Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2087429 original size:38 final size:36
Alignment explanation
Indices: 2087239--2087470 Score: 270
Period size: 37 Copynumber: 6.2 Consensus size: 36
2087229 TATATATATA
* ***
2087239 TATATATATATATAGTTTTCAAATGGTTTTTGAAAATACT
1 TATATA-ATATATAGTTTTTAAA-ACATTTTG-AAA-ACT
2087279 TATATAATATATAGTTTTTAAAACATGTTTGAAAAC-
1 TATATAATATATAGTTTTTAAAACAT-TTTGAAAACT
*
2087315 TATATAATATATAGTTTTTTAAACATTTTAGAAAA-T
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAACT
2087351 ATATATAATATATAGTTTTTAAAATCATTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAA-CATTTTGAAAACT
2087389 TATATAATATATAGTTTTTGAAAACAGTTTTGAAAACTT
1 TATATAATATATAGTTTTT-AAAACA-TTTTGAAAAC-T
* * *
2087428 ATATATAATATATAATTTTTAAAACATTTTTAAAAAT
1 -TATATAATATATAGTTTTTAAAACATTTTGAAAACT
2087465 TATATA
1 TATATA
2087471 GTTTTTAAAA
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
35 3 0.02
36 36 0.21
37 51 0.29
38 33 0.19
39 26 0.15
40 24 0.14
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAACT
Found at i:2087484 original size:30 final size:30
Alignment explanation
Indices: 2087436--2087533 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 30
2087426 TTATATATAA
*
2087436 TATATAATTTTT-AAAACATTTTTAAAAAT
1 TATATAGTTTTTAAAAACATTTTTAAAAAT
2087465 TATATAGTTTTTAAAAACATTTTTTAAAAAT
1 TATATAGTTTTTAAAAACA-TTTTTAAAAAT
* *
2087496 TATATAGTTTTAAAAAAACATTTTTGAAAATT
1 TATATAGTTTT-TAAAAACATTTTT-AAAAAT
2087528 TATATA
1 TATATA
2087534 TAATATATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 11 0.18
30 6 0.10
31 27 0.44
32 18 0.29
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
TATATAGTTTTTAAAAACATTTTTAAAAAT
Found at i:2087489 original size:31 final size:31
Alignment explanation
Indices: 2087436--2087533 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 31
2087426 TTATATATAA
*
2087436 TATATAATTTTT-AAAACA-TTTTTAAAAAT
1 TATATAGTTTTTAAAAACATTTTTTAAAAAT
2087465 TATATAGTTTTTAAAAACATTTTTTAAAAAT
1 TATATAGTTTTTAAAAACATTTTTTAAAAAT
* * *
2087496 TATATAGTTTTAAAAAAACATTTTTGAAAATT
1 TATATAGTTTT-TAAAAACATTTTTTAAAAAT
2087528 TATATA
1 TATATA
2087534 TAATATATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 11 0.18
30 6 0.10
31 22 0.35
32 23 0.37
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATAGTTTTTAAAAACATTTTTTAAAAAT
Found at i:2087584 original size:36 final size:38
Alignment explanation
Indices: 2087532--2087612 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
2087522 AAAATTTATA
*
2087532 TATAATATATAG-TTTTTAAAAAA-AAATTTAAAAATT
1 TATATTATATAGTTTTTTAAAAAATAAATTTAAAAATT
* **
2087568 TATATTATATGGTTTTTTAAAAAATAAATTTTTAAATT
1 TATATTATATAGTTTTTTAAAAAATAAATTTAAAAATT
2087606 TAT-TTAT
1 TATATTAT
2087613 TGTTATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 10 0.26
37 15 0.38
38 14 0.36
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (38 bp):
TATATTATATAGTTTTTTAAAAAATAAATTTAAAAATT
Found at i:2087602 original size:40 final size:41
Alignment explanation
Indices: 2087496--2087603 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 41
2087486 TTTTAAAAAT
* * *
2087496 TATATAGTTTTAAAAAAACATTTTTGAAAATTTATATATAA
1 TATATATTTTTAAAAAAAAATTTTTAAAAATTTATATATAA
2087537 TATATAGTTTTTAAAAAAAAA--TTTAAAAATTTATAT-T-A
1 TATATA-TTTTTAAAAAAAAATTTTTAAAAATTTATATATAA
*
2087575 TATGGT-TTTTTAAAAAATAAATTTTTAAA
1 TAT-ATATTTTTAAAAAA-AAATTTTTAAA
2087604 TTTATTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
37 11 0.19
38 7 0.12
39 2 0.03
40 20 0.34
41 6 0.10
42 12 0.21
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (41 bp):
TATATATTTTTAAAAAAAAATTTTTAAAAATTTATATATAA
Found at i:2087635 original size:17 final size:17
Alignment explanation
Indices: 2087609--2087653 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2087599 TTAAATTTAT
*
2087609 TTATTGTTATTATATTA-
1 TTATTTTTATT-TATTAC
2087626 TTATTTTTA-TTATTAC
1 TTATTTTTATTTATTAC
2087642 TTATTTTTATTT
1 TTATTTTTATTT
2087654 TTTGTTTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 5 0.20
16 10 0.40
17 10 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTTATTTATTAC
Found at i:2088196 original size:23 final size:24
Alignment explanation
Indices: 2088170--2088214 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2088160 AAAACAGAGA
2088170 CCAAACA-CAACAA-AAAACCAAAG
1 CCAAACACCAA-AACAAAACCAAAG
2088193 CCAAACACCAAAACAAAACCAA
1 CCAAACACCAAAACAAAACCAA
2088215 GAAACAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.64, C:0.33, G:0.02, T:0.00
Consensus pattern (24 bp):
CCAAACACCAAAACAAAACCAAAG
Found at i:2088978 original size:14 final size:13
Alignment explanation
Indices: 2088954--2089001 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2088944 TTTTCTTTAT
*
2088954 TTTTAATTATTTC
1 TTTTATTTATTTC
2088967 TTTTATTCTATTT-
1 TTTTATT-TATTTC
2088980 TTTTATTTATTATC
1 TTTTATTTATT-TC
*
2088994 TTCTATTT
1 TTTTATTT
2089002 GTTATGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 4 0.13
13 14 0.47
14 12 0.40
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATTTATTTC
Found at i:2096212 original size:19 final size:20
Alignment explanation
Indices: 2096184--2096222 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2096174 ACGTGTATAA
2096184 TAAATAAAATT-ATAAAATT
1 TAAATAAAATTCATAAAATT
*
2096203 TAAATTAAATTCATAAAATT
1 TAAATAAAATTCATAAAATT
2096223 GATACTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATAAAATTCATAAAATT
Found at i:2096796 original size:15 final size:15
Alignment explanation
Indices: 2096766--2096802 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2096756 TTTAAAAAAA
*
2096766 TATTATT-ATTTTTT
1 TATTATTAATATTTT
2096780 TATTATTAATATTTT
1 TATTATTAATATTTT
2096795 TATTATTA
1 TATTATTA
2096803 TGTTTGCAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTAATATTTT
Found at i:2097037 original size:34 final size:34
Alignment explanation
Indices: 2096970--2097040 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
2096960 AAATAATGTT
* *
2096970 GGGGGAGAATCCAAAAACCCAACAGATCAACAAC
1 GGGGGAGAATCCAAAAAACCAACAGACCAACAAC
* *
2097004 GGGGG-GAATCGAAAAAACCAACAGAACCCACAAC
1 GGGGGAGAATCCAAAAAACCAACAG-ACCAACAAC
2097038 GGG
1 GGG
2097041 AACAAACGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.45, C:0.25, G:0.25, T:0.04
Consensus pattern (34 bp):
GGGGGAGAATCCAAAAAACCAACAGACCAACAAC
Found at i:2097928 original size:34 final size:34
Alignment explanation
Indices: 2097874--2097938 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2097864 ACGACTCTTC
* *
2097874 TATTTTTGTCCTCTATGTTTTTATTTTATTTATA
1 TATTTTTGTCCTCTATGTTTTAATTTAATTTATA
2097908 TATTTTT-TCCT-TCATGGTTTTAATTTAATTT
1 TATTTTTGTCCTCT-AT-GTTTTAATTTAATTT
2097939 TGTTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 6 0.22
34 20 0.74
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.66
Consensus pattern (34 bp):
TATTTTTGTCCTCTATGTTTTAATTTAATTTATA
Found at i:2098039 original size:21 final size:21
Alignment explanation
Indices: 2098014--2098062 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
2098004 TTAACTAATC
2098014 TTTTATTA-ATATTTTTTATTA
1 TTTTATTATAT-TTTTTTATTA
*
2098035 TTTTATTTTATTTTTTTATTA
1 TTTTATTATATTTTTTTATTA
2098056 TTTTATT
1 TTTTATT
2098063 TTCTTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTATATTTTTTTATTA
Found at i:2098042 original size:5 final size:5
Alignment explanation
Indices: 2098023--2098069 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
2098013 CTTTTATTAA
* *
2098023 TATTT T-TTAT TATTT TATTT TATTT TTTTAT TATTT TATTT TCTTT T
1 TATTT TATT-T TATTT TATTT TATTT TATT-T TATTT TATTT TATTT T
2098070 TCCTTCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:2098043 original size:13 final size:13
Alignment explanation
Indices: 2098014--2098069 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
2098004 TTAACTAATC
*
2098014 TTTTATTAATATT-
1 TTTTATT-ATTTTA
2098027 TTTTATTATTTTA
1 TTTTATTATTTTA
*
2098040 TTTTATTTTTTTA
1 TTTTATTATTTTA
*
2098053 TTATT-TTATTTTC
1 TT-TTATTATTTTA
2098066 TTTT
1 TTTT
2098070 TCCTTCTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 6 0.16
13 29 0.78
14 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:2098063 original size:21 final size:21
Alignment explanation
Indices: 2098025--2098070 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2098015 TTTATTAATA
2098025 TTTTTTATTATTTTATTTTAT
1 TTTTTTATTATTTTATTTTAT
*
2098046 TTTTTTATTATTTTATTTTCT
1 TTTTTTATTATTTTATTTTAT
2098067 TTTT
1 TTTT
2098071 CCTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTATTATTTTATTTTAT
Found at i:2098629 original size:20 final size:21
Alignment explanation
Indices: 2098593--2098631 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2098583 AGAACTATTT
2098593 TAATTAGTATAATTTTAAACA
1 TAATTAGTATAATTTTAAACA
*
2098614 TAATTA-TATTATTTTAAA
1 TAATTAGTATAATTTTAAA
2098632 TTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
TAATTAGTATAATTTTAAACA
Found at i:2099861 original size:20 final size:20
Alignment explanation
Indices: 2099818--2099861 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2099808 AAAAATAAAC
*
2099818 TAAATAAAATACAAATCCAA
1 TAAATAAAATACAAATCAAA
2099838 -AAATAAAACTACAAA-CAAA
1 TAAATAAAA-TACAAATCAAA
2099857 TAAAT
1 TAAAT
2099862 TTATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAATAAAATACAAATCAAA
Found at i:2099896 original size:2 final size:2
Alignment explanation
Indices: 2099889--2099917 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2099879 ATTTAAGTTT
2099889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2099918 TTTAATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2100141 original size:14 final size:14
Alignment explanation
Indices: 2100122--2100151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2100112 ATAATTTTAA
2100122 TTTTGTGATATATT
1 TTTTGTGATATATT
*
2100136 TTTTGTGGTATATT
1 TTTTGTGATATATT
2100150 TT
1 TT
2100152 CGGTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (14 bp):
TTTTGTGATATATT
Found at i:2112194 original size:28 final size:28
Alignment explanation
Indices: 2112163--2112221 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
2112153 CAGAGGGTTT
2112163 TATGGTATCATGAAAGAAGGACCATGTC
1 TATGGTATCATGAAAGAAGGACCATGTC
2112191 TATGGTATCATGAAAGAAGGACCATGTC
1 TATGGTATCATGAAAGAAGGACCATGTC
2112219 TAT
1 TAT
2112222 TCACTGGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (28 bp):
TATGGTATCATGAAAGAAGGACCATGTC
Found at i:2116669 original size:16 final size:17
Alignment explanation
Indices: 2116640--2116672 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2116630 GAGAATTTAT
2116640 TAATTTATTTTTTAAAA
1 TAATTTATTTTTTAAAA
2116657 TAATTTA-TTTTTAAAA
1 TAATTTATTTTTTAAAA
2116673 ACTTTATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTATTTTTTAAAA
Found at i:2116673 original size:17 final size:17
Alignment explanation
Indices: 2116640--2116673 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2116630 GAGAATTTAT
*
2116640 TAATTTATTTTTTAAAA
1 TAATTTATTTTTAAAAA
2116657 TAATTTATTTTTAAAAA
1 TAATTTATTTTTAAAAA
2116674 CTTTATGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTATTTTTAAAAA
Found at i:2117619 original size:42 final size:42
Alignment explanation
Indices: 2117563--2117651 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 42
2117553 GTACTTTGAC
2117563 CTTTACTTTAGTTAAATGTTGTTTG-TTTGAATTCAATCTAT
1 CTTTACTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTAT
2117604 CTTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTAT
1 CTTTAC-TTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTAT
2117647 CTTTA
1 CTTTA
2117652 GTAATTTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 6 0.13
42 19 0.41
43 21 0.46
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (42 bp):
CTTTACTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTAT
Found at i:2118214 original size:2 final size:2
Alignment explanation
Indices: 2118207--2118235 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2118197 TGTTAATGTA
2118207 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2118236 TCAATTCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2121508 original size:30 final size:30
Alignment explanation
Indices: 2121472--2121549 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
2121462 TTAATCAAAA
2121472 TAAGTACCTAAAGTATTTA-TCTTTGTCATC
1 TAAGTACCTAAAGTATTTACT-TTTGTCATC
* * * *
2121502 TAAGTACATAAAGTAATCACTTTTTTCATC
1 TAAGTACCTAAAGTATTTACTTTTGTCATC
**
2121532 TGGGTACCTAAAGTATTT
1 TAAGTACCTAAAGTATTT
2121550 TTAATTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTACTTTTGTCATC
Found at i:2124605 original size:42 final size:41
Alignment explanation
Indices: 2124515--2124605 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
2124505 TTATTTTTAT
* *
2124515 ATTATTAAAATATATTATTTAATTATTGAAAAAATATAAATT
1 ATTA-TAAAATATATTATTTAATTAGTGAAAAAATATAAATG
*
2124557 ACTATAAAATATATTATTTTAATT-GT-AAAAATATAATAAATG
1 ATTATAAAATATATTA-TTTAATTAGTGAAAAA-AT-ATAAATG
2124599 ATTATAA
1 ATTATAA
2124606 GCATGTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
40 5 0.12
41 15 0.36
42 22 0.52
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (41 bp):
ATTATAAAATATATTATTTAATTAGTGAAAAAATATAAATG
Found at i:2127205 original size:74 final size:75
Alignment explanation
Indices: 2127084--2127232 Score: 275
Period size: 74 Copynumber: 2.0 Consensus size: 75
2127074 TTTCGATCGA
2127084 GAATGTATTTGTAATAGGGGGTGGCCAGATATTAGGTGCAGAGCATACATATTAAAATTTGCAAG
1 GAATGTATTTGTAATAGGGGGTGGCCAGATATTAGGTGCAGAGCATACATATTAAAATTTGCAAG
2127149 A-TCTTAATT
66 ATTCTTAATT
2127158 GAATGTATTTGTAATA-GGGGTGGCCAGATATTTAGGTGCAGAGCATACATATTAAAATTTGCAA
1 GAATGTATTTGTAATAGGGGGTGGCCAGATA-TTAGGTGCAGAGCATACATATTAAAATTTGCAA
2127222 GATTCTTAATT
65 GATTCTTAATT
2127233 CTTATTTTCC
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 14 0.19
74 51 0.70
75 8 0.11
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (75 bp):
GAATGTATTTGTAATAGGGGGTGGCCAGATATTAGGTGCAGAGCATACATATTAAAATTTGCAAG
ATTCTTAATT
Found at i:2130582 original size:20 final size:20
Alignment explanation
Indices: 2130557--2130598 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2130547 CAACAAATTT
2130557 GCCAACTGATATTGCGTTTC
1 GCCAACTGATATTGCGTTTC
2130577 GCCAACTGATATTGCGTTTC
1 GCCAACTGATATTGCGTTTC
2130597 GC
1 GC
2130599 TTCTCGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (20 bp):
GCCAACTGATATTGCGTTTC
Found at i:2136611 original size:12 final size:12
Alignment explanation
Indices: 2136577--2136614 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2136567 ATTAGGATAA
* *
2136577 TATTGTTATTGT
1 TATTATTATTTT
2136589 TATTATTATTTT
1 TATTATTATTTT
2136601 TATTATTATTTT
1 TATTATTATTTT
2136613 TA
1 TA
2136615 AGCATTAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:2148659 original size:19 final size:20
Alignment explanation
Indices: 2148630--2148667 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2148620 CACTCACAAC
*
2148630 TGTATTACTTACACTGATTG
1 TGTATTACTTACACAGATTG
2148650 TGTA-TACTTACACAGATT
1 TGTATTACTTACACAGATT
2148668 TTTCTGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATTACTTACACAGATTG
Found at i:2150109 original size:33 final size:33
Alignment explanation
Indices: 2150072--2150134 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
2150062 GTTGAACATA
2150072 TTCGTCAAATGCTAACTCCCTTGAAGCTTCTCT
1 TTCGTCAAATGCTAACTCCCTTGAAGCTTCTCT
2150105 TTCGTCAAATGCTAACTCCCTTGAAGCTTC
1 TTCGTCAAATGCTAACTCCCTTGAAGCTTC
2150135 GACAAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (33 bp):
TTCGTCAAATGCTAACTCCCTTGAAGCTTCTCT
Found at i:2150219 original size:21 final size:21
Alignment explanation
Indices: 2150194--2150240 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2150184 TCATCAATTA
* *
2150194 AAAGTCAATGAACACTT-TTGT
1 AAAGTCAATCAAC-CTTATTGC
2150215 AAAGTCAATCAACCTTATTGC
1 AAAGTCAATCAACCTTATTGC
2150236 AAAGT
1 AAAGT
2150241 TATAGCTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (21 bp):
AAAGTCAATCAACCTTATTGC
Found at i:2156382 original size:11 final size:11
Alignment explanation
Indices: 2156366--2156415 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
2156356 TTTTCAACAA
2156366 AAAAAAGGCAC
1 AAAAAAGGCAC
* *
2156377 AAAAAAGGTAA
1 AAAAAAGGCAC
2156388 AAAAAAGGCAC
1 AAAAAAGGCAC
*
2156399 AAAAAAAGCA-
1 AAAAAAGGCAC
2156409 AAAAAAG
1 AAAAAAG
2156416 CCAAAATTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 6 0.18
11 27 0.82
ACGTcount: A:0.72, C:0.10, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAGGCAC
Found at i:2156392 original size:22 final size:22
Alignment explanation
Indices: 2156363--2156414 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2156353 TTTTTTTCAA
*
2156363 CAAAAAAAAGGCACAAAAAAGG
1 CAAAAAAAAGGCACAAAAAAAG
*
2156385 TAAAAAAAAGGCACAAAAAAAG
1 CAAAAAAAAGGCACAAAAAAAG
2156407 CAAAAAAA
1 CAAAAAAA
2156415 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.73, C:0.12, G:0.13, T:0.02
Consensus pattern (22 bp):
CAAAAAAAAGGCACAAAAAAAG
Found at i:2167939 original size:33 final size:33
Alignment explanation
Indices: 2167892--2167965 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
2167882 AGAGAAAGTT
* *
2167892 TAAGAACACTTTAGTAAATCCTGTCTGGCAGAA
1 TAAGCACACTTTAGTAAATCCTGTCTGACAGAA
2167925 TAAGCACACTTTAGTAAATCCTGTCTGACAGAA
1 TAAGCACACTTTAGTAAATCCTGTCTGACAGAA
*
2167958 TAGGCACA
1 TAAGCACA
2167966 ACATTCTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (33 bp):
TAAGCACACTTTAGTAAATCCTGTCTGACAGAA
Found at i:2175282 original size:19 final size:19
Alignment explanation
Indices: 2175241--2175297 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 19
2175231 TATGCTAATT
2175241 AAAAT-TTGAAATAATATTCAA
1 AAAATATTGAAATAA-A-T-AA
2175262 AAAATATTGAAATAAAT--
1 AAAATATTGAAATAAATAA
2175279 AAAATATT-AAA-AAATAA
1 AAAATATTGAAATAAATAA
2175296 AA
1 AA
2175298 TAATTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 10 0.30
20 1 0.03
21 6 0.18
22 9 0.27
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAATATTGAAATAAATAA
Found at i:2175295 original size:15 final size:17
Alignment explanation
Indices: 2175262--2175299 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
2175252 TAATATTCAA
2175262 AAAATATTGAAATAAAT
1 AAAATATTGAAATAAAT
2175279 AAAATATT-AAA-AAAT
1 AAAATATTGAAATAAAT
2175294 AAAATA
1 AAAATA
2175300 ATTTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATTGAAATAAAT
Found at i:2175305 original size:17 final size:17
Alignment explanation
Indices: 2175262--2175305 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2175252 TAATATTCAA
*
2175262 AAAATATTGAAATAAAT
1 AAAATATTTAAATAAAT
2175279 AAAATA-TTAAA-AAAT
1 AAAATATTTAAATAAAT
2175294 AAAATAATTTAA
1 AAAAT-ATTTAA
2175306 TTTCATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 10 0.42
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTTAAATAAAT
Found at i:2177759 original size:23 final size:23
Alignment explanation
Indices: 2177725--2177800 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
2177715 AGAATAATTA
2177725 TGTCTTTGTGACATGTTTATCTC
1 TGTCTTTGTGACATGTTTATCTC
* * *
2177748 TGTCTTTATGACATATTTATCTA
1 TGTCTTTGTGACATGTTTATCTC
* *
2177771 TGTCTTTGTGACACGTTTTTCTC
1 TGTCTTTGTGACATGTTTATCTC
2177794 TGTCTTT
1 TGTCTTT
2177801 TGGTAGTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.54
Consensus pattern (23 bp):
TGTCTTTGTGACATGTTTATCTC
Found at i:2180499 original size:3 final size:3
Alignment explanation
Indices: 2180473--2180555 Score: 114
Period size: 3 Copynumber: 27.7 Consensus size: 3
2180463 TTTAGTTTTC
* * * *
2180473 AAT ATAT AAT AAT TAT TAT TAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2180519 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2180556 CTAAAACCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2181945 original size:24 final size:21
Alignment explanation
Indices: 2181884--2181951 Score: 55
Period size: 24 Copynumber: 3.0 Consensus size: 21
2181874 CAAGGTTTTT
*
2181884 TAAAAAATAATAATATAATAA
1 TAAAAAATAATAAAATAATAA
** *
2181905 TAATGAATAAAAAAAATGAAATAA
1 TAAAAAAT-AATAAAAT--AATAA
2181929 TAAAAAATAATATAAATATATAA
1 TAAAAAATAATA-AAATA-ATAA
2181952 AGTTATAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.17
22 7 0.20
23 7 0.20
24 15 0.43
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (21 bp):
TAAAAAATAATAAAATAATAA
Found at i:2182217 original size:18 final size:17
Alignment explanation
Indices: 2182194--2182236 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2182184 ATATATACAT
2182194 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2182212 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2182229 ATAA-AATA
1 ATAATAATA
2182237 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2183574 original size:105 final size:105
Alignment explanation
Indices: 2183387--2184110 Score: 1149
Period size: 105 Copynumber: 7.0 Consensus size: 105
2183377 GCATTGTTCA
* * **
2183387 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
2183447 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2183487 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2183552 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
2183592 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
2183657 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2183697 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
2183762 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
2183802 AAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGTTCTAAAATTGAGAA---GTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
2183864 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2183904 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
2183969 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2184009 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* ** * *
2184074 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2184111 CCTCGAGTGC
Statistics
Matches: 584, Mismatches: 31, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 36 0.06
101 1 0.00
102 99 0.17
103 2 0.00
104 2 0.00
105 403 0.69
106 41 0.07
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2183906 original size:207 final size:208
Alignment explanation
Indices: 2183387--2184110 Score: 1141
Period size: 207 Copynumber: 3.5 Consensus size: 208
2183377 GCATTGTTCA
* * ** *
2183387 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AATTTTGTTGACAAGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
2183449 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
* *
2183514 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
2183579 CTTGCATTGTCTG
196 CTTGCGTTGTCTG
** *
2183592 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
2183657 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
2183722 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
2183787 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
* * * * * *
2183802 AAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGTTCTAAAATTGAGAA-GTTGTTGACAGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
* *
2183866 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
*
2183931 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
2183996 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
2184009 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TG-TTGTTGACAA
* ** * *
2184074 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2184111 CCTCGAGTGC
Statistics
Matches: 475, Mismatches: 35, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 200 0.42
208 2 0.00
210 196 0.41
211 40 0.08
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (208 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:2184004 original size:312 final size:313
Alignment explanation
Indices: 2183388--2184110 Score: 1161
Period size: 312 Copynumber: 2.3 Consensus size: 313
2183378 CATTGTTCAG
* * **
2183388 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
2183448 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
* * * *
2183513 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TAAAATTGGCTCTAAAATTGAGAA--TGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* * ** *
2183578 ACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAG
194 ACTTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
2183643 TTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
259 TTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
2183698 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
2183763 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
* *
2183828 TAAAATTGGTTCTAAAATTGAGAA-GTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 TAAAATTGGCTCTAAAATTGAGAATGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
2183892 TTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
196 TTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
* *
2183957 GTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
261 GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
*
2184010 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
** * *
2184075 CAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2184111 CCTCGAGTGC
Statistics
Matches: 383, Mismatches: 24, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
310 35 0.09
311 2 0.01
312 206 0.54
313 44 0.11
314 2 0.01
315 94 0.25
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (313 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
TAAAATTGGCTCTAAAATTGAGAATGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
Found at i:2184601 original size:29 final size:26
Alignment explanation
Indices: 2184536--2184602 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
2184526 GCCTGTCTGG
2184536 AATCTTGATTCTTGAATCTTCAAATTTT
1 AATC-TGA-TCTTGAATCTTCAAATTTT
*
2184564 GATCCCTGATCTTGAATTCTTCAAATGTTT
1 AAT--CTGATCTTGAA-TCTTCAAAT-TTT
2184594 AAATCTGAT
1 -AATCTGAT
2184603 GTGCACATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
28 9 0.28
29 17 0.53
30 4 0.12
31 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (26 bp):
AATCTGATCTTGAATCTTCAAATTTT
Found at i:2184930 original size:36 final size:36
Alignment explanation
Indices: 2184890--2185009 Score: 143
Period size: 36 Copynumber: 3.3 Consensus size: 36
2184880 AAGGTTTTGT
* * *
2184890 TTCAAGGGAAACTGTCTCAAAATAGACGAAAATTGG
1 TTCAAGGGAAACTGTCTCAAGAGAGACGAAAATTAG
* *
2184926 TTCAAGAGAAACTGTCTTAAGAGAGAC-AAAACTTAG
1 TTCAAGGGAAACTGTCTCAAGAGAGACGAAAA-TTAG
* * *
2184962 TTCCAAGGGAAACTATCTCAAGAGAGACGAAATTTAT
1 TT-CAAGGGAAACTGTCTCAAGAGAGACGAAAATTAG
2184999 TTCAAGGGAAA
1 TTCAAGGGAAA
2185010 TGTTTTCAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.06
36 37 0.52
37 27 0.38
38 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACGAAAATTAG
Found at i:2185999 original size:22 final size:22
Alignment explanation
Indices: 2185974--2186017 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2185964 CATTTTTGTT
2185974 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
2185996 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
2186018 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:2186631 original size:23 final size:23
Alignment explanation
Indices: 2186604--2186654 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2186594 TTTGCATGTG
2186604 TTTTTGTCCCTTTTT-CTTTTTT
1 TTTTTGTCCCTTTTTGCTTTTTT
* *
2186626 CTTTTTGTTCTTTTTTGCTTTTTT
1 -TTTTTGTCCCTTTTTGCTTTTTT
2186650 TTTTT
1 TTTTT
2186655 CTTTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTTGTCCCTTTTTGCTTTTTT
Found at i:2186634 original size:29 final size:29
Alignment explanation
Indices: 2186605--2186678 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 29
2186595 TTGCATGTGT
2186605 TTTTGTCCCTTTTTCTTTTTTCTTTTTGTTC
1 TTTT-TCCCTTTTT-TTTTTTCTTTTTGTTC
** *
2186636 TTTTTTGCTTTTTTTTTTTCTTTTTTTTC
1 TTTTTCCCTTTTTTTTTTTCTTTTTGTTC
2186665 TTTTTGCCCTTTTT
1 TTTTT-CCCTTTTT
2186679 ATTCTGATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.54
30 13 0.35
31 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (29 bp):
TTTTTCCCTTTTTTTTTTTCTTTTTGTTC
Found at i:2186636 original size:9 final size:9
Alignment explanation
Indices: 2186620--2186670 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
2186610 TCCCTTTTTC
2186620 TTTT-TTCT
1 TTTTGTTCT
2186628 TTTTGTTCTT
1 TTTTGTTC-T
*
2186638 TTTTGCTTTT
1 TTTTG-TTCT
*
2186648 TTTTTTTCT
1 TTTTGTTCT
*
2186657 TTTTTTTCT
1 TTTTGTTCT
2186666 TTTTG
1 TTTTG
2186671 CCCTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.11
9 19 0.53
10 11 0.31
11 2 0.06
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTGTTCT
Found at i:2186656 original size:20 final size:22
Alignment explanation
Indices: 2186622--2186661 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2186612 CCTTTTTCTT
2186622 TTTTCTTTTTGTTCTTTTTTGC
1 TTTTCTTTTTGTTCTTTTTTGC
2186644 TTTT-TTTTT-TTCTTTTTT
1 TTTTCTTTTTGTTCTTTTTT
2186662 TTCTTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (22 bp):
TTTTCTTTTTGTTCTTTTTTGC
Found at i:2187865 original size:8 final size:8
Alignment explanation
Indices: 2187849--2187887 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2187839 ATTGTAGATG
2187849 AAAATGCA
1 AAAATGCA
*
2187857 AAAAGGCA
1 AAAATGCA
2187865 AAAATGC-
1 AAAATGCA
2187872 AAAATGCA
1 AAAATGCA
*
2187880 AGAATGCA
1 AAAATGCA
2187888 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:2187875 original size:15 final size:15
Alignment explanation
Indices: 2187849--2187887 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2187839 ATTGTAGATG
2187849 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
2187865 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
2187880 AGAATGCA
1 AAAATGCA
2187888 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:2190733 original size:19 final size:19
Alignment explanation
Indices: 2190678--2190740 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
2190668 GGTTTTTTAA
2190678 AAAAAATAATATAATAATAAT
1 AAAAAATAATAT-A-AATAAT
*
2190699 GAAAAAA-AACGA-AAATAAT
1 -AAAAAATAA-TATAAATAAT
2190718 AAAAAATAATATAAATATAT
1 AAAAAATAATATAAATA-AT
2190738 AAA
1 AAA
2190741 GTTATAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
18 7 0.20
19 13 0.37
20 6 0.17
21 2 0.06
22 7 0.20
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAAATAATATAAATAAT
Found at i:2190960 original size:43 final size:45
Alignment explanation
Indices: 2190869--2190973 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 45
2190859 AAGATAATTT
* ** *
2190869 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGA
1 AATATATATATAATAATATTAGAAATATAAGTAAAATATCAAAGA
2190914 AATATATATATAATAATA-TA-AAATAT-AGTAAAA-ATCAAATGA
1 AATATATATATAATAATATTAGAAATATAAGTAAAATATCAAA-GA
*
2190956 AA-ATA-ATTTAATATATAT
1 AATATATATATAATA-ATAT
2190974 ATATACATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
40 7 0.13
41 11 0.21
42 11 0.21
43 4 0.08
44 2 0.04
45 17 0.33
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (45 bp):
AATATATATATAATAATATTAGAAATATAAGTAAAATATCAAAGA
Found at i:2191005 original size:18 final size:17
Alignment explanation
Indices: 2190982--2191024 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2190972 ATATATACAT
2190982 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2191000 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2191017 ATAA-AATA
1 ATAATAATA
2191025 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2191430 original size:30 final size:30
Alignment explanation
Indices: 2191396--2191457 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
2191386 TCTTTAGGAG
* *
2191396 TTTAAATCATAGTAGAACTCTATCCTATTT
1 TTTAAATCATAGCAAAACTCTATCCTATTT
* *
2191426 TTTAAATCCTAGCAAAATTCTATCCTATTT
1 TTTAAATCATAGCAAAACTCTATCCTATTT
2191456 TT
1 TT
2191458 AGGAGTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTAAATCATAGCAAAACTCTATCCTATTT
Found at i:2191617 original size:11 final size:11
Alignment explanation
Indices: 2191601--2191625 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2191591 ACCAACATGC
2191601 TAAAAAGTAAA
1 TAAAAAGTAAA
2191612 TAAAAAGTAAA
1 TAAAAAGTAAA
2191623 TAA
1 TAA
2191626 TTTTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (11 bp):
TAAAAAGTAAA
Found at i:2195802 original size:14 final size:14
Alignment explanation
Indices: 2195783--2195812 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2195773 ATTGAAAGGA
2195783 AGAGCAATTGATAG
1 AGAGCAATTGATAG
*
2195797 AGAGCATTTGATAG
1 AGAGCAATTGATAG
2195811 AG
1 AG
2195813 GGGAGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (14 bp):
AGAGCAATTGATAG
Found at i:2202530 original size:22 final size:22
Alignment explanation
Indices: 2202448--2202522 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
2202438 GGGTCTACGC
* * *
2202448 GGTCCTTCGGGACATATACAGA
1 GGTCATTCGGGACAAATACATA
2202470 GGTCATTCGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
* *
2202492 GGTCCTTTGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
2202514 GGTCATTCG
1 GGTCATTCG
2202523 AGAAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACATA
Found at i:2203160 original size:21 final size:21
Alignment explanation
Indices: 2203134--2203174 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2203124 ATGAAATTAC
* *
2203134 TGTAGCAGTGCATCGGTACAT
1 TGTAGCAATGCATCGATACAT
2203155 TGTAGCAATGCATCGATACA
1 TGTAGCAATGCATCGATACA
2203175 CATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
TGTAGCAATGCATCGATACAT
Found at i:2206438 original size:4 final size:4
Alignment explanation
Indices: 2206429--2206463 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2206419 TACACTGTAA
2206429 TCTT TCTT TCTT TC-T T-TT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
2206464 TCCTCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.14
4 25 0.86
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:2206450 original size:14 final size:14
Alignment explanation
Indices: 2206431--2206459 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2206421 CACTGTAATC
2206431 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
2206445 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
2206459 T
1 T
2206460 CTTTTCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:2206452 original size:18 final size:18
Alignment explanation
Indices: 2206429--2206464 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2206419 TACACTGTAA
2206429 TCTTTCTTTCTTTCTTTT
1 TCTTTCTTTCTTTCTTTT
2206447 TCTTTCTTTCTTTCTTTT
1 TCTTTCTTTCTTTCTTTT
2206465 CCTCCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TCTTTCTTTCTTTCTTTT
Done.