATA
1851324 AATAAA
1 AATAAA
1851330 ATATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
27 1 0.03
28 18 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATAAATATTTAAATATAAAAAATA
Found at i:1851324 original size:21 final size:22
Alignment explanation
Indices: 1851285--1851326 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1851275 AATATTTAAA
*
1851285 TTTAAATATTAATAAATAAATT
1 TTTAAATATTAAAAAATAAATT
1851307 TTTAAATA-TAAAAAATAAAT
1 TTTAAATATTAAAAAATAAAT
1851327 AAAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAATATTAAAAAATAAATT
Found at i:1851338 original size:28 final size:29
Alignment explanation
Indices: 1851276--1851338 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
1851266 TATTTAATAA
*
1851276 ATATTTAAATTTAAATATTAATAAATAAAT
1 ATATTTAAATATAAATA-TAATAAATAAAT
1851306 -T-TTTAAATATAAA-A-AATAAATAAAAT
1 ATATTTAAATATAAATATAATAAAT-AAAT
1851332 ATATTTA
1 ATATTTA
1851339 TACTCAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 7 0.24
26 4 0.14
27 2 0.07
28 15 0.52
29 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATATTTAAATATAAATATAATAAATAAAT
Found at i:1851769 original size:17 final size:15
Alignment explanation
Indices: 1851739--1851786 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1851729 TTTATATAAA
1851739 ATTAAATATATTTAT
1 ATTAAATATATTTAT
1851754 ATTAAATATATGTT-T
1 ATTAAATATAT-TTAT
*
1851769 A-TATATAATATTTAT
1 ATTAAAT-ATATTTAT
1851784 ATT
1 ATT
1851787 CCAAGTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.21
15 19 0.68
16 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:1855555 original size:16 final size:16
Alignment explanation
Indices: 1855512--1855556 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1855502 TTTTAAAAGT
1855512 AAAAATTTAAA-TTTA
1 AAAAATTTAAACTTTA
1855527 AAAAAGTTTAAACTTTA
1 AAAAA-TTTAAACTTTA
* *
1855544 GAAAATTCAAACT
1 AAAAATTTAAACT
1855557 AAAAAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 8 0.31
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (16 bp):
AAAAATTTAAACTTTA
Found at i:1856983 original size:5 final size:5
Alignment explanation
Indices: 1856973--1857004 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1856963 ATTATAAAAT
1856973 TTTAA TTTAA TTTAA TTTAA -TT-A TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1857005 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 1 0.04
4 4 0.16
5 20 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:1856987 original size:51 final size:48
Alignment explanation
Indices: 1856932--1857071 Score: 108
Period size: 57 Copynumber: 2.7 Consensus size: 48
1856922 CAAATAATAT
*
1856932 TTTAAAAGATTTAATATTAGTTTTTATATAAATTATAAAATTTTAATTTAA
1 TTTAAAA-ATTTAATATTA-TTTTTATATAAATTATAAAA-TTTAATGTAA
1856983 TTTAATTTAATTATTTAAT-TTATTTTTTATAATTAAAATTATTAAAATTTAATGTAA
1 TTTAA---AA--ATTTAATATTA-TTTTTAT-A-T-AAATTA-TAAAATTTAATGTAA
* *
1857040 -CTAAAAATTTAATATT-TTATTA-ATAAATTATA
1 TTTAAAAATTTAATATTATTTTTATATAAATTATA
1857072 TAACTATTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
45 2 0.03
46 6 0.08
47 1 0.01
48 1 0.01
50 5 0.07
51 12 0.16
52 2 0.03
53 2 0.03
54 12 0.16
55 8 0.11
56 4 0.05
57 15 0.20
58 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (48 bp):
TTTAAAAATTTAATATTATTTTTATATAAATTATAAAATTTAATGTAA
Found at i:1857152 original size:18 final size:19
Alignment explanation
Indices: 1857112--1857152 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1857102 TATTAATAAA
* *
1857112 TTAAATAATTTTTATTTTG
1 TTAAATAATTTTAATGTTG
1857131 TTAAATAATTTTAATGTT-
1 TTAAATAATTTTAATGTTG
1857149 TTAA
1 TTAA
1857153 CTTTTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAATAATTTTAATGTTG
Found at i:1857586 original size:26 final size:26
Alignment explanation
Indices: 1857540--1857611 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
1857530 TTTTTATTAA
*
1857540 AATTATTTAATAAAATTAATTTAAGT
1 AATTATTTAATAAAATAAATTTAAGT
* *
1857566 AATTTTTTAATAATAA-AAATTTAA-C
1 AATTATTTAATAA-AATAAATTTAAGT
*
1857591 AATGTAATTTGATAAAATAAA
1 AAT-T-ATTTAATAAAATAAA
1857612 AAATTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 3 0.08
26 22 0.59
27 12 0.32
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (26 bp):
AATTATTTAATAAAATAAATTTAAGT
Found at i:1858896 original size:3 final size:3
Alignment explanation
Indices: 1858888--1858931 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1858878 TACTTTTCAT
*
1858888 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1858932 CATTCAATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1859044 original size:18 final size:18
Alignment explanation
Indices: 1859021--1859062 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1859011 CTCAATTTTT
* *
1859021 TTTTAAAATTTTTATTTA
1 TTTTAAAAATTATATTTA
1859039 TTTTAAAAATTATATTTA
1 TTTTAAAAATTATATTTA
*
1859057 TATTAA
1 TTTTAA
1859063 TATTGAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATATTTA
Found at i:1860710 original size:13 final size:13
Alignment explanation
Indices: 1860692--1860717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1860682 GGCCTTTAGG
1860692 GTTTTTTTTTTTA
1 GTTTTTTTTTTTA
1860705 GTTTTTTTTTTTA
1 GTTTTTTTTTTTA
1860718 AATTATACAT
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:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
GTTTTTTTTTTTA
Found at i:1860960 original size:13 final size:13
Alignment explanation
Indices: 1860940--1860971 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1860930 ATTTTACAAA
1860940 TTATTTTTAAGTTT
1 TTATTTTTAA-TTT
1860954 TTATTTTTAATTT
1 TTATTTTTAATTT
1860967 TTATT
1 TTATT
1860972 AAGAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (13 bp):
TTATTTTTAATTT
Found at i:1861892 original size:19 final size:19
Alignment explanation
Indices: 1861868--1861909 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1861858 ATTTTATTAG
1861868 TTATTTTTAAATT-TTTATT
1 TTATTTTTAAATTATTT-TT
1861887 TTATTTTTAAATTATTTTT
1 TTATTTTTAAATTATTTTT
1861906 TTAT
1 TTAT
1861910 AGTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTTTAAATTATTTTT
Found at i:1862150 original size:20 final size:19
Alignment explanation
Indices: 1862100--1862148 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1862090 TGATAGAAAA
1862100 ATTTTATTTTATAGA-TTAT
1 ATTTTATTTTATA-ATTTAT
1862119 -TTTTAGGTTTTATAATTTAT
1 ATTTTA--TTTTATAATTTAT
1862139 ATTTTATTTT
1 ATTTTATTTT
1862149 TAAATTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 11 0.42
21 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (19 bp):
ATTTTATTTTATAATTTAT
Found at i:1862268 original size:33 final size:34
Alignment explanation
Indices: 1862222--1862286 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
1862212 TAAAAAAATA
1862222 TTTTATTTATTATTTATTACTTTTA-TATTTAAG
1 TTTTATTTATTATTTATTACTTTTATTATTTAAG
*
1862255 TTTTATATT-TTATTTATTATTTTTATTATTTA
1 TTTTAT-TTATTATTTATTACTTTTATTATTTA
1862287 TTATCTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (34 bp):
TTTTATTTATTATTTATTACTTTTATTATTTAAG
Found at i:1862369 original size:21 final size:21
Alignment explanation
Indices: 1862345--1862399 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1862335 GTTCGAAAGG
1862345 ATATTTTATTAATT-ATTTTT
1 ATATTTTATTAATTAATTTTT
*
1862365 CATATTTT-TATATTTAATTTTT
1 -ATATTTTAT-TAATTAATTTTT
1862387 ATATTTTTATTAA
1 ATA-TTTTATTAA
1862400 GAGATTGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 14 0.50
22 12 0.43
23 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTTATTAATTAATTTTT
Found at i:1862386 original size:13 final size:13
Alignment explanation
Indices: 1862368--1862392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1862358 TATTTTTCAT
1862368 ATTTTTATATTTA
1 ATTTTTATATTTA
1862381 ATTTTTATATTT
1 ATTTTTATATTT
1862393 TTATTAAGAG
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATATTTA
Found at i:1862730 original size:3 final size:3
Alignment explanation
Indices: 1862722--1862752 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1862712 AACGAGACCT
1862722 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1862753 TATAGGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1863291 original size:17 final size:17
Alignment explanation
Indices: 1863271--1863316 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1863261 TTTTCCTATT
*
1863271 AATAATATTTACTATCA
1 AATAATATTTAATATCA
1863288 AATAA-ATTTGAATATCA
1 AATAATATTT-AATATCA
*
1863305 AATAATTTTTAA
1 AATAATATTTAA
1863317 CTAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.16
17 18 0.72
18 3 0.12
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (17 bp):
AATAATATTTAATATCA
Found at i:1864575 original size:42 final size:40
Alignment explanation
Indices: 1864480--1864578 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 40
1864470 ATTTTATAAT
*
1864480 TAAAATGTCACGAAGTAATTACAATTAGTGGCATTTAAAAG
1 TAAAATGTCACTAA-TAATTACAATTAGTGGCATTTAAAAG
* *
1864521 TAAAAATATCACTAATAAATTA-ATTTAGTGGCATTTTAAATAG
1 T-AAAATGTCACTAAT-AATTACAATTAGTGGCA-TTTAAA-AG
1864564 TAAAATGTCACTAAT
1 TAAAATGTCACTAAT
1864579 GATAGTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
41 12 0.24
42 35 0.70
43 3 0.06
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (40 bp):
TAAAATGTCACTAATAATTACAATTAGTGGCATTTAAAAG
Found at i:1865454 original size:12 final size:12
Alignment explanation
Indices: 1865419--1865591 Score: 78
Period size: 12 Copynumber: 14.6 Consensus size: 12
1865409 AATATATATA
*
1865419 ATATATTATAGT
1 ATATATTATAAT
*
1865431 ATGTATT-T--T
1 ATATATTATAAT
1865440 ATATATTATAAT
1 ATATATTATAAT
*
1865452 ATAGATTATTTAAT
1 ATATATTA--TAAT
* *
1865466 ATATA-TGTGAT
1 ATATATTATAAT
*
1865477 ATATATTATATT
1 ATATATTATAAT
* *
1865489 ATATA-TATTAC
1 ATATATTATAAT
*
1865500 ATACATTATAGTAT
1 ATATATTATA--AT
*
1865514 GTATATTATAAT
1 ATATATTATAAT
*
1865526 GTATA-TA-ACAT
1 ATATATTATA-AT
*
1865537 ATA-ATATATATT
1 ATATAT-TATAAT
1865549 ATAGTATGTAT--T
1 ATA-TAT-TATAAT
1865561 ATATATTATAAT
1 ATATATTATAAT
**
1865573 ATATATGCTAAT
1 ATATATTATAAT
1865585 ATATATT
1 ATATATT
1865592 CCGTTTCTTT
Statistics
Matches: 121, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
9 7 0.06
10 6 0.05
11 25 0.21
12 59 0.49
13 2 0.02
14 22 0.18
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (12 bp):
ATATATTATAAT
Found at i:1865486 original size:7 final size:7
Alignment explanation
Indices: 1865411--1865578 Score: 67
Period size: 7 Copynumber: 25.0 Consensus size: 7
1865401 AGCGAACCAA
1865411 TATATAT
1 TATATAT
*
1865418 AATATAT
1 TATATAT
1865425 TATAGTAT
1 TATA-TAT
1865433 GTAT-T-T
1 -TATATAT
1865439 TATATAT
1 TATATAT
1865446 TATA-A-
1 TATATAT
*
1865451 TATAGAT
1 TATATAT
* *
1865458 TATTTAA
1 TATATAT
1865465 TATATAT
1 TATATAT
1865472 GTGATATA-
1 -T-ATATAT
1865480 TATTATAT
1 TA-TATAT
1865488 TATATA-
1 TATATAT
1865494 TAT-TA-
1 TATATAT
* *
1865499 CATACAT
1 TATATAT
1865506 TATAGTA-
1 TATA-TAT
*
1865513 TGTATAT
1 TATATAT
1865520 TATA-AT
1 TATATAT
*
1865526 GTATATAA
1 -TATATAT
* *
1865534 CATATAA
1 TATATAT
1865541 TATATA-
1 TATATAT
*
1865547 T-TATAG
1 TATATAT
*
1865553 TATGTAT
1 TATATAT
1865560 TATATAT
1 TATATAT
1865567 TATA-A-
1 TATATAT
1865572 TATATAT
1 TATATAT
1865579 GCTAATATAT
Statistics
Matches: 122, Mismatches: 19, Indels: 40
0.67 0.10 0.22
Matches are distributed among these distances:
5 19 0.16
6 17 0.14
7 70 0.57
8 8 0.07
9 8 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (7 bp):
TATATAT
Found at i:1866738 original size:19 final size:18
Alignment explanation
Indices: 1866717--1866752 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1866707 AAATATTTCT
1866717 TTTTACAAAAATCCTAAG
1 TTTTACAAAAATCCTAAG
* *
1866735 TTTTATAAAAATGCTAAG
1 TTTTACAAAAATCCTAAG
1866753 AAGATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (18 bp):
TTTTACAAAAATCCTAAG
Done.