Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000799.1 Hibiscus syriacus cultivar Beakdansim tig00001553_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: 92502
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5745 original size:7 final size:7
Alignment explanation
Indices: 5733--5759 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5723 TCCAAGAACC
5733 GCGGTAA
1 GCGGTAA
5740 GCGGTAA
1 GCGGTAA
5747 GCGGTAA
1 GCGGTAA
5754 GCGGTA
1 GCGGTA
5760 TTTGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (7 bp):
GCGGTAA
Found at i:6123 original size:3 final size:3
Alignment explanation
Indices: 6115--6162 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6105 TCTAAATTTC
6115 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6163 CGTACAAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:7314 original size:22 final size:22
Alignment explanation
Indices: 7286--7327 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
7276 TGTTATGTTG
7286 TTTATAATATTTTAGGTCACAC
1 TTTATAATATTTTAGGTCACAC
7308 TTTATAATATTTTAGGTCAC
1 TTTATAATATTTTAGGTCAC
7328 GTATTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTATAATATTTTAGGTCACAC
Found at i:9955 original size:49 final size:46
Alignment explanation
Indices: 9856--9956 Score: 130
Period size: 46 Copynumber: 2.1 Consensus size: 46
9846 ATGAAATTCG
* **
9856 TTATACTCACGTGACAAATTATAAAAAAATTATATTTTAAAAGTTG
1 TTATACTCACGTGACAAATTATAAAAAAATTATATTTTAAAACTCA
* *
9902 TTATACTCATGTGACAAATTCTAATAAAAATTATATTTTATAAAACTCA
1 TTATACTCACGTGACAAATTATAA-AAAAATTATA-TTT-TAAAACTCA
9951 TTATAC
1 TTATAC
9957 ATACGATTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
46 22 0.47
47 10 0.21
48 3 0.06
49 12 0.26
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.39
Consensus pattern (46 bp):
TTATACTCACGTGACAAATTATAAAAAAATTATATTTTAAAACTCA
Found at i:18589 original size:19 final size:19
Alignment explanation
Indices: 18567--18604 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18557 AATAAACCAA
*
18567 ATAAGGTAATATAACATTC
1 ATAAGGTAATACAACATTC
18586 ATAAGGTAATACAACATTC
1 ATAAGGTAATACAACATTC
18605 CCGTAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
ATAAGGTAATACAACATTC
Found at i:18929 original size:31 final size:30
Alignment explanation
Indices: 18891--18960 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
18881 TGATGAATTT
* *
18891 TTAATTTGACTCATGAACTTTAGATAAAATA
1 TTAATTTGACTCAT-AAATTTAGAAAAAATA
* *
18922 TTAATTTGA-TCCTAAATTTATAAAAAATA
1 TTAATTTGACTCATAAATTTAGAAAAAATA
*
18951 TTATTTTGAC
1 TTAATTTGAC
18961 CCTAAACATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 21 0.64
30 3 0.09
31 9 0.27
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (30 bp):
TTAATTTGACTCATAAATTTAGAAAAAATA
Found at i:19037 original size:26 final size:26
Alignment explanation
Indices: 19005--19060 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
18995 AAGTTCTTTC
19005 CATCGATCGCCACTCACAATTGTCTT
1 CATCGATCGCCACTCACAATTGTCTT
19031 CATCGATCGCCACTCACAATTGTCTT
1 CATCGATCGCCACTCACAATTGTCTT
19057 CATC
1 CATC
19061 AATTAGCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.11, T:0.30
Consensus pattern (26 bp):
CATCGATCGCCACTCACAATTGTCTT
Found at i:26363 original size:19 final size:20
Alignment explanation
Indices: 26331--26369 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
26321 TTTTTTCTCG
*
26331 GGGATCGATCCTTTTGAAAA
1 GGGATCGATCCTTTTCAAAA
*
26351 GGGATC-ATTCTTTTCAAAA
1 GGGATCGATCCTTTTCAAAA
26370 CAAAAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
GGGATCGATCCTTTTCAAAA
Found at i:32262 original size:158 final size:158
Alignment explanation
Indices: 31859--32379 Score: 633
Period size: 157 Copynumber: 3.3 Consensus size: 158
31849 CATGTAGTTT
* * * *
31859 AAATTTGGTAAAAACAA--ACTTAAAATAAATGGCAAATTGAAGGAATAAAGAGATTATGAAAAG
1 AAATTTGGTAAAAA-AATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAA
* * * * *
31922 TTGAAGGACTAAATTGAAAAATAAAACATTTTTTTATCAAAAAGAGGATTTGAAATTACACATGT
65 TTGAAGGACTAAATTGAAAAATAAAA-ATTTTATTATAAAAAAGAGGAATTGAAAGTACATATGT
* * * *
31987 ATTATACTATGGTTTAGGAGAATGTGGCTC
129 ATTCTATTATGGTTTAGGAGCATGTGACTC
* *
32017 AAATTT-G-ATAAAACTGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAAT
1 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAAT
* * * * *
32080 TGAAGGGCTAAATTGAAAAATAAAAATTTTGTTATAAAAAAGATGAGTTGAAAGTACATGTGTAT
66 TGAAGGACTAAATTGAAAAATAAAAATTTTATTATAAAAAAGAGGAATTGAAAGTACATATGTAT
*
32145 TCTATTATGGTTTAGGACCATGTGACTC
131 TCTATTATGGTTTAGGAGCATGTGACTC
* * * * *
32173 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTAAAGAAACAAGGAGATTATGGAAACT
1 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAAT
* * *
32238 TTAAGGACTAAATTGAAAAATAAAAA--TTATTATCAAGAAAGAGGAATTGAAAGTATATATGTA
66 TGAAGGACTAAATTGAAAAATAAAAATTTTATTAT-AAAAAAGAGGAATTGAAAGTACATATGTA
* * *
32301 TTCTATGATGTTTTAGGAGCATGTGA-TT
130 TTCTATTATGGTTTAGGAGCATGTGACTC
* * *
32329 AAAGTTTGGTAAAAAAATGGACTTAAAATGAAGGAGGAATTGAAGAAATAA
1 AAA-TTTGGTAAAAAAAT-GACTTAAAATAAATGACGAATTGAAGAAATAA
32380 TGAAACCAGG
Statistics
Matches: 313, Mismatches: 43, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
155 1 0.00
156 76 0.24
157 130 0.42
158 106 0.34
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (158 bp):
AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAAT
TGAAGGACTAAATTGAAAAATAAAAATTTTATTATAAAAAAGAGGAATTGAAAGTACATATGTAT
TCTATTATGGTTTAGGAGCATGTGACTC
Found at i:34779 original size:20 final size:20
Alignment explanation
Indices: 34754--34826 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
34744 GGACTCTATG
34754 GAGTATCGATACCAAGGGAT
1 GAGTATCGATACCAAGGGAT
***** *
34774 GAGTATCGATACTCCCTATAG
1 GAGTATCGATAC-CAAGGGAT
*
34795 GGGTATCGATACCAAGGGAT
1 GAGTATCGATACCAAGGGAT
34815 GAGTATCGATAC
1 GAGTATCGATAC
34827 TCCCCATAGG
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (20 bp):
GAGTATCGATACCAAGGGAT
Found at i:34813 original size:41 final size:41
Alignment explanation
Indices: 34756--34847 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
34746 ACTCTATGGA
*
34756 GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
1 GTATCGATACCAAGGGATGAGTATCGATACTCCCCATAGGG
34797 GTATCGATACCAAGGGATGAGTATCGATACTCCCCATAGGG
1 GTATCGATACCAAGGGATGAGTATCGATACTCCCCATAGGG
*
34838 GTATCTATAC
1 GTATCGATAC
34848 TTCCCCTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (41 bp):
GTATCGATACCAAGGGATGAGTATCGATACTCCCCATAGGG
Found at i:34927 original size:20 final size:21
Alignment explanation
Indices: 34882--34931 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
34872 TTAGCACTGG
**
34882 GGTATCGATACCTTGGGAGAA
1 GGTATCGATACCTTAAGAGAA
*
34903 -TTATCGATA-CTTAAGAGAA
1 GGTATCGATACCTTAAGAGAA
34922 GGTATCGATA
1 GGTATCGATA
34932 TTGTAAGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCTTAAGAGAA
Found at i:39213 original size:35 final size:35
Alignment explanation
Indices: 39167--39245 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
39157 TCTTTCGAGA
*
39167 GGGGAATACAATACGGAGAATGCTCCATCAATATC
1 GGGGATTACAATACGGAGAATGCTCCATCAATATC
39202 GGGGATTACAATACGGAGAATGCTCCATCAATATC
1 GGGGATTACAATACGGAGAATGCTCCATCAATATC
39237 GGGGATTAC
1 GGGGATTAC
39246 CTCGGGTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (35 bp):
GGGGATTACAATACGGAGAATGCTCCATCAATATC
Found at i:42241 original size:22 final size:21
Alignment explanation
Indices: 42217--42256 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42207 GAGAAATTAT
42217 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
42238 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
42257 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:44534 original size:18 final size:17
Alignment explanation
Indices: 44513--44546 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44503 CAAGGGAAAA
*
44513 ATAAAATAAATAAGTAAG
1 ATAAAAAAAAT-AGTAAG
44531 ATAAAAAAAATAGTAA
1 ATAAAAAAAATAGTAA
44547 AGTAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
ATAAAAAAAATAGTAAG
Found at i:44590 original size:2 final size:2
Alignment explanation
Indices: 44585--44616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44575 AAAAACGAAA
44585 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
44617 CAAAGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45115 original size:19 final size:19
Alignment explanation
Indices: 45065--45118 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
45055 ATATATATAT
45065 ATATATAAT-AATAACATGA
1 ATATATAATAAATAA-ATGA
45084 ATA-ATAA-AAATAAATGA
1 ATATATAATAAATAAATGA
45101 ATATATAATAAATAAATG
1 ATATATAATAAATAAATG
45119 GACTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.22
18 13 0.41
19 12 0.38
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (19 bp):
ATATATAATAAATAAATGA
Found at i:45506 original size:37 final size:37
Alignment explanation
Indices: 45456--45560 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
45446 GTGCTTGTGG
* * * *
45456 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
45493 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
45530 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
45561 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:47572 original size:23 final size:21
Alignment explanation
Indices: 47520--47581 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
47510 TTTTGGTGCA
*
47520 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
47540 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
47561 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
47582 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:47607 original size:20 final size:20
Alignment explanation
Indices: 47522--47607 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
47512 TTGGTGCAGA
* *
47522 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
47541 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
47565 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
47586 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
47606 GG
1 GG
47608 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:52563 original size:40 final size:40
Alignment explanation
Indices: 52512--52596 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
52502 CCAGTAGGTT
* * *
52512 GGTGGCTAACTTGTACACATTAGAAAATTCATCTTTGGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
* *
52552 GGTGGCCAACTTGTATACATTGGAAAATTCAACTTTAGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
52592 GGTGG
1 GGTGG
52597 TCAAACTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (40 bp):
GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
Found at i:53934 original size:30 final size:28
Alignment explanation
Indices: 53900--54041 Score: 97
Period size: 30 Copynumber: 4.6 Consensus size: 28
53890 AAAAATAAAT
*
53900 TATATTGTTTAAGTTAAGATAAGTCAAAAA
1 TATATT-TTTAAGTTAAAATAAGT-AAAAA
53930 TATATTTTTTAAGTTAAAATAAG-AATAATA
1 TATA-TTTTTAAGTTAAAATAAGTAA-AA-A
*
53960 TATATTTTTAAGTTTAAAATAAAATAAAATAAAA
1 TATATTTTTAAG-TTAAAAT-AAGT---A-AAAA
* **
53994 TATATTTTTAAGTTAAGATAAAAATAAAA
1 TATATTTTTAAGTTAAAATAAGTA-AAAA
54023 TATATCTTTTGATAGTTAA
1 TATAT-TTTT-A-AGTTAA
54042 TATATGAATT
Statistics
Matches: 95, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
28 2 0.02
29 21 0.22
30 35 0.37
31 5 0.05
32 9 0.09
33 6 0.06
34 13 0.14
35 3 0.03
36 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (28 bp):
TATATTTTTAAGTTAAAATAAGTAAAAA
Found at i:53997 original size:34 final size:33
Alignment explanation
Indices: 53884--54024 Score: 127
Period size: 34 Copynumber: 4.4 Consensus size: 33
53874 TTGTAAAAGG
* *
53884 TAAAATAAAAATAAATTATATTGTTTAAGTTAAGA
1 TAAAAT-AAAATAAAATATATT-TTTAAGTTAAAA
* * *
53919 T-AAGTCAAA-AATATAT-TTTTTAAGTTAAAA
1 TAAAATAAAATAAAATATATTTTTAAGTTAAAA
53949 TAAGAAT--AAT---ATATATTTTTAAGTTTAAAA
1 TAA-AATAAAATAAAATATATTTTTAAG-TTAAAA
*
53979 TAAAATAAAATAAAATATATTTTTAAGTTAAGA
1 TAAAATAAAATAAAATATATTTTTAAGTTAAAA
54012 TAAAAATAAAATA
1 T-AAAATAAAATA
54025 TATCTTTTGA
Statistics
Matches: 88, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
28 4 0.05
29 11 0.12
30 23 0.26
31 6 0.07
32 7 0.08
33 9 0.10
34 27 0.31
35 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (33 bp):
TAAAATAAAATAAAATATATTTTTAAGTTAAAA
Found at i:59882 original size:52 final size:52
Alignment explanation
Indices: 59820--59926 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
59810 TGTACAAATA
59820 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
*
59872 TATGAGTGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
59924 TAT
1 TAT
59927 CCTCATGTGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (52 bp):
TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
Found at i:69124 original size:42 final size:42
Alignment explanation
Indices: 69016--69136 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
69006 CTTAGTAAGA
**
69016 CCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATGATTAAAT
1 CCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAAT
* * * *
69058 CCTCCGCGTTATCAGTAAGTCTTTCAATCATGATGATTAAAT
1 CCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAAT
* * *
69100 CCTTCGGGTCATCTA-TAAGCCTTTCGAGCAAGATGAT
1 CCTTCGGGTCATC-AGTAAGTCTTTCAAGCATGATGAT
69137 AAGTTCTCTG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
CCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGATTAAAT
Found at i:69209 original size:37 final size:37
Alignment explanation
Indices: 69155--69262 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 37
69145 TGGGCTATCT
*
69155 TAAGCCTTCACGGAAGAGTCGTGAAGCAAATCAATCA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
* * * * *
69192 TATGCCTTCACGAAAGAGTATTGAAACAAATCAATCT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
**
69229 TAAGCCTTCACGGAAGAAAAGTGAAGCAAATCAA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAA
69263 GATCGAGTCC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (37 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
Found at i:69339 original size:55 final size:55
Alignment explanation
Indices: 69265--69682 Score: 428
Period size: 55 Copynumber: 7.6 Consensus size: 55
69255 CAAATCAAGA
* ** *
69265 TCGAGTCCTATACTGTCTGAAAGAATAGGGAGTTGACATGTTTGATGAAGATTG-
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATTGT
*
69319 TCTGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
1 TC-GAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATTGT
* * *
69375 TCGTGTCCTATACTCTCTGAAAGAATAGGGAGTAGACATGTTT-ACTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGA-TGAAGATTGT
* * *
69430 TCGAGTCCTATACTCTTTGAAAGAATAGGGAGCAGACACGTTCGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATTGT
* * * * * * * *
69485 TTGAGTCCTATACTCCCCGAAAGATTAGGAAGCATATACGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATTGT
* * * * * * *
69540 TTGAGTCTTGTACTCCCTGAAATAATAGGGAGCGGATACGTTT-ACTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGA-TGAAGATTGT
* * * * * * *** *
69595 TCGAGTCATATACTCCCTGAAAAAATAGGGAGCGGACCCATTTTCCGAAGATTATT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATT-GT
* * *
69651 TCAAGTCATATACTCCCTGAAAGAATAGGGAG
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAG
69683 AGAACCCGTT
Statistics
Matches: 311, Mismatches: 46, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
54 2 0.01
55 276 0.89
56 33 0.11
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGATGAAGATTGT
Found at i:69537 original size:165 final size:165
Alignment explanation
Indices: 69265--69627 Score: 483
Period size: 165 Copynumber: 2.2 Consensus size: 165
69255 CAAATCAAGA
* ** * *
69265 TCGAGTCCTATACTGTCTGAAAGAATAGGGAGTTGACATGTTTGATGAAGATTGTCTGAGTCCTA
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTCGATGAAGATTGTCTGAGTCCTA
* * * * *
69330 TACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCGTGTCCTATACTCTCTGA
66 TACTCCCCGAAAGAATAGGAAGCAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGA
* *
69395 AAGAATAGGGAGTAGACATGTTTACTGAAGATTGT
131 AAGAATAGGGAGCAGACACGTTTACTGAAGATTGT
* * *
69430 TCGAGTCCTATACTCTTTGAAAGAATAGGGAGCAGACACGTTCGTTGAAGATTGTTTGAGTCCTA
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTCGATGAAGATTGTCTGAGTCCTA
* * * * * *
69495 TACTCCCCGAAAGATTAGGAAGCATATACGTTTGCTGAAGATTGTTTGAGTCTTGTACTCCCTGA
66 TACTCCCCGAAAGAATAGGAAGCAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGA
* * *
69560 AATAATAGGGAGCGGATACGTTTACTGAAGATTGT
131 AAGAATAGGGAGCAGACACGTTTACTGAAGATTGT
* * *
69595 TCGAGTCATATACTCCCTGAAAAAATAGGGAGC
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGC
69628 GGACCCATTT
Statistics
Matches: 170, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
165 170 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (165 bp):
TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTCGATGAAGATTGTCTGAGTCCTA
TACTCCCCGAAAGAATAGGAAGCAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGA
AAGAATAGGGAGCAGACACGTTTACTGAAGATTGT
Found at i:73443 original size:7 final size:7
Alignment explanation
Indices: 73431--73460 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
73421 AAATTAACTT
73431 AATAAAA
1 AATAAAA
73438 AATAAAA
1 AATAAAA
*
73445 GATAAAA
1 AATAAAA
73452 AATAAAA
1 AATAAAA
73459 AA
1 AA
73461 AATGTAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:75146 original size:21 final size:21
Alignment explanation
Indices: 75120--75182 Score: 56
Period size: 27 Copynumber: 2.7 Consensus size: 21
75110 ACCCAAAGGT
75120 CAATATCGATACTATGAGGCA
1 CAATATCGATACTATGAGGCA
75141 CAATATCAGTACCGATACTATGAGGCA
1 C-A-AT-A-T--CGATACTATGAGGCA
75168 CAATATC-AGTACTAT
1 CAATATCGA-TACTAT
75183 CATCATGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
20 1 0.03
21 8 0.23
22 1 0.03
23 3 0.09
24 2 0.06
25 3 0.09
26 1 0.03
27 16 0.46
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (21 bp):
CAATATCGATACTATGAGGCA
Found at i:75192 original size:27 final size:27
Alignment explanation
Indices: 75126--75179 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
75116 AGGTCAATAT
75126 CGATACTATGAGGCACAATATCAGTAC
1 CGATACTATGAGGCACAATATCAGTAC
75153 CGATACTATGAGGCACAATATCAGTAC
1 CGATACTATGAGGCACAATATCAGTAC
75180 TATCATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
CGATACTATGAGGCACAATATCAGTAC
Found at i:77638 original size:18 final size:18
Alignment explanation
Indices: 77612--77677 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
77602 TTTTTCGTTC
*
77612 TTTTGGTTTAGCTCTCTA
1 TTTTGGTTTGGCTCTCTA
*
77630 TTTTTGTTTTTTGGCTCTCTA
1 -TTTTG--GTTTGGCTCTCTA
*
77651 TTTCGGTTTGGCTCTCTA
1 TTTTGGTTTGGCTCTCTA
*
77669 TTTTTGTTT
1 TTTTGGTTT
77678 CGGTTTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 19 0.49
19 5 0.13
20 4 0.10
21 11 0.28
ACGTcount: A:0.06, C:0.15, G:0.17, T:0.62
Consensus pattern (18 bp):
TTTTGGTTTGGCTCTCTA
Found at i:77648 original size:21 final size:21
Alignment explanation
Indices: 77622--77677 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 21
77612 TTTTGGTTTA
77622 GCTCTCTATTTTTGTTTTTTG
1 GCTCTCTATTTTTGTTTTTTG
* *
77643 GCTCTCTA-TTTCG--GTTTG
1 GCTCTCTATTTTTGTTTTTTG
77661 GCTCTCTATTTTTGTTT
1 GCTCTCTATTTTTGTTT
77678 CGGTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 4 0.14
21 8 0.29
ACGTcount: A:0.05, C:0.18, G:0.16, T:0.61
Consensus pattern (21 bp):
GCTCTCTATTTTTGTTTTTTG
Found at i:78978 original size:134 final size:134
Alignment explanation
Indices: 78759--79218 Score: 617
Period size: 134 Copynumber: 3.5 Consensus size: 134
78749 CTATTTCTGC
* * * *
78759 AGGGAAGATCAGA-TCGAG-AAACTTTGATTCA-TTCCACTGTTCTTCATGGAAGATTAAATCGG
1 AGGG-AGATCAGAGTCGAGAAAACTTTGATCCACTT-CACTGTTCTTCAGGGAAGATTGAATCAG
** **
78821 AATCGATTTGCTTCACTAATCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTGCTCCACTAC
64 AATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTAC
78886 TCTTTA
129 TCTTTA
* * * *
78892 TGGGAGATCAGAGTCGAGAAAAATTTGATCCACTTCACTATTCTTCAGGGAAGATTGAATTAGAA
1 AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGAA
* *
78957 TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTCTGCTTCACTACTC
66 TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACTC
79022 TTTA
131 TTTA
* * * * * * *
79026 GGGGATATCATAGTCAAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGAT
1 AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGAA
* *
79091 TTGATTTGCTTCACTGCTCTTTAGGAAGACCAAATATG-AAGAAGAAGCGTCTGCTCCACTACT-
66 TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACTC
79154 TTTA
131 TTTA
* * *
79158 AGGGAGATCAAACTCGAGAAATCTTTGATCCACTTCACT-TCTCTTCAGGGAAGATTGAATC
1 AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGT-TCTTCAGGGAAGATTGAATC
79219 TGAAAATCAA
Statistics
Matches: 288, Mismatches: 35, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
132 64 0.22
133 32 0.11
134 190 0.66
135 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (134 bp):
AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGAA
TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACTC
TTTA
Found at i:79817 original size:45 final size:45
Alignment explanation
Indices: 79750--80087 Score: 219
Period size: 45 Copynumber: 7.6 Consensus size: 45
79740 GATATTACCG
* *
79750 AAAAG-TTGACTCATCTCCGCGAGAAAAACAA-AATGGACAACACC
1 AAAAGATTGACTCATCTTCGCGAGAAAAACAAGAA-GGACAACACT
* ***
79794 AAAAGATTGACTCATCTTGGCGAGAATGTCAAGGAA-GACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAAACAA-GAAGGACAACACT
* ** *
79839 AAAATATTGACTCATCTTCATGAGAAAGTAA-AGGAA-GACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAA--AACAAGAAGGACAACACT
* * * **
79884 GAAAGATTGACTCCTCTTTGCGAGAAAGTCAAGAAGGACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAAACAAGAAGGACAACACT
* * *
79929 AAAAGATTGAATCCTCTTTGCGA-AAAAATCAAGAAGGACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAAA-CAAGAAGGACAACACT
* * * * ** * * *
79974 GAAATATTGACTCCTCTTCGCAAGAAAGTCAAAAAAGACAATACT
1 AAAAGATTGACTCATCTTCGCGAGAAAAACAAGAAGGACAACACT
* * * * ** * *
80019 GAAATATTGACTTC-TCTTCACAAGAAAGTCATGAA-TA-AA-ACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAAACAAGAAGGACAACACT
* *
80061 GAAAGATTGACTCCTCTTCGCGAGAAA
1 AAAAGATTGACTCATCTTCGCGAGAAA
80088 GTCAAGAATA
Statistics
Matches: 239, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.01
42 24 0.10
43 2 0.01
44 13 0.05
45 190 0.79
46 6 0.03
47 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
AAAAGATTGACTCATCTTCGCGAGAAAAACAAGAAGGACAACACT
Found at i:79961 original size:135 final size:136
Alignment explanation
Indices: 79784--80093 Score: 362
Period size: 135 Copynumber: 2.3 Consensus size: 136
79774 AAAACAAAAT
* * * *
79784 GGACAACACCAAAAGATTGACTCATCTTGGCGAGAATGTCAAGGAA-GACAACACTAAAATATTG
1 GGACAACACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGGAAGGACAACACTAAAATATTG
** * ** *
79848 ACTCATCTTCATGAGAAAGT-AAAGGAAGACAACACTGAAAGATTGACTCCTCTTTGCGAGAAAG
66 ACTCATCTTCACAAGAAAGTCAAA-AAAGACAACACTGAAAGATTGACTCCTCTTCACAAGAAAG
79912 TCAAGAA
130 TCAAGAA
* * * * *
79919 GGACAACACTAAAAGATTGAATCCTCTTTGCGAAAAAATCAA-GAAGGACAACACTGAAATATTG
1 GGACAACACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGGAAGGACAACACTAAAATATTG
* * * * *
79983 ACTCCTCTTCGCAAGAAAGTCAAAAAAGACAATACTGAAATATTGACTTCTCTTCACAAGAAAGT
66 ACTCATCTTCACAAGAAAGTCAAAAAAGACAACACTGAAAGATTGACTCCTCTTCACAAGAAAGT
*
80048 CATGAA
131 CAAGAA
* *
80054 -TA-AA-ACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAG
1 GGACAACACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAG
80094 AATAACAAAG
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
132 30 0.21
133 2 0.01
134 4 0.03
135 107 0.73
136 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (136 bp):
GGACAACACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGGAAGGACAACACTAAAATATTG
ACTCATCTTCACAAGAAAGTCAAAAAAGACAACACTGAAAGATTGACTCCTCTTCACAAGAAAGT
CAAGAA
Found at i:79969 original size:90 final size:88
Alignment explanation
Indices: 79785--80095 Score: 331
Period size: 90 Copynumber: 3.5 Consensus size: 88
79775 AAACAAAATG
** * * *
79785 GACAACACCAAAAGATTGACTCATCTTGGCGAGAATGTCAAGGAAGACAACACTAAAATATTGAC
1 GACAACACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAA-GAAGACAACACTAAAATATTGAC
* * * * *
79850 TCATCTTCATGAGAAAGTAAAGGAA
65 TCCTCTTCACGAAAAAATCAA-GAA
* * *
79875 GACAACACTGAAAGATTGACTCCTCTTTGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAA
1 GACAACACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA-GACAACACTAAAATATTGAC
**
79940 TCCTCTTTGCGAAAAAATCAAGAA
65 TCCTCTTCACGAAAAAATCAAGAA
* * * * *
79964 GGACAACACTGAAATATTGACTCCTCTTCGCAAGAAAGTCAAAAAAGACAATACTGAAATATTGA
1 -GACAACACTGAAAGATTGACTCCTCTTCGCGAGAAAGTC-AAGAAGACAACACTAAAATATTGA
* * *
80029 CTTCTCTTCAC-AAGAAAGTCATGAA
64 CTCCTCTTCACGAA-AAAATCAAGAA
*
80054 TA-AA-ACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA
1 GACAACACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA
80096 TAACAAAGAT
Statistics
Matches: 186, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
86 4 0.02
87 31 0.17
88 2 0.01
89 9 0.05
90 136 0.73
91 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (88 bp):
GACAACACTGAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGACAACACTAAAATATTGACT
CCTCTTCACGAAAAAATCAAGAA
Found at i:80116 original size:38 final size:38
Alignment explanation
Indices: 80024--80931 Score: 798
Period size: 38 Copynumber: 22.9 Consensus size: 38
80014 ATACTGAAAT
* * *
80024 ATTGACTTCTCTTCACAAGAAAGTCATGAATAAAACTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AAC--AAAG
* * *
80066 ATTGACTCCTCTTCGCGAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * * *
80104 ATCGAGTTCTCTTCATGAGGAAGTTAATAATAAAAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
80142 ATCGACTTCTCTTTATGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
80180 ATTGACTTCTCGTCACGAGGATGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
80218 ATTAATTGA-TTCCTCTTCGCGAGGGAGTCAAGAATAACAAAG
1 ----ATTGACTT-CTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
80260 ATTGACTTCTCTTCATGAAGAAGTCAAGAATAACAAAGATTG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--G
* ** * *
80302 ATTGACTCCTCTTTGCGAGGGAGTCAAGAATAATAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
80340 ATTGACCTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--G
* *
80382 ATTGACTCCTCTTCACGAGGGAGTCAAGAATAA-AATAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA-AG
* *
80420 AATGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
80458 ATTGACCTCTCTTCACGAGGAAATCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * * * *
80500 ATTTACTCCTCTTCGCGAGGGAGTCAAGAACAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * *
80538 ATTAACTTATCTTCACGAGGAAGTCAATAATAACATTGAAAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * * * *
80580 ATTTGACTCCTCTTCGCGAGGGAGTCAAGAATAATATAG
1 A-TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * **
80619 ATTGACTTCACTTCACGAGGAATTCAAGGTTAATATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAA-G--AATA-ACAAAG
* *
80661 ATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
80699 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAA-
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA---AAG
* * *
80739 ATGTTGACTTCTCTTCGCGAGGGAGTCAAGAACAACAAAG
1 A--TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
80779 ATTGACTTCTCTTCAAGAGGAAGTTAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
80817 ATTGATTTCTCTTCACGAGGATGTCAAGGATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* ** * *
80859 ATTGACTCCTCTTCTTGA-GAGAGTCAGGAGTAACAAAG
1 ATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAG
* *
80897 ATTAACTTTTCTTCACGAGGAAGTCAAGAATAACA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA
80932 TTGAAAGATT
Statistics
Matches: 700, Mismatches: 126, Indels: 84
0.77 0.14 0.09
Matches are distributed among these distances:
38 397 0.57
39 19 0.03
40 11 0.02
41 12 0.02
42 235 0.34
43 26 0.04
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:80254 original size:118 final size:117
Alignment explanation
Indices: 80024--80931 Score: 742
Period size: 118 Copynumber: 7.6 Consensus size: 117
80014 ATACTGAAAT
* * * * * *
80024 ATTGACTTCTCTTCACAAGAAAGTCATGAATAAAACTGAAAGATTGACTCCTCTTCGCGAGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AAC--AAAGATTGACTTCTCTTCACGAGGAAG
* * * *
80089 TCAAGAATAAC-AA-AGATCGAGTT-CTCTTCATGAGGAAGTTAATAATAA-AAAAG
62 TCAAGAATAACAAAGAGATTGA-TTCCTCTTCACGAGGAAGTCAAGAATAACAAAAG
* * * * *
80142 ATCGACTTCTCTTTATGAGGAAGTCAAGAATAACAAAGATTGACTTCTCGTCACGAGGATGTCAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * *
80207 GAATAACAAAGATTAATTGATTCCTCTTCGCGAGGGAGTCAAGAATAAC-AAAG
66 GAATAACAAAGA--GATTGATTCCTCTTCACGAGGAAGTCAAGAATAACAAAAG
* * * ** *
80260 ATTGACTTCTCTTCATGAAGAAGTCAAGAATAACAAAGATTGATTGACTCCTCTTTGCGAGGGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--GATTGACTTCTCTTCACGAGGAAG
* *
80325 TCAAGAATAA-TAA-AGATTGA-CCTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTG
62 TCAAGAATAACAAAGAGATTGATTC-CTCTTCACGAGGAAGTCAAGAATAACAAA-A--G
* * *
80382 ATTGACTCCTCTTCACGAGGGAGTCAAGAATAA-AATAGAATGACTTCTCTTCACGAGGAAGTCA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA-AGATTGACTTCTCTTCACGAGGAAGTCA
* *
80446 AGAATAAC--AGAGATTGA-CCTCTCTTCACGAGGAAATCAAGAATAACATTGAAAG
65 AGAATAACAAAGAGATTGATTC-CTCTTCACGAGGAAGTCAAGAATAACA---AAAG
* * * * * * *
80500 ATTTACTCCTCTTCGCGAGGGAGTCAAGAACAACAAAGATTAACTTATCTTCACGAGGAAGTCAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * * * * * *
80565 TAATAACATTGAA-AAATTTGACTCCTCTTCGCGAGGGAGTCAAGAATAA-TATAG
66 GAATAACA---AAGAGA-TTGATTCCTCTTCACGAGGAAGTCAAGAATAACAAAAG
* * ** *
80619 ATTGACTTCACTTCACGAGGAATTCAAGGTTAATATTGAAAGATTAACTTCTCTTCACGAGGAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAA-G--AATA-ACAAAGATTGACTTCTCTTCACGAGGAAG
*
80684 TCAAGAATAAC--AGAGATTGACTT-CTCTTCATGAGGAAGTCAAGAATAACATTGAAATG
62 TCAAGAATAACAAAGAGATTGA-TTCCTCTTCACGAGGAAGTCAAGAATAACA---AAA-G
* * * * *
80742 -TTGACTTCTCTTCGCGAGGGAGTCAAGAACAACAAAGATTGACTTCTCTTCAAGAGGAAGTTAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
* * *
80806 GAATAAC-AA-AGATTGATTTCTCTTCACGAGGATGTCAAGGATAACATTGAAAG
66 GAATAACAAAGAGATTGATTCCTCTTCACGAGGAAGTCAAGAATAACA---AAAG
* ** * * * *
80859 ATTGACTCCTCTTCTTGA-GAGAGTCAGGAGTAACAAAGATTAACTTTTCTTCACGAGGAAGTCA
1 ATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
80923 AGAATAACA
65 AGAATAACA
80932 TTGAAAGATT
Statistics
Matches: 647, Mismatches: 99, Indels: 87
0.78 0.12 0.10
Matches are distributed among these distances:
114 33 0.05
115 2 0.00
116 4 0.01
117 8 0.01
118 398 0.62
119 37 0.06
120 8 0.01
121 5 0.01
122 87 0.13
123 64 0.10
124 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (117 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAA
GAATAACAAAGAGATTGATTCCTCTTCACGAGGAAGTCAAGAATAACAAAAG
Found at i:80932 original size:80 final size:78
Alignment explanation
Indices: 80024--80966 Score: 772
Period size: 80 Copynumber: 11.9 Consensus size: 78
80014 ATACTGAAAT
* * * * * *
80024 ATTGACTTCTCTTCACAAGAAAGTCATGAATAAAACTGAAAGATTGACTCCTCTTCGCGAGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AACAGAAAGATTGACTCCTCTTCACGAGGAAG
80089 TCAAGAATAACAAAG
64 TCAAGAATAACAAAG
* * * * * * * * *
80104 ATCGAGTTCTCTTCATGAGGAAGTTAATAATAA-A-AAAGATCGACTTCTCTTTATGAGGAAGTC
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAGTC
80167 AAGAATAACAAAG
66 AAGAATAACAAAG
* * * * * *
80180 ATTGACTTCTCGTCACGAGGATGTCAAGAATAACA-AAGATTAATTGATTCCTCTTCGCGAGGGA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAA-A--GATTGACTCCTCTTCACGAGGAA
80244 GTCAAGAATAACAAAG
63 GTCAAGAATAACAAAG
* * ** *
80260 ATTGACTTCTCTTCATGAAGAAGTCAAGAATAACA-AAGATTGATTGACTCCTCTTTGCGAGGGA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAA-A--GATTGACTCCTCTTCACGAGGAA
*
80324 GTCAAGAATAATAAAG
63 GTCAAGAATAACAAAG
* *
80340 ATTGACCTCTCTTCACGAGGAAGTCAAGAATAACA-AAGATTGATTGACTCCTCTTCACGAGGGA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAA-A--GATTGACTCCTCTTCACGAGGAA
80404 GTCAAGAATAA-AATAG
63 GTCAAGAATAACAA-AG
* *
80420 AATGACTTCTCTTCACGAGGAAGTCAAGAATAACAG--AGATTGAC-CTCTCTTCACGAGGAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTC-CTCTTCACGAGGAAGT
80482 CAAGAATAACATTGAAAG
65 CAAGAATAAC----AAAG
* * * * * * **
80500 ATTTACTCCTCTTCGCGAGGGAGTCAAGAACAAC--AAAGATTAACTTATCTTCACGAGGAAGTC
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAGTC
* *
80563 AATAATAACATTGAAAA
66 AAGAATAAC----AAAG
* * * * * * * *
80580 ATTTGACTCCTCTTCGCGAGGGAGTCAAGAAT-A-ATATAGATTGACTTCACTTCACGAGGAATT
1 A-TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAGT
**
80643 CAAGGTTAATATTGAAAG
65 CAA-G--AATA-ACAAAG
* * *
80661 ATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAG--AGATTGACTTCTCTTCATGAGGAAGTC
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAGTC
80724 AAGAATAACATTGAA-
66 AAGAATAACA---AAG
* * * * *
80739 ATGTTGACTTCTCTTCGCGAGGGAGTCAAGAACAAC--AAAGATTGACTTCTCTTCAAGAGGAAG
1 A--TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAG
*
80802 TTAAGAATAACAAAG
64 TCAAGAATAACAAAG
* * * **
80817 ATTGATTTCTCTTCACGAGGATGTCAAGGATAACATTGAAAGATTGACTCCTCTTCTTGA-GAGA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA--GAAAGATTGACTCCTCTTCACGAGGA-A
* *
80881 GTCAGGAGTAACAAAG
63 GTCAAGAATAACAAAG
* * * * * *
80897 ATTAACTTTTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTAACTCCTCTTTATGAGGGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA--GAAAGATTGACTCCTCTTCACGAGGAAG
80962 TCAAG
64 TCAAG
80967 TTGAAGCTTC
Statistics
Matches: 717, Mismatches: 108, Indels: 76
0.80 0.12 0.08
Matches are distributed among these distances:
75 1 0.00
76 120 0.17
77 9 0.01
78 6 0.01
79 7 0.01
80 507 0.71
81 62 0.09
82 1 0.00
84 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (78 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAAAGATTGACTCCTCTTCACGAGGAAGTC
AAGAATAACAAAG
Found at i:82793 original size:17 final size:16
Alignment explanation
Indices: 82771--82841 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
82761 AAATACTTGA
82771 TTTATTTTCTCTCATTT
1 TTTATTTTCT-TCATTT
*
82788 TTTATTTTCTTTATTTT
1 TTTATTTTCTTCA-TTT
* *
82805 CTTTATTTTATTCTTTCT
1 -TTTATTTTCTTCATT-T
*
82823 TTTCTTTTCTCTC-TTT
1 TTTATTTTCT-TCATTT
82839 TTT
1 TTT
82842 CTTCTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 6 0.14
17 25 0.57
18 13 0.30
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTCTTCATTT
Found at i:82801 original size:26 final size:26
Alignment explanation
Indices: 82771--82890 Score: 87
Period size: 26 Copynumber: 4.9 Consensus size: 26
82761 AAATACTTGA
*
82771 TTTATTTTCTCTCATTTTTTATTT-T
1 TTTATTTTCTCTCATTTTTTCTTTCT
*
82796 CTTTATTTTCT-TTATTTTATTCTTTCT
1 -TTTATTTTCTCTCATTTT-TTCTTTCT
*
82823 TTTCTTTTCTCTC-TTTTTTC-TTCT
1 TTTATTTTCTCTCATTTTTTCTTTCT
* * * *
82847 TAT-TTTTCTATC-TTTTCTCTTTCA
1 TTTATTTTCTCTCATTTTTTCTTTCT
*
82871 TTT-TTTTATCT--TTTTTTCTT
1 TTTATTTTCTCTCATTTTTTCTT
82891 CTCTCTCCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
23 22 0.28
24 17 0.22
25 9 0.12
26 28 0.36
27 2 0.03
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTTCTCTCATTTTTTCTTTCT
Found at i:82802 original size:9 final size:9
Alignment explanation
Indices: 82771--82813 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
82761 AAATACTTGA
82771 TTTATTTTC
1 TTTATTTTC
*
82780 TCTCA-TTT-
1 T-TTATTTTC
82788 TTTATTTTC
1 TTTATTTTC
82797 TTTATTTTC
1 TTTATTTTC
82806 TTTATTTT
1 TTTATTTT
82814 ATTCTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 4 0.14
9 21 0.72
10 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTC
Found at i:82838 original size:30 final size:29
Alignment explanation
Indices: 82804--82915 Score: 79
Period size: 28 Copynumber: 3.7 Consensus size: 29
82794 TTCTTTATTT
82804 TCTTTATTTTATTCTTTCTTTTCTTTTCTC
1 TCTTTATTTTATTCTTT-TTTTCTTTTCTC
* *
82834 TC-TT-TTTTCTTCTTATTTTTCTATCTTTTC
1 TCTTTATTTTATTCTT-TTTTTCT-T-TTCTC
* *
82864 TCTTTCATTTTTTTATCTTTTTTTCTTCTCTC
1 TCTTT-A-TTTTAT-TCTTTTTTTCTTTTCTC
*
82896 TC-CT-TTTTATCTCTTTTTTT
1 TCTTTATTTTAT-TCTTTTTTT
82916 ATGAATTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
28 29 0.44
29 4 0.06
30 8 0.12
31 3 0.05
32 5 0.08
33 1 0.02
34 12 0.18
35 4 0.06
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (29 bp):
TCTTTATTTTATTCTTTTTTTCTTTTCTC
Found at i:82842 original size:21 final size:22
Alignment explanation
Indices: 82818--82886 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
82808 TATTTTATTC
*
82818 TTTCTTTT-CTTTTCTCTCTTT
1 TTTCTTTTACTTTTCTATCTTT
*
82839 TTTCTTCTTATTTTTCTATCTTT
1 TTTCTT-TTACTTTTCTATCTTT
* * * *
82862 TCTCTTTCATTTTTTTATCTTT
1 TTTCTTTTACTTTTCTATCTTT
82884 TTT
1 TTT
82887 TCTTCTCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.15
22 18 0.45
23 16 0.40
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCTTTTACTTTTCTATCTTT
Found at i:82860 original size:23 final size:23
Alignment explanation
Indices: 82827--82893 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
82817 CTTTCTTTTC
* *
82827 TTTTCTCTCTTTTTTCTTCTTAT
1 TTTTCTATCTTTTTTCTTCTCAT
*
82850 TTTTCTATCTTTTCTCTT-TCAT
1 TTTTCTATCTTTTTTCTTCTCAT
*
82872 TTTTTTATCTTTTTTTCTTCTC
1 TTTTCTATC-TTTTTTCTTCTC
82894 TCTCCTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.30
23 24 0.65
24 2 0.05
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTCTATCTTTTTTCTTCTCAT
Found at i:82862 original size:22 final size:22
Alignment explanation
Indices: 82827--82890 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
82817 CTTTCTTTTC
*
82827 TTTTCTCTCTTTTTTCTTCTTAT
1 TTTTCTATC-TTTTTCTTCTTAT
*
82850 TTTTCTATCTTTTCTCTT-TCAT
1 TTTTCTATCTTTT-TCTTCTTAT
*
82872 TTTTTTATCTTTTT-TTCTT
1 TTTTCTATCTTTTTCTTCTT
82891 CTCTCTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 19 0.54
23 12 0.34
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCTATCTTTTTCTTCTTAT
Found at i:89239 original size:21 final size:21
Alignment explanation
Indices: 89198--89239 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
89188 GTTCTTTATG
**
89198 TTTGGCTCTCTATTTTTGTTT
1 TTTGGCTCTCTATTTCGGTTT
89219 TTTGGCTCTCTATTTCGGTTT
1 TTTGGCTCTCTATTTCGGTTT
89240 GTCTCTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.17, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTGGCTCTCTATTTCGGTTT
Found at i:89523 original size:13 final size:12
Alignment explanation
Indices: 89504--89537 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
89494 GGAAAAGGGC
89504 TTGAAAAAATCT
1 TTGAAAAAATCT
89516 TTGAAAAAATCT
1 TTGAAAAAATCT
89528 TTGAAAAAAT
1 TTGAAAAAAT
89538 GCTTATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (12 bp):
TTGAAAAAATCT
Done.