Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1617782 original size:7 final size:7
Alignment explanation
Indices: 1617742--1617789 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
1617732 ATTTTTCATA
1617742 ACATATC
1 ACATATC
* *
1617749 ACACATA
1 ACATATC
1617756 ACATATC
1 ACATATC
*
1617763 ACACATAC
1 ACATAT-C
1617771 ACATATC
1 ACATATC
1617778 ACATAT-
1 ACATATC
1617784 ACATAT
1 ACATAT
1617790 AATATATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
6 6 0.18
7 22 0.65
8 6 0.18
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (7 bp):
ACATATC
Found at i:1618009 original size:30 final size:31
Alignment explanation
Indices: 1617929--1618029 Score: 177
Period size: 31 Copynumber: 3.3 Consensus size: 31
1617919 CTAAAAAACC
* *
1617929 TAGGTAATCAGTCCATATGTCCTGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1617960 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1617991 TAGGTAAACAGT-CATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1618021 TAGGTAAAC
1 TAGGTAAAC
1618030 CCTCGACCCT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 27 0.40
31 41 0.60
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:1618312 original size:27 final size:29
Alignment explanation
Indices: 1618267--1618340 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 29
1618257 ATATGTCCTT
*
1618267 ATCACATAGCTT-ATTTCACATT-CATAT-
1 ATCACATAG-TTCATATCACATTGCATATA
* * *
1618294 GTCACATAGTTCATATCACTTTGCATGTA
1 ATCACATAGTTCATATCACATTGCATATA
*
1618323 ATCACATAGATCATATCA
1 ATCACATAGTTCATATCA
1618341 TATATCCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 2 0.05
27 16 0.42
28 4 0.11
29 16 0.42
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (29 bp):
ATCACATAGTTCATATCACATTGCATATA
Found at i:1622797 original size:15 final size:14
Alignment explanation
Indices: 1622773--1622811 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1622763 ATCCATTTTT
1622773 CATAACATATCACA
1 CATAACATATCACA
1622787 CATACACATATCACA
1 CATA-ACATATCACA
* *
1622802 TATAATATAT
1 CATAACATAT
1622812 ATTTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CATAACATATCACA
Found at i:1622964 original size:31 final size:31
Alignment explanation
Indices: 1622926--1623172 Score: 347
Period size: 31 Copynumber: 8.0 Consensus size: 31
1622916 TCCGAAGGAC
* * *
1622926 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1622957 CAGTCCATATGTCCCGAAGAACACAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1622988 CAATCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1623019 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
**
1623050 CAGTATATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1623081 CGGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1623112 CAGT-C-TATATCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1623141 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1623172 C
1 C
1623173 CCCGGTCCTT
Statistics
Matches: 194, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
29 26 0.13
30 2 0.01
31 165 0.85
32 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1627571 original size:19 final size:19
Alignment explanation
Indices: 1627520--1627608 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
1627510 TCAAAACTCA
*
1627520 TTTCGAAATTCATA-ATTAT
1 TTTC-AAATTCATATCTTAT
* * * *
1627539 TTTTAGACTCATATCTTAC
1 TTTCAAATTCATATCTTAT
* *
1627558 TGTCAGATTCATATCTTAT
1 TTTCAAATTCATATCTTAT
* *
1627577 TTTCATATTCATAGCTTAT
1 TTTCAAATTCATATCTTAT
1627596 TTTCAAATTCATA
1 TTTCAAATTCATA
1627609 GCCCAATGCA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
18 7 0.12
19 49 0.88
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (19 bp):
TTTCAAATTCATATCTTAT
Found at i:1639638 original size:23 final size:23
Alignment explanation
Indices: 1639608--1639651 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1639598 GAGTAGAGGG
*
1639608 TCTATGTGGTCTTTCGGGACAAT
1 TCTATGTGGTCCTTCGGGACAAT
1639631 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1639652 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.36
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAT
Found at i:1639950 original size:13 final size:13
Alignment explanation
Indices: 1639934--1639963 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1639924 ATGAATTTAT
1639934 AAGTGTTAAATCA
1 AAGTGTTAAATCA
1639947 AAGTGTTAAATCA
1 AAGTGTTAAATCA
1639960 AAGT
1 AAGT
1639964 TTGGATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (13 bp):
AAGTGTTAAATCA
Found at i:1640792 original size:23 final size:23
Alignment explanation
Indices: 1640759--1640802 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1640749 GAGTAGAGGG
1640759 TCTACGCGGTCCTTAGGGATAAT
1 TCTACGCGGTCCTTAGGGATAAT
* *
1640782 TCTACGTGGTCCTTCGGGATA
1 TCTACGCGGTCCTTAGGGATA
1640803 TATATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
TCTACGCGGTCCTTAGGGATAAT
Found at i:1641578 original size:21 final size:21
Alignment explanation
Indices: 1641552--1641593 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1641542 CGATGTTTTT
1641552 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
*
1641573 GTGCATCGGTACATTGTAGCA
1 GTGCATCGGTACACTGTAGCA
1641594 TTGTTCATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
GTGCATCGGTACACTGTAGCA
Found at i:1641612 original size:12 final size:12
Alignment explanation
Indices: 1641595--1641635 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1641585 ATTGTAGCAT
1641595 TGTTCATGGTAC
1 TGTTCATGGTAC
1641607 TGTTCAT--TAC
1 TGTTCATGGTAC
*
1641617 TGTTCATGGTAT
1 TGTTCATGGTAC
1641629 TGTTCAT
1 TGTTCAT
1641636 ACCGTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 10 0.38
12 16 0.62
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.49
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:1651872 original size:21 final size:21
Alignment explanation
Indices: 1651843--1651886 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1651833 AATTTAGTTA
1651843 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* * *
1651864 ATTATTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1651885 AT
1 AT
1651887 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1651887 original size:28 final size:28
Alignment explanation
Indices: 1651856--1651921 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
1651846 AGTTTGTTAG
*
1651856 TATAAATTATTATTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTGTTAGTTTAAGT
*
1651884 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGTTAGTTTAAGT
*
1651912 TATATATTAT
1 TATAAATTAT
1651922 ATTATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (28 bp):
TATAAATTATTAGTTTGTTAGTTTAAGT
Found at i:1652549 original size:20 final size:20
Alignment explanation
Indices: 1652524--1652588 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1652514 TATAATCTTA
1652524 AAATTTATTTGATATTTAAC
1 AAATTTATTTGATATTTAAC
*
1652544 AAATTTGA-TTGATTAATTAAC
1 AAATTT-ATTTGA-TATTTAAC
* * *
1652565 AAATTTGTTTTATATTTAAA
1 AAATTTATTTGATATTTAAC
1652585 AAAT
1 AAAT
1652589 AAAAATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (20 bp):
AAATTTATTTGATATTTAAC
Found at i:1653389 original size:20 final size:20
Alignment explanation
Indices: 1653341--1653402 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1653331 AACTTAAATC
*
1653341 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1653361 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1653379 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1653398 AAAAT
1 AAAAT
1653403 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1653435 original size:14 final size:14
Alignment explanation
Indices: 1653418--1653520 Score: 78
Period size: 14 Copynumber: 7.8 Consensus size: 14
1653408 ATCTATAATA
1653418 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
1653432 TAATATT---TAAT
1 TAATATTAAAAAAT
* *
1653443 TTAT-TTAAAATAT
1 TAATATTAAAAAAT
1653456 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
1653468 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
1653482 TAATATT-AAAAAT
1 TAATATTAAAAAAT
*
1653495 TAAATATTTAAAAAT
1 T-AATATTAAAAAAT
1653510 TAATATTAAAA
1 TAATATTAAAA
1653521 TTAAAATCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.03
11 6 0.09
12 13 0.19
13 8 0.12
14 30 0.43
15 10 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:1653524 original size:54 final size:51
Alignment explanation
Indices: 1653444--1653551 Score: 164
Period size: 54 Copynumber: 2.1 Consensus size: 51
1653434 ATATTTAATT
*
1653444 TATTTAAAATATTAATATTAAAATTAATATCTATAATATAATATTAAAAATTAAA
1 TATTTAAAATATTAATATTAAAATTAAAATC-A-AATATAATA-T-AAAATTAAA
1653499 TATTTAAAA-ATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAA
1 TATTTAAAATATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAA
1653549 TAT
1 TAT
1653552 AAAACCTCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
50 12 0.23
51 1 0.02
52 9 0.17
53 1 0.02
54 20 0.38
55 9 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (51 bp):
TATTTAAAATATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAA
Found at i:1653525 original size:6 final size:6
Alignment explanation
Indices: 1653454--1653548 Score: 50
Period size: 6 Copynumber: 15.0 Consensus size: 6
1653444 TATTTAAAAT
* * * *
1653454 ATTAAT ATTAAA ATTAAT ATCTATA ATATAAT ATTAAAA ATTAAA TATTTAAAA
1 ATTAAA ATTAAA ATTAAA AT-TAAA AT-TAAA ATT-AAA ATTAAA -A-TT-AAA
* * *
1653508 ATTAAT ATTAAA ATTAAA A-TCAA A-TATA ATATAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT-TAAA ATTAAA
1653549 TATAAAACCT
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
5 7 0.10
6 34 0.50
7 21 0.31
8 3 0.04
9 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (6 bp):
ATTAAA
Found at i:1653550 original size:12 final size:12
Alignment explanation
Indices: 1653490--1653555 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 12
1653480 TATAATATTA
1653490 AAAATTAAATATTT
1 AAAATTAAATA--T
1653504 AAAAATT-AATATT
1 -AAAATTAAATA-T
1653517 AAAATTAAA-AT
1 AAAATTAAATAT
*
1653528 CAAA-TATAATAT
1 AAAATTA-AATAT
1653540 AAAATTAAATAT
1 AAAATTAAATAT
1653552 AAAA
1 AAAA
1653556 CCTCTTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 21 0.47
13 6 0.13
14 4 0.09
15 6 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1656869 original size:15 final size:15
Alignment explanation
Indices: 1656849--1656887 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1656839 AATGAATTAA
*
1656849 TAATGATTTTATTTT
1 TAATGATTTTATATT
1656864 TAATGATTTTATATT
1 TAATGATTTTATATT
1656879 TAATGATTT
1 TAATGATTT
1656888 AGTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (15 bp):
TAATGATTTTATATT
Found at i:1657246 original size:59 final size:59
Alignment explanation
Indices: 1657169--1657329 Score: 295
Period size: 59 Copynumber: 2.7 Consensus size: 59
1657159 GATTTGATAG
* *
1657169 TAATAATTTATTATTAATATTTAATTATTTGATAGTAATGATTTAGTCATGATTACTAA
1 TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTCATGATTACTAA
*
1657228 TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTTATGATTACTAA
1 TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTCATGATTACTAA
1657287 TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATT
1657330 AATAATAATG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 99 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.50
Consensus pattern (59 bp):
TAATGATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTCATGATTACTAA
Found at i:1657266 original size:21 final size:22
Alignment explanation
Indices: 1657228--1657272 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1657218 TGATTACTAA
*
1657228 TAATGATTTATTATTAAT-ATT
1 TAATGATTTATTAGTAATGATT
1657249 TAATGATTTGA-TAGTAATGATT
1 TAATGATTT-ATTAGTAATGATT
1657271 TA
1 TA
1657273 GTTATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
TAATGATTTATTAGTAATGATT
Found at i:1657327 original size:14 final size:14
Alignment explanation
Indices: 1657308--1657377 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
1657298 TATTAATATT
*
1657308 TAATGATTTGATAG
1 TAATGATTTGATAA
*
1657322 TAATGA-TTAATAA
1 TAATGATTTGATAA
*
1657335 TAATGAAATT-ATAA
1 TAATG-ATTTGATAA
*
1657349 TAATGATTTGATAC
1 TAATGATTTGATAA
*
1657363 TAATGATTTAATAA
1 TAATGATTTGATAA
1657377 T
1 T
1657378 TATTACTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
13 13 0.28
14 32 0.68
15 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.41
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:1657390 original size:41 final size:40
Alignment explanation
Indices: 1657294--1657395 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
1657284 TAATAATGAT
* * *
1657294 TTATTATTAATATTTAATGATTTGATAGTAATGATTAATAA
1 TTATTAATAATA-ATAATGATTTGATACTAATGATTAATAA
* * *
1657335 TAATGAAATTATAATAATGATTTGATACTAATGATTTAATAA
1 TTAT-TAATAATAATAATGATTTGATACTAATGA-TTAATAA
* *
1657377 TTATTACTAATAATTATGA
1 TTATTAATAATAATAATGA
1657396 AATAATAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
41 33 0.69
42 15 0.31
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (40 bp):
TTATTAATAATAATAATGATTTGATACTAATGATTAATAA
Found at i:1657571 original size:10 final size:11
Alignment explanation
Indices: 1657516--1657573 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
1657506 TGATATGATT
1657516 TGATTTAGTAA
1 TGATTTAGTAA
*
1657527 TGATTTAAAAATAA
1 TGATTT---AGTAA
*
1657541 TGATTTAATAA
1 TGATTTAGTAA
1657552 TGATTTAGTAA
1 TGATTTAGTAA
1657563 TGA-TTAGTAA
1 TGATTTAGTAA
1657573 T
1 T
1657574 AATAAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 8 0.19
11 24 0.57
14 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (11 bp):
TGATTTAGTAA
Found at i:1657912 original size:11 final size:11
Alignment explanation
Indices: 1657882--1658119 Score: 58
Period size: 11 Copynumber: 19.7 Consensus size: 11
1657872 TCTAGCTATT
1657882 TAATGATTTGATA
1 TAATGATTT-A-A
*
1657895 CTAATGATTTAG
1 -TAATGATTTAA
1657907 TAATGATTACTAA
1 TAATGATT--TAA
*
1657920 TAATGATTTAT
1 TAATGATTTAA
* *
1657931 TATTAATATT--
1 TAATGAT-TTAA
1657941 TAATGATTTGATA
1 TAATGATTT-A-A
*
1657954 TTAATGATTTAG
1 -TAATGATTTAA
*
1657966 TATTGATTAGTAA
1 TAATGATT--TAA
* *
1657979 TAATAATTTAT
1 TAATGATTTAA
* *
1657990 TATTAATATT--
1 TAATGAT-TTAA
1658000 TAATGATTTGATA
1 TAATGATTT-A-A
*
1658013 GTAATGATTTAT
1 -TAATGATTTAA
* *
1658025 TAGTAATATT--
1 TAATGAT-TTAA
1658035 TAATGATTTGATA
1 TAATGATTT-A-A
1658048 CTAATGATTTAA
1 -TAATGATTTAA
1658060 TAATGATTAGTAA
1 TAATGATT--TAA
1658073 TAATGAAACTATT-A
1 TAATG--A-T-TTAA
1658087 TAATGATTTGATA
1 TAATGATTT-A-A
1658100 CTAATGATTTAA
1 -TAATGATTTAA
1658112 TAATGATT
1 TAATGATT
1658120 ACTAATAGTT
Statistics
Matches: 171, Mismatches: 21, Indels: 67
0.66 0.08 0.26
Matches are distributed among these distances:
9 6 0.04
10 17 0.10
11 52 0.30
12 9 0.05
13 32 0.19
14 51 0.30
15 2 0.01
16 1 0.01
17 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:1657941 original size:59 final size:59
Alignment explanation
Indices: 1657878--1658023 Score: 247
Period size: 59 Copynumber: 2.5 Consensus size: 59
1657868 GATTTCTAGC
*
1657878 TATTTAATGATTTGATACTAATGATTTAGTAATGATTACTAATAATGATTTATTATTAA
1 TATTTAATGATTTGATACTAATGATTTAGTAATGATTACTAATAATAATTTATTATTAA
* * *
1657937 TATTTAATGATTTGATATTAATGATTTAGTATTGATTAGTAATAATAATTTATTATTAA
1 TATTTAATGATTTGATACTAATGATTTAGTAATGATTACTAATAATAATTTATTATTAA
*
1657996 TATTTAATGATTTGATAGTAATGATTTA
1 TATTTAATGATTTGATACTAATGATTTA
1658024 TTAGTAATAT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 82 1.00
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (59 bp):
TATTTAATGATTTGATACTAATGATTTAGTAATGATTACTAATAATAATTTATTATTAA
Found at i:1657946 original size:21 final size:21
Alignment explanation
Indices: 1657920--1658008 Score: 82
Period size: 21 Copynumber: 4.4 Consensus size: 21
1657910 TGATTACTAA
1657920 TAATGATTTATTATTAATATT
1 TAATGATTTATTATTAATATT
1657941 TAATGATTTGA-TATTAATGATT
1 TAATGATTT-ATTATTAAT-ATT
* * *
1657963 TAGT-ATTGATTAGT-A-A--
1 TAATGATTTATTATTAATATT
*
1657979 TAATAATTTATTATTAATATT
1 TAATGATTTATTATTAATATT
1658000 TAATGATTT
1 TAATGATTT
1658009 GATAGTAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
16 3 0.06
17 8 0.15
18 2 0.04
19 1 0.02
20 2 0.04
21 30 0.57
22 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TAATGATTTATTATTAATATT
Found at i:1658019 original size:14 final size:14
Alignment explanation
Indices: 1658000--1658036 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1657990 TATTAATATT
1658000 TAATGATTTGA-TAG
1 TAATGATTT-ATTAG
1658014 TAATGATTTATTAG
1 TAATGATTTATTAG
1658028 TAAT-ATTTA
1 TAATGATTTA
1658037 ATGATTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (14 bp):
TAATGATTTATTAG
Found at i:1658023 original size:35 final size:35
Alignment explanation
Indices: 1657979--1658058 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1657969 TGATTAGTAA
* * *
1657979 TAATAATTTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTATTAGTAATATTTAATGATTTGATAC
1658014 TAATGATTTATTAGTAATATTTAATGATTTGATAC
1 TAATGATTTATTAGTAATATTTAATGATTTGATAC
1658049 TAATGATTTA
1 TAATGATTTA
1658059 ATAATGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (35 bp):
TAATGATTTATTAGTAATATTTAATGATTTGATAC
Found at i:1658039 original size:21 final size:21
Alignment explanation
Indices: 1658014--1658074 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1658004 GATTTGATAG
1658014 TAATGATTTATTAGTAATATT
1 TAATGATTTATTAGTAATATT
*
1658035 TAATGATTTGA-TACTAATGATT
1 TAATGATTT-ATTAGTAAT-ATT
* *
1658057 TAAT-AATGATTAGTAATA
1 TAATGATTTATTAGTAATA
1658075 ATGAAACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.06
21 23 0.70
22 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (21 bp):
TAATGATTTATTAGTAATATT
Found at i:1658054 original size:14 final size:13
Alignment explanation
Indices: 1658035--1658119 Score: 56
Period size: 14 Copynumber: 6.6 Consensus size: 13
1658025 TAGTAATATT
1658035 TAATGATTTGATA
1 TAATGATTTGATA
1658048 CTAATGATTT-A-A
1 -TAATGATTTGATA
*
1658060 TAATGATTAG-TAA
1 TAATGATTTGAT-A
**
1658073 TAATGAAACT-ATTA
1 TAATG-ATTTGA-TA
1658087 TAATGATTTGATA
1 TAATGATTTGATA
1658100 CTAATGATTT-A-A
1 -TAATGATTTGATA
1658112 TAATGATT
1 TAATGATT
1658120 ACTAATAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 16 0.28
12 2 0.04
13 12 0.21
14 26 0.46
15 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (13 bp):
TAATGATTTGATA
Found at i:1658256 original size:22 final size:23
Alignment explanation
Indices: 1658231--1658274 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1658221 AATTGTTGAA
*
1658231 TTTATAACTA-GTCGAATTTATC
1 TTTATAAATATGTCGAATTTATC
1658253 TTTATAAATATGTCGAATTTAT
1 TTTATAAATATGTCGAATTTAT
1658275 ATTTTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTATAAATATGTCGAATTTATC
Found at i:1658337 original size:17 final size:15
Alignment explanation
Indices: 1658303--1658342 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1658293 AGAGACATGC
1658303 ATATTTAATATTATA
1 ATATTTAATATTATA
*
1658318 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
1658335 ATATTTAA
1 ATATTTAA
1658343 CATTTGCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:1660909 original size:44 final size:39
Alignment explanation
Indices: 1660859--1660964 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 39
1660849 TTAACTATCT
1660859 ACAAACTAATTAAATATTTTTTATATATAACTAACGACTAACAA
1 ACAAACTAATTAAATATTTTTTATATAT-A-T-A--ACTAACAA
* *
1660903 ACAAACTAATTAATTA-TTTTTA-ATATATAACTATCAA
1 ACAAACTAATTAAATATTTTTTATATATATAACTAACAA
1660940 ACAAACTAATTAAATAATTTTTTAT
1 ACAAACTAATTAAAT-ATTTTTTAT
1660965 TTATGTATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
37 21 0.38
38 1 0.02
39 7 0.12
40 1 0.02
41 1 0.02
42 4 0.07
43 6 0.11
44 15 0.27
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (39 bp):
ACAAACTAATTAAATATTTTTTATATATATAACTAACAA
Found at i:1661027 original size:21 final size:21
Alignment explanation
Indices: 1660974--1661013 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1660964 TTTATGTATG
1660974 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1660995 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1661014 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1661329 original size:22 final size:23
Alignment explanation
Indices: 1661304--1661353 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1661294 CAATAATTGT
1661304 TGCATGAAGCAAC-AAATGATAC
1 TGCATGAAGCAACAAAATGATAC
*
1661326 TGCATGAAGCAACGAAAATGATGC
1 TGCATGAAGCAAC-AAAATGATAC
1661350 TGCA
1 TGCA
1661354 ATAATGCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.52
24 12 0.48
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (23 bp):
TGCATGAAGCAACAAAATGATAC
Found at i:1666464 original size:7 final size:7
Alignment explanation
Indices: 1666452--1666477 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1666442 ATTTTATTAT
1666452 TTTTAAA
1 TTTTAAA
1666459 TTTTAAA
1 TTTTAAA
1666466 TTTTAAA
1 TTTTAAA
1666473 TTTTA
1 TTTTA
1666478 TTTATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:1667609 original size:22 final size:22
Alignment explanation
Indices: 1667584--1667633 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1667574 TAATTATTTA
*
1667584 ATTATCAAGATATGATATTACG
1 ATTATCAAGAGATGATATTACG
*
1667606 ATTATCAAGAGATGATATTATG
1 ATTATCAAGAGATGATATTACG
1667628 ATTATC
1 ATTATC
1667634 TCACAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (22 bp):
ATTATCAAGAGATGATATTACG
Found at i:1673406 original size:21 final size:21
Alignment explanation
Indices: 1673390--1673464 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1673380 CTGTCATTTT
* *
1673390 ACATGCCACCATCGTCAATTT
1 ACATGCCACCATCGTCAGTTC
** * * *
1673411 TGATGGCACCACCGCCAGTTC
1 ACATGCCACCATCGTCAGTTC
1673432 ACATGCCACCA-CTGTCAGTTC
1 ACATGCCACCATC-GTCAGTTC
*
1673453 ACAAGCCACCAT
1 ACATGCCACCAT
1673465 TATAAGGTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (21 bp):
ACATGCCACCATCGTCAGTTC
Found at i:1674059 original size:26 final size:26
Alignment explanation
Indices: 1674005--1674061 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1673995 TTTTTGCTTT
* *
1674005 TATTAAGTTTTAATATTGTTTTTTCA
1 TATTAAGTTTTAATATTATCTTTTCA
*
1674031 TATTAAGTTTTTATATTATGCTTTT-A
1 TATTAAGTTTTAATATTAT-CTTTTCA
1674057 TATTA
1 TATTA
1674062 TTTGTTTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (26 bp):
TATTAAGTTTTAATATTATCTTTTCA
Found at i:1684369 original size:53 final size:53
Alignment explanation
Indices: 1684214--1684370 Score: 224
Period size: 53 Copynumber: 3.0 Consensus size: 53
1684204 TTTGAGGTAC
* * * * *
1684214 TAAGATATTGAGGGATGTATATACTTACACCAATATAAGTATGTGTTAAATGT
1 TAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTGT
* * *
1684267 TAAGGTATTGAGAGATGTACATACTTACACTAGTGTAAGTATTTGTTAATTGT
1 TAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTGT
* *
1684320 TAAGATATTGAGAGATGTACATACTTACTCCGGTGTAAGTATGTGTTAATT
1 TAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATT
1684371 ACTACCTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 91 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (53 bp):
TAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTGT
Found at i:1685095 original size:21 final size:21
Alignment explanation
Indices: 1685069--1685358 Score: 166
Period size: 21 Copynumber: 13.5 Consensus size: 21
1685059 GTTTCCAGAT
*
1685069 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
1685090 TCGCAATGAGAGCTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1685111 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* * *
1685131 TTGCAATGCGATA-GTCGAGTA
1 TCGCAATGCGA-ACTTCGACTA
*
1685152 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
1685173 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1685194 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
* *
1685215 TCGCAATGCGACAATGCGAACT-
1 TCGCAATGCGA-ACTTCG-ACTA
* * * *
1685237 TGGACTAT-CGCAA-TGCGAATATGTAAA
1 TCG-CAATGCG-AACTTCG---A-CT--A
*
1685264 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1685285 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1685306 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
1685327 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1685348 TCGCATTGCGA
1 TCGCAATGCGA
1685359 TAGTCCAAAA
Statistics
Matches: 214, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
20 17 0.08
21 167 0.78
22 8 0.04
23 9 0.04
24 2 0.01
26 4 0.02
27 7 0.03
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1685155 original size:62 final size:62
Alignment explanation
Indices: 1685083--1685317 Score: 301
Period size: 62 Copynumber: 3.6 Consensus size: 62
1685073 AACGCGAACT
* *
1685083 TCGACTATCGCAATGAGAGCTTGGACTATCGCAATGCGAATATGTAAATTGCAATGCGATAG
1 TCGACTATCGCAATGAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
* * * * *
1685145 TCGAGTATCGCAATGCGAACTTGGACTATCGCAATGCAAACT-TGGACTATCGCAATGCGATAG
1 TCGACTATCGCAATGAGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATAG
1685208 TCGACTATCGCAATGCGACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
1 TCGACTATCGCAAT--G---A---GAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
1685273 GATAG
58 GATAG
*
1685278 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 TCGACTATCGCAATGAGAACTTGGACTATCGCAATGCGAA
1685318 CTTGGACTAT
Statistics
Matches: 149, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
62 63 0.42
63 28 0.19
65 1 0.01
68 1 0.01
70 30 0.20
71 26 0.17
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (62 bp):
TCGACTATCGCAATGAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
Found at i:1685358 original size:133 final size:133
Alignment explanation
Indices: 1685093--1685334 Score: 439
Period size: 133 Copynumber: 1.8 Consensus size: 133
1685083 TCGACTATCG
* * *
1685093 CAATGAGAGCTTGGACTATCGCAATGCGAATATGTAAATTGCAATGCGATAGTCGAGTATCGCAA
1 CAATGAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
1685158 TGCGAACTTGGACTATCGCAATGCAAACTTGGACTATCGCAATGCGATAGTCGACTATCGCAATG
66 TGCGAACTTGGACTATCGCAATGCAAACTTGGACTATCGCAATGCGATAGTCGACTATCGCAATG
1685223 CGA
131 CGA
*
1685226 CAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
1 CAATGAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
*
1685291 TGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATG
66 TGCGAACTTGGACTATCGCAATGCAAACTTGGACTATCGCAATG
1685335 TGAACTTGGA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 104 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (133 bp):
CAATGAGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
TGCGAACTTGGACTATCGCAATGCAAACTTGGACTATCGCAATGCGATAGTCGACTATCGCAATG
CGA
Found at i:1685994 original size:5 final size:5
Alignment explanation
Indices: 1685986--1686026 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1685976 CCGTCTCGTC
1685986 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
1686027 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:1686015 original size:6 final size:6
Alignment explanation
Indices: 1685989--1686030 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1685979 TCTCGTCTCG
1685989 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1686031 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1686148 original size:21 final size:21
Alignment explanation
Indices: 1686123--1686333 Score: 250
Period size: 21 Copynumber: 10.0 Consensus size: 21
1686113 ATTTTGGACT
1686123 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1686144 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
1686165 ATCGTAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
1686186 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1686207 ATCGCAATGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
1686230 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1686251 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1686272 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1686293 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1686314 ATCGCAACGAACTTGGAATA
1 ATCGCAACGAACTTGGAATA
1686334 TCGCAATGCG
Statistics
Matches: 165, Mismatches: 16, Indels: 19
0.82 0.08 0.09
Matches are distributed among these distances:
19 19 0.12
21 108 0.65
23 38 0.23
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1694180 original size:17 final size:17
Alignment explanation
Indices: 1694160--1694195 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1694150 TGTCCGGGTC
1694160 TTTT-TTTTATTTTATTA
1 TTTTGTTTTA-TTTATTA
1694177 TTTTGTTTTATTTATTA
1 TTTTGTTTTATTTATTA
1694194 TT
1 TT
1694196 ATCGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTGTTTTATTTATTA
Found at i:1694783 original size:13 final size:13
Alignment explanation
Indices: 1694765--1694792 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1694755 GATTCGAACC
1694765 AAAAAAGAAAGAG
1 AAAAAAGAAAGAG
1694778 AAAAAAGAAAGAG
1 AAAAAAGAAAGAG
1694791 AA
1 AA
1694793 GGAGATACCT
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:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAG
Found at i:1702028 original size:31 final size:31
Alignment explanation
Indices: 1701993--1702071 Score: 77
Period size: 36 Copynumber: 2.4 Consensus size: 31
1701983 TCCATAAATT
* *
1701993 TTGAGAATTTTAAAAACAAATTTTGTCTCGC
1 TTGAGAATTTTAAAAACAAATTTCGTCTCAC
*
1702024 TTGAGACAATTTCTTTCAAAACAAATTTCGTCTCAC
1 TTGAG--AA--T-TTTAAAAACAAATTTCGTCTCAC
1702060 TTGAGACATTTT
1 TTGAGA-ATTTT
1702072 CCCTTTGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
31 5 0.13
32 3 0.08
33 3 0.08
34 1 0.03
35 2 0.05
36 25 0.64
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
TTGAGAATTTTAAAAACAAATTTCGTCTCAC
Found at i:1702389 original size:30 final size:31
Alignment explanation
Indices: 1702355--1702413 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1702345 AAAATATATC
1702355 ATCTTTGAGTC-ATTTCTTTTGAAACAAAGG
1 ATCTTTGAGTCTATTTCTTTTGAAACAAAGG
1702385 ATCTTTGAGTCTATTTCTTTTGAAACAAA
1 ATCTTTGAGTCTATTTCTTTTGAAACAAA
1702414 ACTTTGTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCTTTTGAAACAAAGG
Found at i:1702485 original size:36 final size:36
Alignment explanation
Indices: 1702445--1702516 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
1702435 ATTTTCTTAA
1702445 AAAAAATCTTTGAGGC-TGTTTCACTGAAAACAAAAT
1 AAAAAATCTTTGA-GCATGTTTCACTGAAAACAAAAT
** *
1702481 AAAAAATCTTTGAGCATGTTTCTTTGATAACAAAAT
1 AAAAAATCTTTGAGCATGTTTCACTGAAAACAAAAT
1702517 TTTGTCTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (36 bp):
AAAAAATCTTTGAGCATGTTTCACTGAAAACAAAAT
Found at i:1702733 original size:29 final size:30
Alignment explanation
Indices: 1702689--1702750 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
1702679 AAAATTTACA
*
1702689 ATCTTTGAGTCTGTTTCTTTTGAAA-CATC
1 ATCTTTGAGTCGGTTTCTTTTGAAATCATC
1702718 ATCTTTGAGTCGGTTTCTTTTGAAATCATC
1 ATCTTTGAGTCGGTTTCTTTTGAAATCATC
1702748 ATC
1 ATC
1702751 CCTAAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.47
Consensus pattern (30 bp):
ATCTTTGAGTCGGTTTCTTTTGAAATCATC
Found at i:1702817 original size:40 final size:40
Alignment explanation
Indices: 1702762--1702972 Score: 158
Period size: 40 Copynumber: 5.0 Consensus size: 40
1702752 CTAAATATGG
1702762 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
* *
1702802 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCT-G---A
* * * * *
1702845 CCAG-ACGTCCTCATCACGTAGGAACTGTGTTATCGCCCTTTCTATAGATGA
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT--CCC---C------TGA
* *
1702896 CCAGAACTTTTCATCACGTATGAGCCGTGTCATCCCCCGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
* *
1702936 CCAGATCTCATCATCACGTATGAGCCGTGTCA-CCCCT
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCT
1702973 AGATAACCAG
Statistics
Matches: 135, Mismatches: 18, Indels: 37
0.71 0.09 0.19
Matches are distributed among these distances:
39 9 0.07
40 62 0.46
42 1 0.01
43 26 0.19
46 4 0.03
49 4 0.03
51 25 0.19
52 2 0.01
54 1 0.01
55 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
Found at i:1703077 original size:108 final size:108
Alignment explanation
Indices: 1702888--1703083 Score: 284
Period size: 108 Copynumber: 1.8 Consensus size: 108
1702878 CGCCCTTTCT
* *
1702888 ATAGATGACCAGAACTTTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCATCATCAC
1 ATAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATCTCATCATCAC
* * **
1702953 GTATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGC
66 ATAGGAAACGTGTCACCCCTAGATAACCAGCCGTCCTCATCGC
* * * *
1702996 ATAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGAGCAGATTTCCTCATCAC
1 ATAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATCTCATCATCAC
* *
1703061 ATAGGAAATGTGTCACCCTTAGA
66 ATAGGAAACGTGTCACCCCTAGA
1703084 CGACCAGACT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
108 76 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (108 bp):
ATAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATCTCATCATCAC
ATAGGAAACGTGTCACCCCTAGATAACCAGCCGTCCTCATCGC
Found at i:1703296 original size:3 final size:3
Alignment explanation
Indices: 1703290--1703336 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1703280 TTTGTTTTAT
**
1703290 TTA TTA TTA TCG TTA TT- TATA TTA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
1703334 TTA
1 TTA
1703337 CTAATTACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 3 0.08
3 33 0.89
4 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1706144 original size:7 final size:7
Alignment explanation
Indices: 1706134--1706158 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1706124 TTTTAAAAAT
1706134 ATTTAAA
1 ATTTAAA
1706141 ATTTAAA
1 ATTTAAA
1706148 ATTTAAA
1 ATTTAAA
1706155 ATTT
1 ATTT
1706159 CTAAATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:1706805 original size:17 final size:17
Alignment explanation
Indices: 1706780--1706820 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1706770 CGGTCATGTT
*
1706780 ATCGTTTTATTGATTTA
1 ATCGGTTTATTGATTTA
1706797 ATCGGTTTATTGATTTA
1 ATCGGTTTATTGATTTA
1706814 ATCGGTT
1 ATCGGTT
1706821 GAACCGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (17 bp):
ATCGGTTTATTGATTTA
Found at i:1708974 original size:20 final size:20
Alignment explanation
Indices: 1708951--1709002 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1708941 AACGCGATCC
1708951 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1708971 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1708991 CCAAAATCGCAA
1 CCAGAATCGCAA
1709003 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1709083 original size:20 final size:20
Alignment explanation
Indices: 1709058--1709251 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1709048 GATTTTCCAT
* *
1709058 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1709078 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1709098 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1709118 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1709138 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1709158 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1709178 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1709198 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1709219 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1709239 AATCGCAACGCGA
1 AATCGCAACGCGA
1709252 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1709103 original size:40 final size:39
Alignment explanation
Indices: 1709054--1709251 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1709044 TTGCGATTTT
* ** *
1709054 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1709092 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1709133 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1709173 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1709212 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1709252 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1709141 original size:60 final size:60
Alignment explanation
Indices: 1709058--1709250 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1709048 GATTTTCCAT
* ** * *
1709058 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1709118 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1709178 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1709239 AATCGCAACGCG
1 AATCGCAACGCG
1709251 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1709671 original size:33 final size:33
Alignment explanation
Indices: 1709632--1709702 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1709622 TTCACTTAGA
*
1709632 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1709665 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1709698 TTTCA
1 TTTCA
1709703 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1709877 original size:32 final size:33
Alignment explanation
Indices: 1709823--1709892 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
1709813 AGAATGACTG
**
1709823 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1709856 TCGCAACGAGAG-ATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1709888 TCGCA
1 TCGCA
1709893 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.43, C:0.26, G:0.23, T:0.09
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1709910 original size:19 final size:19
Alignment explanation
Indices: 1709888--1709985 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1709878 GAAACCAAAA
*
1709888 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1709907 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1709921 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1709940 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1709954 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1709973 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1709986 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1709929 original size:14 final size:14
Alignment explanation
Indices: 1709910--1709999 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1709900 TTTCATTTCG
1709910 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1709924 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1709943 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1709957 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1709974 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1709990 CGTTGCGATT
1 CGTTGCGATT
1710000 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1709935 original size:33 final size:33
Alignment explanation
Indices: 1709893--1710007 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1709883 CAAAATCGCA
1709893 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1709926 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1709959 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1709992 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1710008 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1712018 original size:93 final size:93
Alignment explanation
Indices: 1711704--1712174 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
1711694 TAGATTGCTT
*
1711704 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1711769 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1711797 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1711861 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1711889 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1711954 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1711982 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1712046 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1712073 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1712138 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1712166 AGTAAATTT
1 AGTAAATTT
1712175 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 89 0.24
92 95 0.26
93 188 0.51
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1712171 original size:184 final size:185
Alignment explanation
Indices: 1711704--1712174 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
1711694 TAGATTGCTT
*
1711704 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1711769 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1711834 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1711889 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1711954 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
1712019 GTGTATTCTTTAACACTGTGAAATATA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1712073 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1712138 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1712175 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 129 0.45
185 155 0.55
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1712319 original size:19 final size:19
Alignment explanation
Indices: 1712218--1712313 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
1712208 TAGTTTACTT
* *
1712218 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1712238 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1712257 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1712276 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1712290 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1712309 TCGCA
1 TCGCA
1712314 TTGCGATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 36 0.56
20 13 0.20
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1712331 original size:19 final size:19
Alignment explanation
Indices: 1712309--1712443 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1712299 GAAACCAAAA
*
1712309 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1712328 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1712344 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1712361 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1712377 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1712394 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1712413 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1712433 TCGTGTTGCGA
1 TCGCGTTGCGA
1712444 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1712350 original size:14 final size:14
Alignment explanation
Indices: 1712331--1712387 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1712321 TTTCATTTCG
1712331 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1712345 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1712362 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1712378 CGTTGCGATT
1 CGTTGCGATT
1712388 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1712356 original size:33 final size:33
Alignment explanation
Indices: 1712314--1712406 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1712304 CAAAATCGCA
*
1712314 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1712347 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1712380 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1712407 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1714362 original size:14 final size:14
Alignment explanation
Indices: 1714343--1714378 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1714333 ATTGTTTAAT
1714343 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1714357 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1714371 TGATTTGT
1 TGATTTGT
1714379 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1714561 original size:20 final size:19
Alignment explanation
Indices: 1714485--1714567 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1714475 AAAAATGACT
1714485 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1714504 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1714523 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1714537 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1714557 ATCGCAATGCG
1 ATCGCAATGCG
1714568 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 3 0.05
19 28 0.50
20 13 0.23
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1714620 original size:19 final size:19
Alignment explanation
Indices: 1714596--1714888 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
1714586 GATTATCTCG
1714596 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714615 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714634 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1714648 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714667 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714686 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714705 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714724 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1714743 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1714762 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1714776 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1714795 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1714814 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1714828 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1714848 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1714862 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1714881 TTGCGATT
1 TTGCGATT
1714889 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1714631 original size:52 final size:52
Alignment explanation
Indices: 1714574--1714888 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
1714564 TGCGTTTATA
*
1714574 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1714626 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1714678 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
1714735 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
1714787 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1714839 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
1714889 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1714744 original size:128 final size:122
Alignment explanation
Indices: 1714596--1714860 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
1714586 GATTATCTCG
*
1714596 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
1714658 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1714722 CA
121 CA
* * *
1714724 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
1714786 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
1714846 CA
121 CA
1714848 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1714861 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:1717182 original size:12 final size:12
Alignment explanation
Indices: 1717167--1717191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1717157 TTCTTCGGGA
1717167 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1717179 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1717191 C
1 C
1717192 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1717400 original size:24 final size:24
Alignment explanation
Indices: 1717366--1717412 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1717356 CTGAAACATC
1717366 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1717390 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1717413 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1718123 original size:20 final size:20
Alignment explanation
Indices: 1718095--1718463 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1718085 AAATTTAAGT
* * * *
1718095 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1718115 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1718135 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1718155 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1718175 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1718195 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1718215 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1718235 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1718255 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1718275 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1718295 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
1718315 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1718335 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1718355 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1718375 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1718395 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1718415 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1718435 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1718455 GTTGCGATT
1 GTTGCGATT
1718464 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1719422 original size:19 final size:19
Alignment explanation
Indices: 1719400--1719455 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1719390 TTCAGAATTC
1719400 ATTTTCAAATTCATAACTG
1 ATTTTCAAATTCATAACTG
* * * *
1719419 ATTTCCAAACTCATAATTT
1 ATTTTCAAATTCATAACTG
* *
1719438 ACTTTCAGATTCATAACT
1 ATTTTCAAATTCATAACT
1719456 TTACTTTTGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.41
Consensus pattern (19 bp):
ATTTTCAAATTCATAACTG
Found at i:1719467 original size:19 final size:19
Alignment explanation
Indices: 1719429--1719471 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1719419 ATTTCCAAAC
1719429 TCATAATTTACTTTCAGAT
1 TCATAATTTACTTTCAGAT
*
1719448 TCATAACTTTACTTT-TGAT
1 TCATAA-TTTACTTTCAGAT
1719467 TCATA
1 TCATA
1719472 GCCTAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (19 bp):
TCATAATTTACTTTCAGAT
Found at i:1719583 original size:29 final size:30
Alignment explanation
Indices: 1719512--1719571 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1719502 CAATTTAAGG
1719512 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1719543 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1719572 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1719686 original size:21 final size:21
Alignment explanation
Indices: 1719661--1719741 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1719651 TTCAAGATTG
* *
1719661 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
1719682 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
1719700 CCC---GGGTACAGATACCCCC
1 CCCAGGGGGTACAGATA-CCCC
*
1719719 CCCAGGGGGTACAAATACCCC
1 CCCAGGGGGTACAGATACCCC
1719740 CC
1 CC
1719742 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
15 11 0.22
18 4 0.08
19 4 0.08
21 21 0.42
22 10 0.20
ACGTcount: A:0.23, C:0.38, G:0.26, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:1719708 original size:15 final size:15
Alignment explanation
Indices: 1719688--1719717 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1719678 CCCCCCCAGG
1719688 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1719703 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1719718 CCCCAGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:1719816 original size:21 final size:22
Alignment explanation
Indices: 1719775--1719819 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1719765 AACAGAATGT
1719775 CCAGGGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
1719797 CCAGGGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
1719819 C
1 C
1719820 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (22 bp):
CCAGGGGGTACCGATTCCCCCC
Found at i:1719881 original size:21 final size:21
Alignment explanation
Indices: 1719855--1719897 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1719845 ATTTGAATAT
*
1719855 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1719876 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1719897 T
1 T
1719898 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1719963 original size:20 final size:22
Alignment explanation
Indices: 1719925--1719964 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1719915 TTTAAGTATA
1719925 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1719947 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1719965 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1720219 original size:34 final size:32
Alignment explanation
Indices: 1720180--1720249 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1720170 TTTTGTAAAG
* *
1720180 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1720214 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1720246 GGGA
1 GGGA
1720250 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1722910 original size:29 final size:30
Alignment explanation
Indices: 1722839--1722898 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1722829 CAATTTAAGG
1722839 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1722870 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1722899 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1723016 original size:20 final size:21
Alignment explanation
Indices: 1722988--1723031 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1722978 TTCAAGATTG
*
1722988 CCCAGGGGGTATAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1723009 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1723030 CC
1 CC
1723032 TGTAGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:1723094 original size:21 final size:21
Alignment explanation
Indices: 1723068--1723107 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1723058 AGAATGTCCA
1723068 GGGGTACCGATTCCCCCCCAG
1 GGGGTACCGATTCCCCCCCAG
*
1723089 GGGGTACCGATTCTCCCCC
1 GGGGTACCGATTCCCCCCC
1723108 TGTTCAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.42, G:0.28, T:0.17
Consensus pattern (21 bp):
GGGGTACCGATTCCCCCCCAG
Found at i:1723169 original size:21 final size:21
Alignment explanation
Indices: 1723143--1723185 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1723133 ATTTGAATAT
*
1723143 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1723164 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1723185 T
1 T
1723186 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1723251 original size:20 final size:22
Alignment explanation
Indices: 1723213--1723252 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1723203 TTTGAGTATA
1723213 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1723235 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1723253 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1728769 original size:3 final size:3
Alignment explanation
Indices: 1728761--1728789 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1728751 GAATTAGGTT
1728761 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1728790 TATATAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1732395 original size:18 final size:18
Alignment explanation
Indices: 1732371--1732435 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
1732361 GAGTAGTTAA
*
1732371 TCGGGACGTAGTGGTCCT
1 TCGGGACATAGTGGTCCT
*
1732389 ACGGGACATATACAGTGGTCCT
1 TCGGGAC--AT--AGTGGTCCT
*
1732411 TCGGGACATAGTGGTCAT
1 TCGGGACATAGTGGTCCT
1732429 TCGGGAC
1 TCGGGAC
1732436 GAATACTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 21 0.54
20 3 0.08
22 15 0.38
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.25
Consensus pattern (18 bp):
TCGGGACATAGTGGTCCT
Found at i:1738367 original size:64 final size:65
Alignment explanation
Indices: 1738265--1738389 Score: 155
Period size: 64 Copynumber: 1.9 Consensus size: 65
1738255 GATGCACTTC
* * * * *
1738265 TTAATAATAGAGACATCGAATGCAATTAGTGCATCGATGCATAAGGCGTGCATCGATGCATCCCA
1 TTAATAATAGAAACATCGAATGCAATTAGTGAACCGATGCACAAGGAGTGCATCGATGCATCCCA
* * *
1738330 TTAATAATA-AAACATCGAATGCATTTTA-TGAACCGATGCACGAGTAGTGCATCGATGCAT
1 TTAATAATAGAAACATCGAATGCA-ATTAGTGAACCGATGCACAAGGAGTGCATCGATGCAT
1738390 TCCTTCATTG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 39 0.76
65 12 0.24
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (65 bp):
TTAATAATAGAAACATCGAATGCAATTAGTGAACCGATGCACAAGGAGTGCATCGATGCATCCCA
Found at i:1740918 original size:13 final size:13
Alignment explanation
Indices: 1740900--1740924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740890 CATAACTATT
1740900 TCTATAAAAAAAA
1 TCTATAAAAAAAA
1740913 TCTATAAAAAAA
1 TCTATAAAAAAA
1740925 TTAATTTAAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
TCTATAAAAAAAA
Found at i:1741161 original size:22 final size:21
Alignment explanation
Indices: 1741131--1741173 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1741121 CAGTGGTCTT
1741131 TGATGGAAATAAT-ATGTTTTAA
1 TGATGGAAA-AATGAT-TTTTAA
*
1741153 TGATTGAAAAATGATTTTTAA
1 TGATGGAAAAATGATTTTTAA
1741174 ATCGAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (21 bp):
TGATGGAAAAATGATTTTTAA
Found at i:1749112 original size:25 final size:25
Alignment explanation
Indices: 1749078--1749126 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1749068 CCTCCATGGT
1749078 GAGCGGCGTTCATGAGATGGAGAGA
1 GAGCGGCGTTCATGAGATGGAGAGA
*
1749103 GAGCGGCGTTCGTGAGATGGAGAG
1 GAGCGGCGTTCATGAGATGGAGAG
1749127 GGAGAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.47, T:0.16
Consensus pattern (25 bp):
GAGCGGCGTTCATGAGATGGAGAGA
Found at i:1751631 original size:16 final size:16
Alignment explanation
Indices: 1751610--1751642 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1751600 CCCAATCTAT
1751610 ATTTAGGGATAATTAC
1 ATTTAGGGATAATTAC
1751626 ATTTAGGGATAATTAC
1 ATTTAGGGATAATTAC
1751642 A
1 A
1751643 ATAATACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
ATTTAGGGATAATTAC
Found at i:1763084 original size:20 final size:20
Alignment explanation
Indices: 1763061--1763098 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1763051 AGTTTTCAAA
*
1763061 TTCGCAAAGCGATTTTCGTT
1 TTCGCAAAGCGAATTTCGTT
*
1763081 TTCGCAATGCGAATTTCG
1 TTCGCAAAGCGAATTTCG
1763099 CAACGCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTCGCAAAGCGAATTTCGTT
Found at i:1763302 original size:91 final size:91
Alignment explanation
Indices: 1763147--1763478 Score: 431
Period size: 91 Copynumber: 3.7 Consensus size: 91
1763137 AAAACGATAT
* * * *
1763147 TCGCGTTGC-AATTTTGGAAAA-CGCGTTGTGTGTTTACCTATATCGGCAATTAGTGTTGCGAAA
1 TCGCGTTGCGAA-TTT-GAAAACCGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
*
1763210 ACGATATTCGCGTTGCAATTTTGGAGAA
64 ACGAAATTCGCGTTGCAATTTTGGAGAA
* * *
1763238 TCGCGTTGCGAATTTGAAAACCGCGTTGTGTGTTTACCTACATCGGTAATTAGCGTTGCGAAAAC
1 TCGCGTTGCGAATTTGAAAACCGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC
*
1763303 GAAATTCGCGTTGCGATTTTGGAGAA
66 GAAATTCGCGTTGCAATTTTGGAGAA
*
1763329 TCGCGTTGCGAATTTG--AACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC
1 TCGCGTTGCGAATTTGAAAACCGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC
* * * * *
1763392 AAAATTCGCATTGTAAATTT-GAAAA
66 GAAATTCGCGTTGCAATTTTGGAGAA
* * * **
1763417 CCGCATTGCGAATTTAAAAATTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAA
1 TCGCGTTGCGAATTTGAAAACCGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAA
1763479 TTTGAAAATC
Statistics
Matches: 218, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
88 17 0.08
89 58 0.27
90 48 0.22
91 93 0.43
92 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (91 bp):
TCGCGTTGCGAATTTGAAAACCGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC
GAAATTCGCGTTGCAATTTTGGAGAA
Found at i:1763501 original size:90 final size:90
Alignment explanation
Indices: 1763171--1763517 Score: 398
Period size: 91 Copynumber: 3.9 Consensus size: 90
1763161 TGGAAAACGC
* * * * *
1763171 GTTGTGTGTTTACCTATATCGGCAATTAGTGTTGCGAAAACGATATTCGCGTTGC-AATTTTGGA
1 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAATCGCGTTGCGAA-TTTGGA
* * * *
1763235 GAATCGCGTTGCGAATTTGAAAACCGC
65 AAACCGCGTTGCGAATTT-AAAACTGA
* * * * *
1763262 GTTGTGTGTTTACCTACATCGGTAATTAGCGTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAG
1 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAATCGCGTTGCGAATTTGGAA
* *
1763327 AATCGCGTTGCGAATTT-GAACTGA
66 AACCGCGTTGCGAATTTAAAACTGA
* **
1763351 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAAC-AAAATTCGCATTGTAAATTT-GA
1 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAA-TCGCGTTGCGAATTTGGA
* *
1763414 AAACCGCATTGCGAATTTAAAAATTGA
65 AAACCGCGTTGCGAATTT-AAAACTGA
*** *
1763441 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCGAATTT-GAA
1 GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAATCGCGTTGCGAATTTGGAA
1763505 AACCGCGTTGCGA
66 AACCGCGTTGCGA
1763518 TTTTGGAGAA
Statistics
Matches: 223, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
88 20 0.09
89 54 0.24
90 69 0.31
91 79 0.35
92 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (90 bp):
GTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAAATCGCGTTGCGAATTTGGAA
AACCGCGTTGCGAATTTAAAACTGA
Found at i:1763534 original size:21 final size:20
Alignment explanation
Indices: 1763469--1763547 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
1763459 TCGGTAATTA
1763469 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
1763489 ACGTTGCGAATTTGAAAACC
1 GCGTTGCGAATTTGAAAATC
* *
1763509 GCGTTGCGATTTTGGAGAATC
1 GCGTTGCGAATTT-GAAAATC
*
1763530 GCGTTACGAATTTGAAAA
1 GCGTTGCGAATTTGAAAA
1763548 ATGAGTTGCG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 33 0.67
21 16 0.33
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1763544 original size:41 final size:40
Alignment explanation
Indices: 1763469--1763547 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
1763459 TCGGTAATTA
*
1763469 GCGTTGCGAATTTGAAAATCACGTTGCGAATTTGAAAACC
1 GCGTTGCGAATTTGAAAATCACGTTACGAATTTGAAAACC
* * *
1763509 GCGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAA
1 GCGTTGCGAATTT-GAAAATCACGTTACGAATTTGAAAA
1763548 ATGAGTTGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (40 bp):
GCGTTGCGAATTTGAAAATCACGTTACGAATTTGAAAACC
Found at i:1763556 original size:41 final size:40
Alignment explanation
Indices: 1763471--1763557 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
1763461 GGTAATTAGC
* * *
1763471 GTTGCGAATTTGAAAATCACGTTGCGAATTTGAAAACCGC
1 GTTGCGAATTTGAAAATCACGTTACGAATTTGAAAAACGA
* * * *
1763511 GTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAAATGA
1 GTTGCGAATTT-GAAAATCACGTTACGAATTTGAAAAACGA
1763552 GTTGCG
1 GTTGCG
1763558 CGTTTTCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (40 bp):
GTTGCGAATTTGAAAATCACGTTACGAATTTGAAAAACGA
Found at i:1763573 original size:111 final size:111
Alignment explanation
Indices: 1763425--1763668 Score: 337
Period size: 111 Copynumber: 2.2 Consensus size: 111
1763415 AACCGCATTG
* * ***
1763425 CGAATTT-AAAAATTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
1 CGAATTTGAAAAA-TGAGTTGCGCGTTTACCTATATCGGTAATTAGAGTTGCGAAAACGAAAATC
*
1763489 ACGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTA
65 ACATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTA
* * * *
1763536 CGAATTTGAAAAATGAGTTGCGCGTTTTCCTATATCGGTAATTAGAGTTGTGAAAACGAAATTCG
1 CGAATTTGAAAAATGAGTTGCGCGTTTACCTATATCGGTAATTAGAGTTGCGAAAACGAAAATCA
* * *
1763601 CATTGCTAATTTGAAAACCGCGTTGTGATTTTGGAGAATCGCGTTG
66 CATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTA
* *
1763647 CGAATTTGAAAACTGTGTTGCG
1 CGAATTTGAAAAATGAGTTGCG
1763669 AAACTGGTGT
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
111 112 0.96
112 5 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (111 bp):
CGAATTTGAAAAATGAGTTGCGCGTTTACCTATATCGGTAATTAGAGTTGCGAAAACGAAAATCA
CATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTA
Found at i:1768263 original size:45 final size:44
Alignment explanation
Indices: 1768154--1768464 Score: 162
Period size: 43 Copynumber: 7.1 Consensus size: 44
1768144 AAATAGTATG
* * * * *
1768154 ATTGAAAAAAATTAAGGACCTCAATTATAAAGGTAAAAATTGAT
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
* *
1768198 ATTG-AAAAAATTAGGGGCCTCAGTTTTAAAGGTAAAAAAGTAAA
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGT-AAAAAGTAAA
* * * * *
1768242 ATTGAAAAAAATTAGGGGCCTCAATTAGAAATGTAAAAAATGAG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
* * * * * *** ***
1768286 ATTGAAAATAATAAGGAG-CTAAATTATAAAAGTACGTAGTGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
* ** * * * * ***
1768329 ATTG-AAAAATTTAGGATCATCAAATATAAATGTAAAAAATGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
* * * * **
1768372 ATTAAAAATAAATTTAAGGGCGTCAATTATAAAGATAAAAAGTAGG
1 ATTGAAAA-AAA-TTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
* * * * *
1768418 ATT-ACAAAATTTAGGGACCTCAATTATAAAGATAAAAAATTAAA
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGT-AAAAAGTAAA
1768462 ATT
1 ATT
1768465 AAAGGGTTAA
Statistics
Matches: 204, Mismatches: 56, Indels: 14
0.74 0.20 0.05
Matches are distributed among these distances:
42 9 0.04
43 86 0.42
44 52 0.25
45 30 0.15
46 27 0.13
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (44 bp):
ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTAAA
Found at i:1768727 original size:20 final size:20
Alignment explanation
Indices: 1768691--1768729 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1768681 AATATAATTT
*
1768691 CAAAAAAATAATTAAATAAC
1 CAAAAAAATAATAAAATAAC
1768711 CAAAATAAA-AATAAAATAA
1 CAAAA-AAATAATAAAATAA
1768730 TAAATAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (20 bp):
CAAAAAAATAATAAAATAAC
Found at i:1775779 original size:2 final size:2
Alignment explanation
Indices: 1775774--1775811 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1775764 AAAAATGAGA
1775774 AT 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 AT
1775812 GGTATGAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1780416 original size:15 final size:15
Alignment explanation
Indices: 1780379--1780416 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
1780369 GAAAAAGATA
1780379 AAGAAGAGACTTTGG
1 AAGAAGAGACTTTGG
1780394 AAGAAAGAGACTTTGG
1 AAG-AAGAGACTTTGG
1780410 AAGAAGA
1 AAGAAGA
1780417 AGACAAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.47, C:0.05, G:0.32, T:0.16
Consensus pattern (15 bp):
AAGAAGAGACTTTGG
Found at i:1785645 original size:31 final size:31
Alignment explanation
Indices: 1785592--1785698 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
1785582 GAGTCAAGGG
*
1785592 TTACATATGTTCTTCG-GAACATATGGACTGA
1 TTACCTATGTTCTTCGAG-ACATATGGACTGA
* *
1785623 TTACCTATGTTATTCGAGACATATAGACTGA
1 TTACCTATGTTCTTCGAGACATATGGACTGA
1785654 TTACCTATGTTCTTC-AGGACATATGGACTGA
1 TTACCTATGTTCTTCGA-GACATATGGACTGA
* *
1785685 TTACTTAGGTTCTT
1 TTACCTATGTTCTT
1785699 ATGGACCTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.01
31 65 0.97
32 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGAGACATATGGACTGA
Found at i:1785710 original size:31 final size:30
Alignment explanation
Indices: 1785592--1785713 Score: 136
Period size: 31 Copynumber: 3.9 Consensus size: 30
1785582 GAGTCAAGGG
* *
1785592 TTACATATGTTCTTCGGAACATATGGACTGA
1 TTACCTATGTTCTTAGG-ACATATGGACTGA
* * *
1785623 TTACCTATGTTATTCGAGACATATAGACTGA
1 TTACCTATGTTCTTAG-GACATATGGACTGA
1785654 TTACCTATGTTCTTCAGGACATATGGACTGA
1 TTACCTATGTTCTT-AGGACATATGGACTGA
* * *
1785685 TTACTTAGGTTCTTATGGACCTATGGACT
1 TTACCTATGTTCTTA-GGACATATGGACT
1785714 AGTCCTTCGG
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.01
31 76 0.96
32 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (30 bp):
TTACCTATGTTCTTAGGACATATGGACTGA
Found at i:1786330 original size:21 final size:22
Alignment explanation
Indices: 1786304--1786354 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
1786294 GCCGAAATTA
* *
1786304 CTGTAGCAGGGTATCGGTA-CG
1 CTGTAGCAGGGTATCGATACCC
1786325 CTGTAGCAGGGTATCGATACCC
1 CTGTAGCAGGGTATCGATACCC
1786347 CTGTAGCA
1 CTGTAGCA
1786355 TTACGGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGTATCGATACCC
Found at i:1786414 original size:20 final size:20
Alignment explanation
Indices: 1786389--1786443 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1786379 TACTGTTCAT
1786389 TACTATTTGCACAGTATCGG
1 TACTATTTGCACAGTATCGG
* *
1786409 TACTATTTGCATAGTATTGG
1 TACTATTTGCACAGTATCGG
*
1786429 TACTATCTGCACAGT
1 TACTATTTGCACAGT
1786444 GATGGGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
TACTATTTGCACAGTATCGG
Found at i:1786453 original size:20 final size:19
Alignment explanation
Indices: 1786389--1786455 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
1786379 TACTGTTCAT
1786389 TACTATTTGCACAGTATCGG
1 TACTATTTGCACAGTAT-GG
*
1786409 TACTATTTGCATAGTATTGG
1 TACTATTTGCACAGTA-TGG
*
1786429 TACTATCTGCACAGTGATGG
1 TACTATTTGCACAGT-ATGG
*
1786449 GACTATT
1 TACTATT
1786456 CATATAGTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
TACTATTTGCACAGTATGG
Found at i:1788532 original size:137 final size:137
Alignment explanation
Indices: 1788198--1788605 Score: 500
Period size: 137 Copynumber: 3.0 Consensus size: 137
1788188 AACCTAGGGG
* * *
1788198 ATTAAACCTAAAAATGTAGGTTAT-ATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAA
1 ATTAGACCT-AAAATGAAGGCTATAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAA
* * *
1788262 TAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAGAATTCTCCTAAATTAAAGGACT
65 TAATTAAAATGGAACCTCAAGCATAAGCGAAGACCAAATTAA-AATTCTCCTAAATTAAAAGACT
1788327 AAATATGAA
129 AAATATGAA
* * * * * *
1788336 ATTAGACCTAAAGTGAAGGTTATAACATTAATTCTAATTCATTTTAACCAATTAATGATTCAAAT
1 ATTAGACCTAAAATGAAGGCTATAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAAT
* * * * *
1788401 AATTAATATGGAACCTCAAGCAGAAGCGATGACCAAATTAAAATTCTCCTAAATTAAAAGATTAT
66 AATTAAAATGGAACCTCAAGCATAAGCGAAGACCAAATTAAAATTCTCCTAAATTAAAAGACTAA
*
1788466 ATTTGAA
131 ATATGAA
* * *
1788473 ATTA-AGCCTAAAATGAAGGCCT-TAATATTAATCCTAATTAATTTTAATCGATTATTGATTCGA
1 ATTAGA-CCTAAAATGAAGG-CTATAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGA
* * * * *
1788536 ATAATTAAAATGGAACCTTGAA-TATAAGCGAAGACCAAATTAAAAATTCCCCTAAATTAAATGG
64 ATAATTAAAATGGAACC-TCAAGCATAAGCGAAGACCAAATT-AAAATTCTCCTAAATTAAAAGA
1788600 CTAAAT
127 CTAAAT
1788606 TAAAATGATC
Statistics
Matches: 231, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
136 1 0.00
137 121 0.52
138 109 0.47
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (137 bp):
ATTAGACCTAAAATGAAGGCTATAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAAT
AATTAAAATGGAACCTCAAGCATAAGCGAAGACCAAATTAAAATTCTCCTAAATTAAAAGACTAA
ATATGAA
Done.