Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold400
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: 2847997
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 12 of 17
Found at i:1754394 original size:31 final size:26
Alignment explanation
Indices: 1754245--1754401 Score: 271
Period size: 26 Copynumber: 6.1 Consensus size: 26
1754235 TGTCTCCAAT
*
1754245 TGCAATTTTTATTTCCTTTCCCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
1754271 TGCATTTTTTATTTCCTTTCCCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
*
1754297 TGCATTTTCTATTTCCTTT-CCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
1754322 TGCATTTTTTATTTCCTTTCCCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
1754348 TGCATTTTTTATTTCCTTTCCCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
* *
1754374 TGCATTTTCTATTTTCTTTCCCATGC
1 TGCATTTTTTATTTCCTTTCCCATGC
1754400 TG
1 TG
1754402 TAAGTTTTCA
Statistics
Matches: 125, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
25 24 0.19
26 101 0.81
ACGTcount: A:0.12, C:0.27, G:0.08, T:0.53
Consensus pattern (26 bp):
TGCATTTTTTATTTCCTTTCCCATGC
Found at i:1754569 original size:6 final size:6
Alignment explanation
Indices: 1754535--1754561 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1754525 ATTATTATTT
1754535 TTTGAA TTTGAA TTTGAA TTTGAA TTT
1 TTTGAA TTTGAA TTTGAA TTTGAA TTT
1754562 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:1755503 original size:11 final size:11
Alignment explanation
Indices: 1755489--1755528 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1755479 AAATCTTTCC
1755489 AAACCCATTCG
1 AAACCCATTCG
1755500 AAACCCATTCG
1 AAACCCATTCG
* *
1755511 AAATCTATTCG
1 AAACCCATTCG
1755522 AAACCCA
1 AAACCCA
1755529 AACTCATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (11 bp):
AAACCCATTCG
Found at i:1758927 original size:37 final size:37
Alignment explanation
Indices: 1758863--1758939 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
1758853 ATTATATTTG
* * ** *
1758863 TTTTCATGATTGTAATGAATGTTTGCCTTGCTATATT
1 TTTTCATGAATGCAATGAATGAATGCCTTGATATATT
* *
1758900 TTTTCATGAATGCAATTAATGAATGCCTTGATTTATT
1 TTTTCATGAATGCAATGAATGAATGCCTTGATATATT
1758937 TTT
1 TTT
1758940 CGATGCATGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (37 bp):
TTTTCATGAATGCAATGAATGAATGCCTTGATATATT
Found at i:1760380 original size:63 final size:63
Alignment explanation
Indices: 1760302--1760427 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1760292 CACAAACACC
1760302 AGCCTACTTAAAGGCATTTCGAGTTTGTAAAATCTCTGTATTGTAAAAGATTGTATTCAACCT
1 AGCCTACTTAAAGGCATTTCGAGTTTGTAAAATCTCTGTATTGTAAAAGATTGTATTCAACCT
1760365 AGCCTACTTAAAGGCATTTCGAGTTTGTAAAATCTCTGTATTGTAAAAGATTGTATTCAACCT
1 AGCCTACTTAAAGGCATTTCGAGTTTGTAAAATCTCTGTATTGTAAAAGATTGTATTCAACCT
1760428 TGGGATACAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (63 bp):
AGCCTACTTAAAGGCATTTCGAGTTTGTAAAATCTCTGTATTGTAAAAGATTGTATTCAACCT
Found at i:1761774 original size:21 final size:20
Alignment explanation
Indices: 1761706--1761780 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
1761696 GATCGTGATA
* *
1761706 AAATTAATTATTATAGTAGT
1 AAATTAAATATTATAGCAGT
* *
1761726 AAGATTAAATACTATAGCGGTT
1 AA-ATTAAATATTATAGCAG-T
*
1761748 ATATTAAATATTATAGCAGT
1 AAATTAAATATTATAGCAGT
1761768 GAAATTAAA-ATTA
1 -AAATTAAATATTA
1761781 ATGATCAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.16
21 35 0.80
22 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATTAAATATTATAGCAGT
Found at i:1762057 original size:23 final size:24
Alignment explanation
Indices: 1762018--1762066 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1762008 TTATTTATAA
* * *
1762018 TTTTAAATAAATATAAATACATTT
1 TTTTAAAAAAATATAAAAAAATTT
1762042 TTTTAAAAAAAT-TAAAAAAATTT
1 TTTTAAAAAAATATAAAAAAATTT
1762065 TT
1 TT
1762067 AAACCTCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTAAAAAAATATAAAAAAATTT
Found at i:1762246 original size:14 final size:15
Alignment explanation
Indices: 1762195--1762237 Score: 77
Period size: 15 Copynumber: 2.8 Consensus size: 15
1762185 ATTTTGAATA
1762195 AATATTTTTTAAAATG
1 AATA-TTTTTAAAATG
1762211 AATATTTTTAAAATG
1 AATATTTTTAAAATG
1762226 AATATTTTTAAA
1 AATATTTTTAAA
1762238 TAGATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
AATATTTTTAAAATG
Found at i:1762286 original size:15 final size:15
Alignment explanation
Indices: 1762195--1762287 Score: 71
Period size: 15 Copynumber: 5.7 Consensus size: 15
1762185 ATTTTGAATA
1762195 AATATTTTTTAAAATG
1 AATATTTTTT-AAATG
*
1762211 AATATTTTTAAAATG
1 AATATTTTTTAAATG
1762226 AATA-TTTTTAAATAG
1 AATATTTTTTAAAT-G
**
1762241 ATATTTATTATTCTTAAACAA
1 A-A--TATT-TT-TTAAA-TG
1762262 AATAATTTTTTAAATG
1 AAT-ATTTTTTAAATG
1762278 AATATTTTTT
1 AATATTTTTT
1762288 TATTGATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.13
15 18 0.29
16 13 0.21
17 5 0.08
18 5 0.08
19 4 0.06
20 3 0.05
21 6 0.10
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
AATATTTTTTAAATG
Found at i:1762876 original size:27 final size:28
Alignment explanation
Indices: 1762846--1762934 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
1762836 TATTTAAAAA
1762846 TAATAAAAATA-ATTTTTATTTTAATAT
1 TAATAAAAATATATTTTTATTTTAATAT
** * *
1762873 TAATATTAATATATTTTATAATTAAAT-T
1 TAATAAAAATATATTTT-TATTTTAATAT
*
1762901 TAAATAAAAATATATATTTATTATT-ATA-
1 T-AATAAAAATATATTTTTATT-TTAATAT
1762929 TAATAA
1 TAATAA
1762935 TTTAAATTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
27 14 0.29
28 13 0.27
29 21 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAATAAAAATATATTTTTATTTTAATAT
Found at i:1763885 original size:46 final size:46
Alignment explanation
Indices: 1763830--1763969 Score: 176
Period size: 46 Copynumber: 3.0 Consensus size: 46
1763820 AAAATTTAAC
* *
1763830 TTCTTCATTTATCT-TGTAATTAATTTAATTTCATTAGAGATAAAAT
1 TTCTTCATTTATCTAT-TAATTAATTTAATTTAATTAAAGATAAAAT
* *
1763876 ATT-TTCATTTATCTATTAATTAATTTAATTAAACTAAAGATAAAAT
1 -TTCTTCATTTATCTATTAATTAATTTAATTTAATTAAAGATAAAAT
* * * *
1763922 TTCTTTATTTATCTCTTAATTATTTTAATTTAATTAAAAATAAAAT
1 TTCTTCATTTATCTATTAATTAATTTAATTTAATTAAAGATAAAAT
1763968 TT
1 TT
1763970 GATTGGTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
45 2 0.02
46 76 0.94
47 3 0.04
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (46 bp):
TTCTTCATTTATCTATTAATTAATTTAATTTAATTAAAGATAAAAT
Found at i:1765958 original size:59 final size:60
Alignment explanation
Indices: 1765854--1765968 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
1765844 CTTAAAAAAA
* *
1765854 TAATATGAATGTGATATAAATACATAAACAAATCAAAATATATAAA-ATCATATAAACCTT
1 TAATATGAATATGACATAAATACATAAACAAATCAAAATATATAAAGAT-ATATAAACCTT
* *
1765914 TAATATGATTATGACATAAA-ACATAACACCAAAT-ACAA-ATATAAAGATATATAAA
1 TAATATGAATATGACATAAATACATAA-A-CAAATCAAAATATATAAAGATATATAAA
1765969 TATTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
59 20 0.42
60 23 0.48
61 5 0.10
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (60 bp):
TAATATGAATATGACATAAATACATAAACAAATCAAAATATATAAAGATATATAAACCTT
Found at i:1768118 original size:19 final size:18
Alignment explanation
Indices: 1768086--1768130 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1768076 AAAATTTAAT
1768086 TATTTA-AATTATATTGA
1 TATTTATAATTATATTGA
*
1768103 TATTTATAATTTATATTTA
1 TATTTATAA-TTATATTGA
*
1768122 TATTAATAA
1 TATTTATAA
1768131 ATACAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTTATAATTATATTGA
Found at i:1768175 original size:19 final size:19
Alignment explanation
Indices: 1768151--1768188 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1768141 ATAAAATAAA
1768151 AACTTACAAC-TCATCTAAT
1 AACTTACAACATCAT-TAAT
*
1768170 AACTTATAACATCATTAAT
1 AACTTACAACATCATTAAT
1768189 CATATTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (19 bp):
AACTTACAACATCATTAAT
Found at i:1769773 original size:62 final size:62
Alignment explanation
Indices: 1769672--1769789 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
1769662 CAATTGCAAG
* * * *
1769672 CAATTGGGGTAAAATTTTGCACCTATGGATGCATTAATCATAATCATGATAAGAGGTGGAGC
1 CAATTGGGATAAAATTATGCACCTATGGATGCATCAATCATAATCATCATAAGAGGTGGAGC
* *
1769734 CAATTGGGATAGAATTATGCTCCT-TCGGATGCATCAATCATAATCATCATAAGAGG
1 CAATTGGGATAAAATTATGCACCTAT-GGATGCATCAATCATAATCATCATAAGAGG
1769790 AAAAGTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 1 0.02
62 48 0.98
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (62 bp):
CAATTGGGATAAAATTATGCACCTATGGATGCATCAATCATAATCATCATAAGAGGTGGAGC
Found at i:1770428 original size:28 final size:30
Alignment explanation
Indices: 1770375--1770431 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
1770365 ACATTGGCAC
1770375 TAATTTTGAAAAAGATAAAAAATTTATTTA
1 TAATTTTGAAAAAGATAAAAAATTTATTTA
* *
1770405 TAATTTT-AAAAA-ATAAATACTTTATTT
1 TAATTTTGAAAAAGATAAAAAATTTATTT
1770432 TCATATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.52
29 5 0.20
30 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (30 bp):
TAATTTTGAAAAAGATAAAAAATTTATTTA
Found at i:1771356 original size:18 final size:18
Alignment explanation
Indices: 1771333--1771369 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1771323 ATAAAAAGAA
1771333 ATTAGTCGTACAATTACT
1 ATTAGTCGTACAATTACT
*
1771351 ATTAGTTGTACAATTACT
1 ATTAGTCGTACAATTACT
1771369 A
1 A
1771370 GTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (18 bp):
ATTAGTCGTACAATTACT
Found at i:1772775 original size:21 final size:23
Alignment explanation
Indices: 1772734--1772775 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1772724 TATTTTAATA
1772734 TATATTTTTATATATTAAAAAAC
1 TATATTTTTATATATTAAAAAAC
1772757 TATATTTTTA-ATA-TAAAAA
1 TATATTTTTATATATTAAAAA
1772776 TTAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATTTTTATATATTAAAAAAC
Found at i:1773076 original size:18 final size:17
Alignment explanation
Indices: 1773016--1773077 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
1773006 ACAAAGTAGT
**
1773016 TAAAAATATTTTTCAAA
1 TAAAAATATTTTTTTAA
* *
1773033 TAAATAATATTTCTTTACC
1 TAAA-AATATTTTTTTA-A
*
1773052 TATAAATATTTATTTTAA
1 TAAAAATATTT-TTTTAA
1773070 TAAAAATA
1 TAAAAATA
1773078 AATAATAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 4 0.12
18 23 0.68
19 7 0.21
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAATATTTTTTTAA
Found at i:1773276 original size:61 final size:62
Alignment explanation
Indices: 1773176--1773301 Score: 211
Period size: 61 Copynumber: 2.0 Consensus size: 62
1773166 AATTACAAGT
1773176 AATTCGGGTAGAATTTTGCTCCTTTGGATGCATCAATCATAACCATGATAAGAGGTGAAGCC
1 AATTCGGGTAGAATTTTGCTCCTTTGGATGCATCAATCATAACCATGATAAGAGGTGAAGCC
* *
1773238 AATT-GGGTAGAATTTTGCTCCTTTGCG-TGCATCAATCATAATCATGATAAGAGTTGAAGCC
1 AATTCGGGTAGAATTTTGCTCCTTTG-GATGCATCAATCATAACCATGATAAGAGGTGAAGCC
1773299 AAT
1 AAT
1773302 AATTTTAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 56 0.92
62 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (62 bp):
AATTCGGGTAGAATTTTGCTCCTTTGGATGCATCAATCATAACCATGATAAGAGGTGAAGCC
Found at i:1774387 original size:28 final size:28
Alignment explanation
Indices: 1774355--1774411 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1774345 TCATTGTCTA
1774355 ATATGGCTATTATGGATGTGGAAAATTT
1 ATATGGCTATTATGGATGTGGAAAATTT
1774383 ATATGGCTATTATGGATGTGGAAAATTT
1 ATATGGCTATTATGGATGTGGAAAATTT
1774411 A
1 A
1774412 AACTAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (28 bp):
ATATGGCTATTATGGATGTGGAAAATTT
Found at i:1782641 original size:13 final size:13
Alignment explanation
Indices: 1782623--1782653 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1782613 ACATTTCTTC
1782623 ATGTATCGATACA
1 ATGTATCGATACA
1782636 ATGTATCGATACA
1 ATGTATCGATACA
*
1782649 TTGTA
1 ATGTA
1782654 CCATGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1782659 original size:33 final size:32
Alignment explanation
Indices: 1782603--1782669 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
1782593 GTTACAAGCT
1782603 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTC-TCATGTATCGATACA
*
1782636 ATGTATCGATACATTGTAC-CATGTATTGATACA
1 ATGTATCGATACATT-T-CTCATGTATCGATACA
1782669 A
1 A
1782670 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCGATACA
Found at i:1782743 original size:19 final size:19
Alignment explanation
Indices: 1782698--1782754 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1782688 CTGCCAGTTT
**
1782698 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1782719 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1782738 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1782755 TATGGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1782780 original size:33 final size:32
Alignment explanation
Indices: 1782720--1782784 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1782710 CAATTTGTCC
*
1782720 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
* *
1782752 ATGTATGGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1782785 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1783811 original size:13 final size:13
Alignment explanation
Indices: 1783793--1783818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1783783 ACATTTTGGG
1783793 ATGTATCGATACA
1 ATGTATCGATACA
1783806 ATGTATCGATACA
1 ATGTATCGATACA
1783819 TATTGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1783813 original size:33 final size:32
Alignment explanation
Indices: 1783771--1783838 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1783761 CGTTACAAGC
*
1783771 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
1783804 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
1783836 CAA
1 CAA
1783839 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:1784529 original size:21 final size:23
Alignment explanation
Indices: 1784494--1784536 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1784484 TCTTTTCTCT
*
1784494 TCCCCCTTAATTAAAA-AATTTC
1 TCCCCCTTAAGTAAAATAATTTC
1784516 TCCCCCTT-AGTAAAATAATTT
1 TCCCCCTTAAGTAAAATAATTT
1784537 TGACAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (23 bp):
TCCCCCTTAAGTAAAATAATTTC
Found at i:1786414 original size:13 final size:13
Alignment explanation
Indices: 1786396--1786433 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1786386 ATAAACCCCT
*
1786396 TGTATCGATACAC
1 TGTATCGATACAA
1786409 TGTATCGATACAA
1 TGTATCGATACAA
1786422 TGTATCGATACA
1 TGTATCGATACA
1786434 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1786649 original size:8 final size:8
Alignment explanation
Indices: 1786636--1786661 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1786626 AACATCATTC
1786636 ATCACAAA
1 ATCACAAA
1786644 ATCACAAA
1 ATCACAAA
1786652 ATCACAAA
1 ATCACAAA
1786660 AT
1 AT
1786662 TGAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:1791031 original size:13 final size:13
Alignment explanation
Indices: 1791013--1791038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1791003 CAATTTTTTG
1791013 TGTATCGATACAT
1 TGTATCGATACAT
1791026 TGTATCGATACAT
1 TGTATCGATACAT
1791039 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1791124 original size:20 final size:20
Alignment explanation
Indices: 1791099--1791171 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1791089 AACTTTTTTT
1791099 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1791119 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1791140 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1791160 ATGTATCGATAC
1 ATGTATCGATAC
1791172 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1791150 original size:41 final size:42
Alignment explanation
Indices: 1791077--1791171 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
1791067 CTGCCAAGAA
*
1791077 ATGTATCGATACAACTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
*
1791119 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
1791160 ATGTATCGATAC
1 ATGTATCGATAC
1791172 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 37 0.73
42 14 0.27
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (42 bp):
ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC
Found at i:1791917 original size:62 final size:62
Alignment explanation
Indices: 1791738--1791947 Score: 341
Period size: 62 Copynumber: 3.4 Consensus size: 62
1791728 TTTGTACATT
* ** * **
1791738 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTCTCTCCCCCGTTTATTTGTACATT
1 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTTAAAAAAA
1791800 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTTAAAAAAA
1 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTTAAAAAAA
1791862 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTTAAAAAAAA
1 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTT-AAAAAAA
1791925 CTCCCCCTTAATCAA-GTAATTCA
1 CTCCCCCTTAAT-AAGGTAATTCA
1791948 TATCAAAATT
Statistics
Matches: 140, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
62 111 0.79
63 27 0.19
64 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.07, T:0.36
Consensus pattern (62 bp):
CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTTAAAAAAA
Found at i:1793767 original size:13 final size:13
Alignment explanation
Indices: 1793749--1793786 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1793739 ATAATCACCC
1793749 TGTATCGATACAG
1 TGTATCGATACAG
*
1793762 TGTATCGATACAT
1 TGTATCGATACAG
1793775 TGTATCGATACA
1 TGTATCGATACA
1793787 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1795887 original size:15 final size:15
Alignment explanation
Indices: 1795867--1795897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1795857 ATTTCGTTTG
*
1795867 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1795882 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1795897 G
1 G
1795898 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1799976 original size:13 final size:13
Alignment explanation
Indices: 1799958--1799983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1799948 CAATTTTTTG
1799958 TGTATCGATACAT
1 TGTATCGATACAT
1799971 TGTATCGATACAT
1 TGTATCGATACAT
1799984 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1800069 original size:20 final size:20
Alignment explanation
Indices: 1800044--1800136 Score: 141
Period size: 20 Copynumber: 4.6 Consensus size: 20
1800034 AACTTTTTTT
1800044 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1800064 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1800084 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1800105 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1800125 ATGTATCGATAC
1 ATGTATCGATAC
1800137 TTTGAATTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 48 0.75
21 16 0.25
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1802724 original size:13 final size:13
Alignment explanation
Indices: 1802706--1802731 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1802696 ACATTTTGGG
1802706 ATGTATCGATACA
1 ATGTATCGATACA
1802719 ATGTATCGATACA
1 ATGTATCGATACA
1802732 TATTGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1802726 original size:33 final size:32
Alignment explanation
Indices: 1802684--1802751 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1802674 CGTTACAAGC
*
1802684 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
1802717 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
1802749 CAA
1 CAA
1802752 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:1802830 original size:20 final size:21
Alignment explanation
Indices: 1802783--1802837 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1802773 GCCAATGACC
**
1802783 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1802804 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1802824 TGTATCGATACATT
1 TGTATCGATACATT
1802838 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1803163 original size:26 final size:26
Alignment explanation
Indices: 1803133--1803184 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1803123 TCAATCCTTT
1803133 GTTATATCAAAACCAAGATCCTAACA
1 GTTATATCAAAACCAAGATCCTAACA
*
1803159 GTTATATCAAAACTAAGATCCTAACA
1 GTTATATCAAAACCAAGATCCTAACA
1803185 ATCTCCCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (26 bp):
GTTATATCAAAACCAAGATCCTAACA
Found at i:1803517 original size:42 final size:41
Alignment explanation
Indices: 1803426--1803508 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
1803416 TTCTCCCCTT
* * *
1803426 AAAAAATTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAA
1 AAAAAATTCTCCCCCTTAAACAATTATCTCCCCCCTTAT-AA
1803468 AAAAAATTCTCCCCCTTAAACAATTATCTTCTCCCCCTTAT
1 AAAAAATTCTCCCCCTTAAACAATTATC-TC-CCCCCTTAT
1803509 GTAAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 27 0.75
43 2 0.06
44 7 0.19
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (41 bp):
AAAAAATTCTCCCCCTTAAACAATTATCTCCCCCCTTATAA
Found at i:1805371 original size:13 final size:13
Alignment explanation
Indices: 1805353--1805394 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
1805343 AAATAGTACC
1805353 CAATGTATCGATA
1 CAATGTATCGATA
1805366 CAATGTATCGATA
1 CAATGTATCGATA
1805379 CAATGTATCGATA
1 CAATGTATCGATA
1805392 CAA
1 CAA
1805395 GGAATGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1806490 original size:13 final size:13
Alignment explanation
Indices: 1806472--1806496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1806462 ATATTGCAGA
1806472 GTATCGATACATT
1 GTATCGATACATT
1806485 GTATCGATACAT
1 GTATCGATACAT
1806497 AACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1806614 original size:13 final size:13
Alignment explanation
Indices: 1806596--1806621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1806586 TACACACAAG
1806596 ATGTATCGATACA
1 ATGTATCGATACA
1806609 ATGTATCGATACA
1 ATGTATCGATACA
1806622 TCCCAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1806641 original size:33 final size:32
Alignment explanation
Indices: 1806578--1806641 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1806568 CTTAACTGTT
* *
1806578 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCAATACAA
*
1806610 TGTATCGATACATCCCAAAATGTATCAATACA
1 TGTATCGATACA-CACAAAATGTATCAATACA
1806642 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCAATACAA
Found at i:1812558 original size:8 final size:8
Alignment explanation
Indices: 1812545--1812570 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1812535 ATTTGATTCA
1812545 ATTTTGTG
1 ATTTTGTG
1812553 ATTTTGTG
1 ATTTTGTG
1812561 ATTTTGTG
1 ATTTTGTG
1812569 AT
1 AT
1812571 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1812791 original size:13 final size:13
Alignment explanation
Indices: 1812773--1812797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1812763 CAGCATTCTC
1812773 TGTATCGATACAG
1 TGTATCGATACAG
1812786 TGTATCGATACA
1 TGTATCGATACA
1812798 AGGGGTTTAT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1817701 original size:13 final size:13
Alignment explanation
Indices: 1817683--1817720 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1817673 TAGCATTCTC
*
1817683 TGTATCGATACAT
1 TGTATCGATACAG
1817696 TGTATCGATACAG
1 TGTATCGATACAG
1817709 TGTATCGATACA
1 TGTATCGATACA
1817721 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1817887 original size:20 final size:20
Alignment explanation
Indices: 1817852--1817892 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1817842 CAAATTTCTT
1817852 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1817874 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1817893 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1818179 original size:21 final size:20
Alignment explanation
Indices: 1818154--1818195 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1818144 CATCTAGGCA
*
1818154 GCACCCACAAGGTCGCGACCG
1 GCACCC-CAAGGTCGCAACCG
*
1818175 GCACCCCCAGGTCGCAACCG
1 GCACCCCAAGGTCGCAACCG
1818195 G
1 G
1818196 ATAGCCCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.21, C:0.45, G:0.29, T:0.05
Consensus pattern (20 bp):
GCACCCCAAGGTCGCAACCG
Found at i:1819555 original size:19 final size:22
Alignment explanation
Indices: 1819527--1819571 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1819517 TTCTGCAAAT
1819527 AAATTTT-T-ATTAAGGGGGAG
1 AAATTTTATGATTAAGGGGGAG
1819547 AAATTTTATGATTAAGGGGGAG
1 AAATTTTATGATTAAGGGGGAG
1819569 AAA
1 AAA
1819572 GAAATTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.30
21 1 0.04
22 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (22 bp):
AAATTTTATGATTAAGGGGGAG
Found at i:1820346 original size:32 final size:33
Alignment explanation
Indices: 1820305--1820366 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1820295 CTTAACTGTT
*
1820305 TGTATCGATACA-CACAAGATGTATCGATATAA
1 TGTATCGATACATCACAAAATGTATCGATATAA
*
1820337 TGTATCGATACATCCCAAAATGTATCGATA
1 TGTATCGATACATCACAAAATGTATCGATA
1820367 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCGATACATCACAAAATGTATCGATATAA
Found at i:1824484 original size:19 final size:19
Alignment explanation
Indices: 1824448--1824489 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1824438 CTAATGTTAT
* *
1824448 TTAACTTTTGACTCAAATAA
1 TTAACTTTTGAATAAAAT-A
1824468 TTAA-TTTTGAATAAAATA
1 TTAACTTTTGAATAAAATA
1824486 TTAA
1 TTAA
1824490 AAAAATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 11 0.55
20 4 0.20
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (19 bp):
TTAACTTTTGAATAAAATA
Found at i:1824942 original size:37 final size:36
Alignment explanation
Indices: 1824876--1824945 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
1824866 ATATAAACAT
* * * *
1824876 TAAAAAATTGTTAAATTATTTATTTTTAAAATTTAA
1 TAAAAAATTATTAAATTATTAAATATTAAAATTTAA
1824912 TAAAAAATTTATTAAATTATTAAATATTAAAATT
1 TAAAAAA-TTATTAAATTATTAAATATTAAAATT
1824946 AAAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 7 0.24
37 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (36 bp):
TAAAAAATTATTAAATTATTAAATATTAAAATTTAA
Found at i:1824964 original size:29 final size:26
Alignment explanation
Indices: 1824932--1824991 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
1824922 ATTAAATTAT
1824932 TAAATATTAAAATTAAAAATATATTTTTA
1 TAAATATT-AAATTAAAAAT-TA-TTTTA
* *
1824961 TAAAAATTAATTTAAAAATTATTTTA
1 TAAATATTAAATTAAAAATTATTTTA
1824987 TAAAT
1 TAAAT
1824992 CAACTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.32
27 2 0.07
28 10 0.36
29 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAATATTAAATTAAAAATTATTTTA
Found at i:1824984 original size:11 final size:12
Alignment explanation
Indices: 1824961--1825010 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1824951 TATATTTTTA
1824961 TAAAAATTAATT
1 TAAAAATTAATT
*
1824973 TAAAAATTATTT
1 TAAAAATTAATT
* * *
1824985 TATAAATCAACT
1 TAAAAATTAATT
1824997 TAAAAA--AATT
1 TAAAAATTAATT
1825007 TAAA
1 TAAA
1825011 TTATTTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
10 7 0.23
12 24 0.77
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:1824999 original size:24 final size:27
Alignment explanation
Indices: 1824944--1825002 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 27
1824934 AATATTAAAA
* *
1824944 TTAAAAATATATTTTTATAAAAATTAAT
1 TTAAAAATATATTTTTAT-AAAATCAAC
1824972 TTAAAAAT-TA-TTTTAT-AAATCAAC
1 TTAAAAATATATTTTTATAAAATCAAC
1824996 TTAAAAA
1 TTAAAAA
1825003 AATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 13 0.45
26 6 0.21
27 2 0.07
28 8 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
TTAAAAATATATTTTTATAAAATCAAC
Found at i:1826075 original size:2 final size:2
Alignment explanation
Indices: 1826068--1826099 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1826058 TTTAACATGC
1826068 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
1826100 GCCATAGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826677 original size:3 final size:3
Alignment explanation
Indices: 1826669--1826711 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1826659 TTAATCATGA
1826669 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1826712 TTTAAATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1832498 original size:15 final size:15
Alignment explanation
Indices: 1832478--1832509 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1832468 TGAGGCTTCA
1832478 TGTTCTCATAGATAT
1 TGTTCTCATAGATAT
1832493 TGTTCTCATAGATAT
1 TGTTCTCATAGATAT
1832508 TG
1 TG
1832510 ACATCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (15 bp):
TGTTCTCATAGATAT
Found at i:1833870 original size:20 final size:20
Alignment explanation
Indices: 1833847--1833892 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1833837 GTAATGTAAT
*
1833847 GATATATTGTG-CATTGTATC
1 GATACATTGTGACA-TGTATC
*
1833867 GATACATTTTGACATGTATC
1 GATACATTGTGACATGTATC
1833887 GATACA
1 GATACA
1833893 AATGAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (20 bp):
GATACATTGTGACATGTATC
Found at i:1833925 original size:113 final size:111
Alignment explanation
Indices: 1833734--1833947 Score: 277
Period size: 113 Copynumber: 1.9 Consensus size: 111
1833724 GAGATGTATC
* * ** * * *
1833734 GATACATTGTGTATTGTATTGATACATTTTCATGTGTGTTGATACAAATGGGGATTTTAGGATTT
1 GATACATTGTGCATTGTATCGATACATTTTCACATGTATCGATACAAATGGGGA-TTTAGGACTT
*
1833799 TTTTAGCTACTGCCAACCAAATGTATTGATACATTCACGTAATGTAAT
65 TTTTAGCTACTGCCAA-CAAATGTATCGATACATTCACGTAATGTAAT
* * *
1833847 GATATATTGTGCATTGTATCGATACATTTTGACATGTATCGATACAAATGAGGG-TTTCGGCACT
1 GATACATTGTGCATTGTATCGATACATTTTCACATGTATCGATACAAATG-GGGATTTAGG-ACT
*
1833911 TTTTTAGCTACTGCCAAGAAATGTATCGATACATTCA
64 TTTTTAGCTACTGCCAACAAATGTATCGATACATTCA
1833948 ACCTTAAACA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
112 23 0.26
113 61 0.70
114 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (111 bp):
GATACATTGTGCATTGTATCGATACATTTTCACATGTATCGATACAAATGGGGATTTAGGACTTT
TTTAGCTACTGCCAACAAATGTATCGATACATTCACGTAATGTAAT
Found at i:1836010 original size:21 final size:21
Alignment explanation
Indices: 1835986--1836026 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1835976 AAATATATTG
*
1835986 ACATTATGTGAATGTATCAAA
1 ACATTATGTGAATATATCAAA
1836007 ACATTATGTGAATATATCAA
1 ACATTATGTGAATATATCAA
1836027 TGCATCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
ACATTATGTGAATATATCAAA
Found at i:1840316 original size:18 final size:19
Alignment explanation
Indices: 1840293--1840328 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1840283 TGTTCAAAGA
1840293 CTTATTATTATTA-ATATT
1 CTTATTATTATTATATATT
1840311 CTTATTATTATTATATAT
1 CTTATTATTATTATATAT
1840329 GAGCATGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (19 bp):
CTTATTATTATTATATATT
Found at i:1840441 original size:2 final size:2
Alignment explanation
Indices: 1840434--1840474 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1840424 TGATTGAAGT
*
1840434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1840475 GTTTCTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1846003 original size:34 final size:34
Alignment explanation
Indices: 1845956--1846059 Score: 181
Period size: 34 Copynumber: 3.1 Consensus size: 34
1845946 AATATATTGA
*
1845956 TACACACCCAGATGTATCGATACAAATTGTTAAG
1 TACACACCTAGATGTATCGATACAAATTGTTAAG
1845990 TACACACCTAGATGTATCGATACAAATTGTTAAG
1 TACACACCTAGATGTATCGATACAAATTGTTAAG
* *
1846024 TACACACCTAGATGTATCAATACAAATTGCTAAG
1 TACACACCTAGATGTATCGATACAAATTGTTAAG
1846058 TA
1 TA
1846060 TCGATACACC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (34 bp):
TACACACCTAGATGTATCGATACAAATTGTTAAG
Found at i:1846647 original size:34 final size:34
Alignment explanation
Indices: 1846586--1846651 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1846576 TAATTCTCGG
* * *
1846586 AGTGATTGTGAGGTTCTATCTTAGCCTTGAAAGAT
1 AGTGATTGTAAGGTTATACCTTAGCCTT-AAAGAT
*
1846621 AGTG-TTGTAAGGTTATACCTTTGCCTTAAAG
1 AGTGATTGTAAGGTTATACCTTAGCCTTAAAG
1846652 GTAGCAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 4 0.15
34 19 0.70
35 4 0.15
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (34 bp):
AGTGATTGTAAGGTTATACCTTAGCCTTAAAGAT
Found at i:1849544 original size:183 final size:183
Alignment explanation
Indices: 1849236--1849601 Score: 732
Period size: 183 Copynumber: 2.0 Consensus size: 183
1849226 ATTGATTGTG
1849236 ATAAAGTTTGTGATGCATGCATTAAAGGAAAACATAGAAAGACTTCCTTCAAACCTATAACATTG
1 ATAAAGTTTGTGATGCATGCATTAAAGGAAAACATAGAAAGACTTCCTTCAAACCTATAACATTG
1849301 TCACAACCACTAGAGTTTTGCAATTAGTATGTATCAATTTATTTGGTCCTACTAGGACATAAAGT
66 TCACAACCACTAGAGTTTTGCAATTAGTATGTATCAATTTATTTGGTCCTACTAGGACATAAAGT
1849366 CTAGGTGGTAAATGATATGATTTTGTTATTATGGTTGATTCTTCAAGGTTTAC
131 CTAGGTGGTAAATGATATGATTTTGTTATTATGGTTGATTCTTCAAGGTTTAC
1849419 ATAAAGTTTGTGATGCATGCATTAAAGGAAAACATAGAAAGACTTCCTTCAAACCTATAACATTG
1 ATAAAGTTTGTGATGCATGCATTAAAGGAAAACATAGAAAGACTTCCTTCAAACCTATAACATTG
1849484 TCACAACCACTAGAGTTTTGCAATTAGTATGTATCAATTTATTTGGTCCTACTAGGACATAAAGT
66 TCACAACCACTAGAGTTTTGCAATTAGTATGTATCAATTTATTTGGTCCTACTAGGACATAAAGT
1849549 CTAGGTGGTAAATGATATGATTTTGTTATTATGGTTGATTCTTCAAGGTTTAC
131 CTAGGTGGTAAATGATATGATTTTGTTATTATGGTTGATTCTTCAAGGTTTAC
1849602 TTAGGCTCTC
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (183 bp):
ATAAAGTTTGTGATGCATGCATTAAAGGAAAACATAGAAAGACTTCCTTCAAACCTATAACATTG
TCACAACCACTAGAGTTTTGCAATTAGTATGTATCAATTTATTTGGTCCTACTAGGACATAAAGT
CTAGGTGGTAAATGATATGATTTTGTTATTATGGTTGATTCTTCAAGGTTTAC
Found at i:1850626 original size:33 final size:33
Alignment explanation
Indices: 1850581--1850646 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1850571 CTACCACTGT
* * *
1850581 TTGTATTGATACATGGT-ACATTGTATCGATACA
1 TTGTATTAATACATGATGA-ATTGCATCGATACA
1850614 TTGTATTAATACATGATGAATTGCATCGATACA
1 TTGTATTAATACATGATGAATTGCATCGATACA
1850647 CTGCTTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATTAATACATGATGAATTGCATCGATACA
Found at i:1853186 original size:20 final size:20
Alignment explanation
Indices: 1853163--1853235 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1853153 ACAATTCAAA
1853163 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*****
1853183 GTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1853204 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1853224 GTATCGATACAT
1 GTATCGATACAT
1853236 AAAAAAAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1853214 original size:41 final size:42
Alignment explanation
Indices: 1853163--1853257 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 42
1853153 ACAATTCAAA
1853163 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1853204 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1853246 GTATCGATACAT
1 GTATCGATACAT
1853258 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 32 0.60
42 21 0.40
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:1853314 original size:13 final size:13
Alignment explanation
Indices: 1853296--1853321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1853286 TACAGCAAGT
1853296 ATGTATCGATACA
1 ATGTATCGATACA
1853309 ATGTATCGATACA
1 ATGTATCGATACA
1853322 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1859506 original size:20 final size:21
Alignment explanation
Indices: 1859427--1859505 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1859417 AATGTCCAAA
*
1859427 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1859447 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1859472 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1859492 TTGTATCGATACAT
1 ATGTATCGATACAT
1859506 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1859510 original size:13 final size:13
Alignment explanation
Indices: 1859492--1859530 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1859482 ACATTTTTCT
1859492 TTGTATCGATACA
1 TTGTATCGATACA
1859505 TTGTATCGATACA
1 TTGTATCGATACA
*
1859518 CTGTATCGATACA
1 TTGTATCGATACA
1859531 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1861991 original size:20 final size:20
Alignment explanation
Indices: 1861968--1862040 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1861958 ACAATTCAAA
1861968 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*****
1861988 GTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1862009 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1862029 GTATCGATACAT
1 GTATCGATACAT
1862041 AAAAAAAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1862019 original size:41 final size:42
Alignment explanation
Indices: 1861968--1862062 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 42
1861958 ACAATTCAAA
1861968 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1862009 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1862051 GTATCGATACAT
1 GTATCGATACAT
1862063 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 32 0.60
42 21 0.40
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:1862119 original size:13 final size:13
Alignment explanation
Indices: 1862101--1862126 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1862091 TACAGCAAGT
1862101 ATGTATCGATACA
1 ATGTATCGATACA
1862114 ATGTATCGATACA
1 ATGTATCGATACA
1862127 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1863884 original size:33 final size:33
Alignment explanation
Indices: 1863842--1863907 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1863832 AAGAAATTCT
*
1863842 TTTAAACCCATAAACATTGTCACGACATCTAGA
1 TTTAAACCCATAAACATTGTCACAACATCTAGA
*
1863875 TTTAAACCCATAAATATTGTCACAACATCTAGA
1 TTTAAACCCATAAACATTGTCACAACATCTAGA
1863908 GTCTTGCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (33 bp):
TTTAAACCCATAAACATTGTCACAACATCTAGA
Found at i:1868718 original size:38 final size:38
Alignment explanation
Indices: 1868649--1868721 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
1868639 CTAGAACAAA
*
1868649 AAGGGGGAGAAATATTGTTTTCAAAATAAATTTTTATC
1 AAGGGGGAGAAATATTGTTTTCAAAAAAAATTTTTATC
* *
1868687 AAGGGGGAGAAA-ATTTTTTTTAAAGAAAAATTTTT
1 AAGGGGGAGAAATATTGTTTTCAAA-AAAAATTTTT
1868722 CAAAAAGAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 10 0.32
38 21 0.68
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (38 bp):
AAGGGGGAGAAATATTGTTTTCAAAAAAAATTTTTATC
Found at i:1869283 original size:20 final size:20
Alignment explanation
Indices: 1869258--1869309 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1869248 AAACCCTTGA
1869258 ATGTATCGATACACACCCAG
1 ATGTATCGATACACACCCAG
1869278 ATGTATCGAT--ACACCCAG
1 ATGTATCGATACACACCCAG
1869296 ATTGTATCGATACA
1 A-TGTATCGATACA
1869310 TGTTTATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.31
19 9 0.31
20 10 0.34
21 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
ATGTATCGATACACACCCAG
Found at i:1869303 original size:19 final size:18
Alignment explanation
Indices: 1869258--1869309 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 18
1869248 AAACCCTTGA
1869258 ATGTATCGATACACACCCAG
1 ATGTATCGAT--ACACCCAG
1869278 ATGTATCGATACACCCAG
1 ATGTATCGATACACCCAG
1869296 ATTGTATCGATACA
1 A-TGTATCGATACA
1869310 TGTTTATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.29
19 12 0.39
20 10 0.32
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (18 bp):
ATGTATCGATACACCCAG
Found at i:1869318 original size:19 final size:19
Alignment explanation
Indices: 1869296--1869401 Score: 125
Period size: 19 Copynumber: 5.8 Consensus size: 19
1869286 ATACACCCAG
*
1869296 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGTTC
1869315 ATTGTATCGAT--A----C
1 ATTGTATCGATACATGTTC
1869328 ATTGTATCGATACATGTTC
1 ATTGTATCGATACATGTTC
*
1869347 ATTTTATCGATACATGTTC
1 ATTGTATCGATACATGTTC
**
1869366 ATTGTATCGATACATGGAC
1 ATTGTATCGATACATGTTC
1869385 AATTGTATCGATACATG
1 -ATTGTATCGATACATG
1869402 AAACTAGCAG
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.15
15 1 0.01
17 1 0.01
19 46 0.61
20 16 0.21
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (19 bp):
ATTGTATCGATACATGTTC
Found at i:1869333 original size:13 final size:13
Alignment explanation
Indices: 1869315--1869342 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1869305 ATACATGTTT
1869315 ATTGTATCGATAC
1 ATTGTATCGATAC
1869328 ATTGTATCGATAC
1 ATTGTATCGATAC
1869341 AT
1 AT
1869343 GTTCATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:1869337 original size:32 final size:32
Alignment explanation
Indices: 1869296--1869361 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1869286 ATACACCCAG
*
1869296 ATTGTATCGATACATGTTTATTGTATCGATAC
1 ATTGTATCGATACATGTTCATTGTATCGATAC
*
1869328 ATTGTATCGATACATGTTCATTTTATCGATAC
1 ATTGTATCGATACATGTTCATTGTATCGATAC
1869360 AT
1 AT
1869362 GTTCATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (32 bp):
ATTGTATCGATACATGTTCATTGTATCGATAC
Found at i:1869495 original size:33 final size:33
Alignment explanation
Indices: 1869430--1869497 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1869420 CTACCACTGT
*
1869430 TTGTATCGATACATGGTACATTATATCAATACA
1 TTGTATCGATACATGATACATTATATCAATACA
* *
1869463 TTGTATCGATACATGATGA-ATTTTATCGATACA
1 TTGTATCGATACATGAT-ACATTATATCAATACA
1869496 TT
1 TT
1869498 ACTTTTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATGATACATTATATCAATACA
Found at i:1872251 original size:21 final size:21
Alignment explanation
Indices: 1872227--1872266 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1872217 GATGTTTGAA
* *
1872227 TGATCTTGTGTTGTTAATTGT
1 TGATCTTGCGTGGTTAATTGT
*
1872248 TGATGTTGCGTGGTTAATT
1 TGATCTTGCGTGGTTAATT
1872267 ATCTGTGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.53
Consensus pattern (21 bp):
TGATCTTGCGTGGTTAATTGT
Found at i:1882065 original size:13 final size:13
Alignment explanation
Indices: 1882047--1882072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1882037 TACAGCAAGT
1882047 ATGTATCGATACA
1 ATGTATCGATACA
1882060 ATGTATCGATACA
1 ATGTATCGATACA
1882073 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1884323 original size:21 final size:21
Alignment explanation
Indices: 1884290--1884334 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1884280 TTGCAAGTTG
*
1884290 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1884312 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1884332 AAA
1 AAA
1884335 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1886158 original size:15 final size:15
Alignment explanation
Indices: 1886138--1886168 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1886128 TAAAAATGTC
*
1886138 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1886153 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1886168 C
1 C
1886169 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1888263 original size:20 final size:20
Alignment explanation
Indices: 1888184--1888263 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1888174 AATGTCCAAA
*
1888184 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1888204 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1888229 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1888249 TTGTATCGATACATT
1 ATGTATCGATACATT
1888264 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1888267 original size:13 final size:13
Alignment explanation
Indices: 1888249--1888287 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1888239 ACATTTTTCT
1888249 TTGTATCGATACA
1 TTGTATCGATACA
1888262 TTGTATCGATACA
1 TTGTATCGATACA
* *
1888275 CTCTATCGATACA
1 TTGTATCGATACA
1888288 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1888432 original size:21 final size:21
Alignment explanation
Indices: 1888408--1888454 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1888398 AAATCTTTTG
1888408 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1888429 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1888449 CAAAAT
1 CAAAAT
1888455 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1888451 original size:20 final size:19
Alignment explanation
Indices: 1888410--1888452 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1888400 ATCTTTTGCA
1888410 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1888430 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1888450 AAA
1 AAA
1888453 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1890833 original size:13 final size:13
Alignment explanation
Indices: 1890815--1890840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1890805 TACAGCAAGT
1890815 ATGTATCGATACA
1 ATGTATCGATACA
1890828 ATGTATCGATACA
1 ATGTATCGATACA
1890841 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1901664 original size:10 final size:10
Alignment explanation
Indices: 1901649--1901682 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1901639 CCATTAGGAA
1901649 AAAGATTTTT
1 AAAGATTTTT
1901659 AAAGATTTTT
1 AAAGATTTTT
*
1901669 GAAATATTTTT
1 -AAAGATTTTT
1901680 AAA
1 AAA
1901683 TCGATCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (10 bp):
AAAGATTTTT
Found at i:1902156 original size:27 final size:27
Alignment explanation
Indices: 1902086--1902148 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1902076 TGTCATCATC
1902086 GGGGATACTTTAACCCCATTCCTCCGA
1 GGGGATACTTTAACCCCATTCCTCCGA
1902113 GGGGATACTTTAACCCCATTCCTCCGA
1 GGGGATACTTTAACCCCATTCCTCCGA
1902140 GGGGATACT
1 GGGGATACT
1902149 CCAACCCCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (27 bp):
GGGGATACTTTAACCCCATTCCTCCGA
Found at i:1904979 original size:13 final size:13
Alignment explanation
Indices: 1904961--1904986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1904951 ATTCTTCATT
1904961 TATCGATACAATG
1 TATCGATACAATG
1904974 TATCGATACAATG
1 TATCGATACAATG
1904987 AGCCACGTAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1905078 original size:19 final size:18
Alignment explanation
Indices: 1905032--1905089 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
1905022 ACTGCCAGTT
1905032 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
*
1905051 TGTATGTATCGATACAATG
1 T-CATGTATCGATACAATG
*
1905070 ATCATGTATTGATACAATG
1 -TCATGTATCGATACAATG
1905089 T
1 T
1905090 ATCGATACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:1914073 original size:33 final size:33
Alignment explanation
Indices: 1914036--1914106 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1914026 GTATGCATCG
1914036 ATACAATATATCGATACAAAGCATAATGTATCA
1 ATACAATATATCGATACAAAGCATAATGTATCA
* * * *
1914069 ATACAATGTATCTATACAAAGCATAATGTGTCG
1 ATACAATATATCGATACAAAGCATAATGTATCA
1914102 ATACA
1 ATACA
1914107 TCTCGATGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (33 bp):
ATACAATATATCGATACAAAGCATAATGTATCA
Found at i:1919463 original size:90 final size:90
Alignment explanation
Indices: 1919310--1919488 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
1919300 TGACAACTTC
* * * * *
1919310 ATTTTATTTAAAGATGATAAGATTCCACTAGGAGGGATGATTTCATTGAAAGCCCTACATGTCAT
1 ATTTTATTCAAAGATGATAAGATTCCACTAGAAGGGACGATTTCATTAAAAGCACTACATGTCAT
1919375 GACTAACTATAAGAGGCACATCTTT
66 GACTAACTATAAGAGGCACATCTTT
* * *
1919400 ATTTTATTCAAGGATGATGAGATTCCATTAGAAGGGACGATTTCATTAAAAGCACTACATGTCAT
1 ATTTTATTCAAAGATGATAAGATTCCACTAGAAGGGACGATTTCATTAAAAGCACTACATGTCAT
*
1919465 GACTAACTGTAAGAGGCACATCTT
66 GACTAACTATAAGAGGCACATCTT
1919489 ACTGAGGGTC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (90 bp):
ATTTTATTCAAAGATGATAAGATTCCACTAGAAGGGACGATTTCATTAAAAGCACTACATGTCAT
GACTAACTATAAGAGGCACATCTTT
Found at i:1924868 original size:27 final size:27
Alignment explanation
Indices: 1924830--1924897 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1924820 GTTTAAAAGC
1924830 GGGGTTAGAGTATCTTTTCAGAAGAAT
1 GGGGTTAGAGTATCTTTTCAGAAGAAT
*
1924857 GGGGTTAGAGTATCTTTTTAGAAGAAT
1 GGGGTTAGAGTATCTTTTCAGAAGAAT
*
1924884 GGGGTTAAAGTATC
1 GGGGTTAGAGTATC
1924898 CCCGATGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.34
Consensus pattern (27 bp):
GGGGTTAGAGTATCTTTTCAGAAGAAT
Found at i:1927362 original size:52 final size:51
Alignment explanation
Indices: 1927284--1927400 Score: 153
Period size: 52 Copynumber: 2.3 Consensus size: 51
1927274 CATTGAAGAT
* * * *
1927284 GTATCGATATATTTAGGTCAAAACCCAGAATGTATCGATACAATGAATAAC
1 GTATCGATACATTTAGGTCAAAACCCAGAATATATCGATACAATAAAAAAC
* * *
1927335 GTATCGATACATTTGGGTCCAAAACCCAGAATATATTGATACAATAAAAAAT
1 GTATCGATACATTTAGGT-CAAAACCCAGAATATATCGATACAATAAAAAAC
*
1927387 GTATCAATACATTT
1 GTATCGATACATTT
1927401 TCTTTGTAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 16 0.28
52 41 0.72
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (51 bp):
GTATCGATACATTTAGGTCAAAACCCAGAATATATCGATACAATAAAAAAC
Found at i:1928308 original size:52 final size:52
Alignment explanation
Indices: 1928135--1928452 Score: 252
Period size: 52 Copynumber: 6.1 Consensus size: 52
1928125 CATGCGCTAT
* * * * * *
1928135 TTCAAGGCCAGTAACATTAGG-CTTAAAGGTGATGAGAA-TGCCAATGTGCTGA
1 TTCAAGGCTAGCAACATT-GGACTTAAAGATGATCA-AAGTGCCAATATGTTGA
** * *
1928187 TTCAAGGCTAGTGACATTGGGCTTAAAGATGAT-AAGGGTGCCAATATGTTGA
1 TTCAAGGCTAGCAACATTGGACTTAAAGATGATCAA-AGTGCCAATATGTTGA
* * * *
1928239 TTCAAGGCTAGCGATATTGGACTTAAAGATGATGAAAGTGCCAATATGCTGA
1 TTCAAGGCTAGCAACATTGGACTTAAAGATGATCAAAGTGCCAATATGTTGA
* * * * * *
1928291 TTCAAGGCCAGCAATATTAGATTTAAAGATGA-CAATGATGCCAATATGTTGG
1 TTCAAGGCTAGCAACATTGGACTTAAAGATGATCAAAG-TGCCAATATGTTGA
** * * * *
1928343 TTCAAGGCTAGCGCCATTAGA-TCTAAAGATAATAAAAGGTGCCAATATATTGA
1 TTCAAGGCTAGCAACATTGGACT-TAAAGATGATCAAA-GTGCCAATATGTTGA
** * * *
1928396 TTCAAGGCTAGCAGTATTGGACTTAAATATGA-CAAGAGTGCTAATGTGTTGA
1 TTCAAGGCTAGCAACATTGGACTTAAAGATGATCAA-AGTGCCAATATGTTGA
1928448 TTCAA
1 TTCAA
1928453 AGCCAGCGAC
Statistics
Matches: 218, Mismatches: 38, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
50 1 0.00
51 7 0.03
52 167 0.77
53 41 0.19
54 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (52 bp):
TTCAAGGCTAGCAACATTGGACTTAAAGATGATCAAAGTGCCAATATGTTGA
Found at i:1928317 original size:104 final size:104
Alignment explanation
Indices: 1928148--1928467 Score: 347
Period size: 104 Copynumber: 3.1 Consensus size: 104
1928138 AAGGCCAGTA
* * * ** * *
1928148 ACATTAGGCTTAAAGGTGATGAGAA-TGCCAATGTGCTGATTCAAGGCTAGTGACATTGGGCTTA
1 ACATTAGACTTAAAGATGATGA-AAGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTA
*
1928212 AAGATGATAAGGGTGCCAATATGTTGATTCAAGGCTAGCG
65 AAGATGACAAGGGTGCCAATATGTTGATTCAAGGCTAGCG
* * * * *
1928252 ATATTGGACTTAAAGATGATGAAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTAGATTTAA
1 ACATTAGACTTAAAGATGATGAAAGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTAA
* * *
1928317 AGATGACAATGATGCCAATATGTTGGTTCAAGGCTAGCG
66 AGATGACAAGGGTGCCAATATGTTGATTCAAGGCTAGCG
* * * ** *
1928356 CCATTAGA-TCTAAAGATAATAAAAGGTGCCAATATATTGATTCAAGGCTAGCAGTATTGGACTT
1 ACATTAGACT-TAAAGATGATGAAA-GTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTT
* * * * * *
1928420 AAATATGACAAGAGTGCTAATGTGTTGATTCAAAGCCAGCG
64 AAAGATGACAAGGGTGCCAATATGTTGATTCAAGGCTAGCG
1928461 ACATTAG
1 ACATTAG
1928468 GCTTTGGTGA
Statistics
Matches: 176, Mismatches: 37, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
103 3 0.02
104 102 0.58
105 71 0.40
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (104 bp):
ACATTAGACTTAAAGATGATGAAAGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTAA
AGATGACAAGGGTGCCAATATGTTGATTCAAGGCTAGCG
Found at i:1928645 original size:33 final size:32
Alignment explanation
Indices: 1928605--1928675 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
1928595 CTTGCATGGA
**
1928605 CTTTGAGAAAAGATGCCACCAACTTATGTGGG
1 CTTTGAGAAAAGACACCACCAACTTATGTGGG
* * *
1928637 CTATTGAGAAAGGACACCATCGACTTATGTGGG
1 CT-TTGAGAAAAGACACCACCAACTTATGTGGG
1928670 CTTTGA
1 CTTTGA
1928676 AAGGGTCACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (32 bp):
CTTTGAGAAAAGACACCACCAACTTATGTGGG
Found at i:1928693 original size:31 final size:31
Alignment explanation
Indices: 1928626--1928741 Score: 106
Period size: 33 Copynumber: 3.6 Consensus size: 31
1928616 GATGCCACCA
* *
1928626 ACTTATGTGGGCTATTGAGAAAGGACACCATCG
1 ACTTATGTGGGCT-TTGA-AAGGGTCACCATCG
*
1928659 ACTTATGTGGGCTTTGAAAGGGTCACCATTG
1 ACTTATGTGGGCTTTGAAAGGGTCACCATCG
* * ** * *
1928690 ACTTGTGTAGGCTTTAGAAAAGGGTTGCCACCA
1 ACTTATGTGGGCTTT-G-AAAGGGTCACCATCG
*
1928723 ACTTGTGTGGGCTTTGAAA
1 ACTTATGTGGGCTTTGAAA
1928742 AAGATGTCAC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
31 27 0.39
32 6 0.09
33 37 0.53
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (31 bp):
ACTTATGTGGGCTTTGAAAGGGTCACCATCG
Found at i:1930254 original size:13 final size:13
Alignment explanation
Indices: 1930236--1930261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1930226 CAATTTTTTG
1930236 TGTATCGATACAT
1 TGTATCGATACAT
1930249 TGTATCGATACAT
1 TGTATCGATACAT
1930262 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1932585 original size:20 final size:20
Alignment explanation
Indices: 1932562--1932634 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1932552 ACAATTCAAA
1932562 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1932582 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1932603 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1932623 GTATCGATACAT
1 GTATCGATACAT
1932635 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1932606 original size:21 final size:21
Alignment explanation
Indices: 1932580--1932655 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1932570 ACATGTTGCA
1932580 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1932601 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1932621 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1932642 TTGTATCGATACAT
1 ATGTATCGATACAT
1932656 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1932613 original size:41 final size:41
Alignment explanation
Indices: 1932562--1932655 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1932552 ACAATTCAAA
*
1932562 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1932603 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1932644 GTATCGATACAT
1 GTATCGATACAT
1932656 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1932712 original size:13 final size:13
Alignment explanation
Indices: 1932694--1932719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1932684 TACAGCAAGT
1932694 ATGTATCGATACA
1 ATGTATCGATACA
1932707 ATGTATCGATACA
1 ATGTATCGATACA
1932720 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1938904 original size:20 final size:21
Alignment explanation
Indices: 1938825--1938903 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1938815 AATGTCCAAA
*
1938825 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATATTTTCT
* *
1938845 GTGTATCGATACATATGGAAATTCT
1 ATGTATCGATACATAT----TTTCT
1938870 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATATTTTCT
*
1938890 TTGTATCGATACAT
1 ATGTATCGATACAT
1938904 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATATTTTCT
Found at i:1938908 original size:13 final size:13
Alignment explanation
Indices: 1938890--1938928 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1938880 ACATTTTTCT
1938890 TTGTATCGATACA
1 TTGTATCGATACA
1938903 TTGTATCGATACA
1 TTGTATCGATACA
*
1938916 CTGTATCGATACA
1 TTGTATCGATACA
1938929 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1940735 original size:23 final size:23
Alignment explanation
Indices: 1940705--1940751 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1940695 GTGCAAATAA
*
1940705 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATCACTTGATT
1940728 ATTTTGATATGAATCACTTGATT
1 ATTTTGATATGAATCACTTGATT
1940751 A
1 A
1940752 AGGGGGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (23 bp):
ATTTTGATATGAATCACTTGATT
Found at i:1940814 original size:28 final size:29
Alignment explanation
Indices: 1940782--1940878 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
1940772 AACGGGGGAG
1940782 ATAAA-GGAGAGAATGCGTGAATTACCTT
1 ATAAAGGGAGAGAATGCGTGAATTACCTT
* ****
1940810 ATAAAGGGGGAGAATGTACAAATT--C--
1 ATAAAGGGAGAGAATGCGTGAATTACCTT
*
1940835 GTAAA-GGAGAGAATGCGTGAATTACCTT
1 ATAAAGGGAGAGAATGCGTGAATTACCTT
*
1940863 ATAAAGGGGGAGAATG
1 ATAAAGGGAGAGAATG
1940879 TACAAATTCG
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
24 13 0.26
25 4 0.08
26 1 0.02
27 1 0.02
28 9 0.18
29 22 0.44
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.22
Consensus pattern (29 bp):
ATAAAGGGAGAGAATGCGTGAATTACCTT
Found at i:1940863 original size:53 final size:53
Alignment explanation
Indices: 1940783--1940892 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
1940773 ACGGGGGAGA
1940783 TAAAGGAGAGAATGCGTGAATTACCTTATAAAGGGGGAGAATGTACAAATTCG
1 TAAAGGAGAGAATGCGTGAATTACCTTATAAAGGGGGAGAATGTACAAATTCG
1940836 TAAAGGAGAGAATGCGTGAATTACCTTATAAAGGGGGAGAATGTACAAATTCG
1 TAAAGGAGAGAATGCGTGAATTACCTTATAAAGGGGGAGAATGTACAAATTCG
1940889 TAAA
1 TAAA
1940893 ATTTATTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (53 bp):
TAAAGGAGAGAATGCGTGAATTACCTTATAAAGGGGGAGAATGTACAAATTCG
Found at i:1941466 original size:20 final size:20
Alignment explanation
Indices: 1941443--1941513 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1941433 AATTCAAAGA
1941443 ATCGATACATGTTGCAATGT
1 ATCGATACATGTTGCAATGT
****
1941463 ATCGATACATGAAAAAGATGT
1 ATCGATACATGTTGCA-ATGT
1941484 ATCGATACATGTTGCAATGT
1 ATCGATACATGTTGCAATGT
1941504 ATCGATACAT
1 ATCGATACAT
1941514 AAAAAAGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
ATCGATACATGTTGCAATGT
Found at i:1941485 original size:21 final size:21
Alignment explanation
Indices: 1941459--1941534 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1941449 ACATGTTGCA
1941459 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1941480 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1941500 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1941521 TTGTATCGATACAT
1 ATGTATCGATACAT
1941535 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Done.