Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003567.1 Hibiscus syriacus cultivar Beakdansim tig00007531_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: 95201
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:443 original size:59 final size:59
Alignment explanation
Indices: 319--544 Score: 278
Period size: 59 Copynumber: 3.8 Consensus size: 59
309 TTCCCATACG
* * ** *
319 GAAATTCATACACTTAGGATGAATT-CTTATCATTTTAGCACACATGGTGCCCCATCTA
1 GAAATTCATACACTTAGTATGAATTCCTTCTCATTTTAGCACACAAAGTGCCCTATCTA
* * * * *
377 GAAATTCATAGACTTAGTATGAATTCCTTCTCCTGTTAGCACACAAAGTGCCCTATATC
1 GAAATTCATACACTTAGTATGAATTCCTTCTCATTTTAGCACACAAAGTGCCCTATCTA
* * *
436 GAAATTCATACACTTAGTATGATTTCCTTAC-CATTTTAGCACACTAAGTGCCCTATCTG
1 GAAATTCATACACTTAGTATGAATTCCTT-CTCATTTTAGCACACAAAGTGCCCTATCTA
* *
495 GAAATTCATACACTTAGTATGATTTCCTTAC-CATTTTAGCACACTAAGTG
1 GAAATTCATACACTTAGTATGAATTCCTT-CTCATTTTAGCACACAAAGTG
545 TCCTTTGGTA
Statistics
Matches: 149, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
58 23 0.15
59 125 0.84
60 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTCCTTCTCATTTTAGCACACAAAGTGCCCTATCTA
Found at i:534 original size:118 final size:117
Alignment explanation
Indices: 319--544 Score: 312
Period size: 118 Copynumber: 1.9 Consensus size: 117
309 TTCCCATACG
* *
319 GAAATTCATACACTTAGGATGAATTCTTATCATTTTAGCACACATGGTGCCCCATCTAGAAATTC
1 GAAATTCATACACTTAGGATGAATTCTTACCATTTTAGCACACATAGTGCCCCATCTAGAAATTC
* *
384 ATAGACTTAGTATGAATTCCTTCTCCTGTTAGCACACAAAGTGCCCTATATC
66 ATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGCCCTATATC
* * * *
436 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC-TAAGTGCCCTATCTGGAAAT
1 GAAATTCATACACTTAGGATGAATT-CTTACCATTTTAGCACACAT-AGTGCCCCATCTAGAAAT
* * *
500 TCATACACTTAGTATGATTTCCTTAC-CATTTTAGCACACTAAGTG
64 TCATACACTTAGTATGAATTCCTT-CTCATGTTAGCACACAAAGTG
545 TCCTTTGGTA
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
117 24 0.25
118 70 0.74
119 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (117 bp):
GAAATTCATACACTTAGGATGAATTCTTACCATTTTAGCACACATAGTGCCCCATCTAGAAATTC
ATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGCCCTATATC
Found at i:3549 original size:3 final size:3
Alignment explanation
Indices: 3543--3645 Score: 181
Period size: 3 Copynumber: 34.3 Consensus size: 3
3533 CAATCTGTTG
*
3543 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3591 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3638 TATA TTA T
1 T-TA TTA T
3646 AACATTATGT
Statistics
Matches: 96, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 91 0.95
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3652 original size:15 final size:14
Alignment explanation
Indices: 3575--3653 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 14
3565 TATTATTATT
**
3575 ATTATTATTATTATT
1 ATTATTATTA-TAAC
**
3590 ATTATTATTATTATT
1 ATTATTATTA-TAAC
**
3605 ATTATTATTATTATT
1 ATTATTATTA-TAAC
* *
3620 ATTATTATTATTAT
1 ATTATTATTATAAC
3634 ATTATATATTATAAC
1 ATTAT-TATTATAAC
3649 ATTAT
1 ATTAT
3654 GTTATCGATA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
14 7 0.12
15 52 0.88
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATTATAAC
Found at i:4489 original size:46 final size:46
Alignment explanation
Indices: 4410--4537 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
4400 TTAAATTTTT
* *
4410 ATAAATTAAATTAAT-G-AATCATCGTTAGTGGTGTTCGACGTGTA
1 ATAAATTAAATTAATGGTACTCATCGTTAGTGGTGTTCGACGTATA
4454 ATAAATTAAATTAATGGTACTCATCGTTAGTGGTGTTCGACGTATA
1 ATAAATTAAATTAATGGTACTCATCGTTAGTGGTGTTCGACGTATA
*
4500 ATAAATTAAATTAATGATACTCATCGTTAGTGGTGTTC
1 ATAAATTAAATTAATGGTACTCATCGTTAGTGGTGTTC
4538 AATAGTACTC
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
44 15 0.19
45 1 0.01
46 63 0.80
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (46 bp):
ATAAATTAAATTAATGGTACTCATCGTTAGTGGTGTTCGACGTATA
Found at i:6187 original size:40 final size:39
Alignment explanation
Indices: 6121--6255 Score: 132
Period size: 39 Copynumber: 3.5 Consensus size: 39
6111 AGACGTCATG
* *
6121 CACTCCTAGAGT-TTTATATTTGGCCTGAAGACGTTGTG
1 CACTCCTAAAGTCTTTATATTTGGCCTGAAGACGTTGTA
* *
6159 CGACTCCTAAAGTCTTTATGTTTTGCCTGAAGACGTTGTA
1 C-ACTCCTAAAGTCTTTATATTTGGCCTGAAGACGTTGTA
* * * **
6199 CACTCCTAAAATC-TTATCTATTGGCCTGAAGTCGCCGTA
1 CACTCCTAAAGTCTTTATAT-TTGGCCTGAAGACGTTGTA
*
6238 CACTCTTAGAA-TCTTTAT
1 CACTCCTA-AAGTCTTTAT
6256 GTTTAACCTA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
38 6 0.07
39 45 0.56
40 30 0.37
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (39 bp):
CACTCCTAAAGTCTTTATATTTGGCCTGAAGACGTTGTA
Found at i:7695 original size:35 final size:35
Alignment explanation
Indices: 7650--7742 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
7640 TTACAGTGGT
* *
7650 TAAT-ATTTTGCTTAGGAATTTGCTTAGGTAGGGC
1 TAATAATTTTGCTTAGGAAATTGCTTAAGTAGGGC
* *
7684 TAATAATTTTGCTAAGGAAATTGCTTAAGTAGGGT
1 TAATAATTTTGCTTAGGAAATTGCTTAAGTAGGGC
*
7719 TAATAAATTTGC-TAGGAAATTGCT
1 TAATAATTTTGCTTAGGAAATTGCT
7743 CATCTCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 15 0.29
35 37 0.71
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.39
Consensus pattern (35 bp):
TAATAATTTTGCTTAGGAAATTGCTTAAGTAGGGC
Found at i:9798 original size:13 final size:13
Alignment explanation
Indices: 9780--9813 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
9770 AGCATTGTGA
*
9780 AAAGAAAATAATG
1 AAAGAAAATAACG
9793 AAAGAAAATAACG
1 AAAGAAAATAACG
9806 AAAGAAAA
1 AAAGAAAA
9814 GTGCAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAACG
Found at i:15975 original size:15 final size:15
Alignment explanation
Indices: 15957--15986 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15947 TAATCATTTT
15957 AAATTATAAAAATAA
1 AAATTATAAAAATAA
*
15972 AAATTATATAAATAA
1 AAATTATAAAAATAA
15987 GATTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTATAAAAATAA
Found at i:18159 original size:19 final size:19
Alignment explanation
Indices: 18135--18174 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18125 TTTATATCTC
*
18135 TCATTTCATCTTCTTCCTT
1 TCATTTCATCTACTTCCTT
*
18154 TCATTTCTTCTACTTCCTT
1 TCATTTCATCTACTTCCTT
18173 TC
1 TC
18175 TACACATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (19 bp):
TCATTTCATCTACTTCCTT
Found at i:22688 original size:21 final size:21
Alignment explanation
Indices: 22626--22726 Score: 71
Period size: 23 Copynumber: 4.6 Consensus size: 21
22616 ACACAACAGT
* *
22626 GTGTATCGATGCACATTCAAA
1 GTGTATCGATGCATATTCATA
* * *
22647 GAATGCATCGGTGCATCTTCATA
1 G--TGTATCGATGCATATTCATA
22670 GTGTATCGATGCATATTCA-A
1 GTGTATCGATGCATATTCATA
* *
22690 GGGATGCATCGGTGCACT-TTCATA
1 --G-TGTATCGATGCA-TATTCATA
22714 GTGTATCGATGCA
1 GTGTATCGATGCA
22727 CAGTGTACAA
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.02
21 26 0.43
22 2 0.03
23 30 0.49
24 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
GTGTATCGATGCATATTCATA
Found at i:22688 original size:44 final size:44
Alignment explanation
Indices: 22626--22728 Score: 163
Period size: 44 Copynumber: 2.3 Consensus size: 44
22616 ACACAACAGT
22626 GTGTATCGATGCACATTCAAAGAATGCATCGGTGCA-TCTTCATA
1 GTGTATCGATGCACATTCAAAGAATGCATCGGTGCACT-TTCATA
* * *
22670 GTGTATCGATGCATATTCAAGGGATGCATCGGTGCACTTTCATA
1 GTGTATCGATGCACATTCAAAGAATGCATCGGTGCACTTTCATA
22714 GTGTATCGATGCACA
1 GTGTATCGATGCACA
22729 GTGTACAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (44 bp):
GTGTATCGATGCACATTCAAAGAATGCATCGGTGCACTTTCATA
Found at i:28155 original size:64 final size:64
Alignment explanation
Indices: 28043--28197 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
28033 AGTTGACCTA
** * * * * *
28043 GTGCATCGGTACACTAATTA-CATTCGATGTTTCAAAAGAGCCAGGAGTGTATCGATGTATGGTC
1 GTGCATCGGTACAC-AAAAAGCATTCGATGTTTCAAAAGAACCAAGAGTGCATCGATGCATAGT-
28107 T
64 T
* * * *
28108 GTGCA-CGGTACATAAAATGCTTTCGATGTTTCAATAA-AATCAAGAGTGCATCGATGCATAGTT
1 GTGCATCGGTACACAAAAAGCATTCGATGTTTCAA-AAGAACCAAGAGTGCATCGATGCATAGTT
28171 GTGCATCGGTACACAAAAAGCATTCGA
1 GTGCATCGGTACACAAAAAGCATTCGA
28198 ATTAGGGTGT
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
63 8 0.11
64 58 0.79
65 7 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAAAGCATTCGATGTTTCAAAAGAACCAAGAGTGCATCGATGCATAGTT
Found at i:30229 original size:15 final size:15
Alignment explanation
Indices: 30211--30240 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30201 CACTATGATC
30211 ATCATTACCACCACT
1 ATCATTACCACCACT
*
30226 ATCATTATCACCACT
1 ATCATTACCACCACT
30241 TAACGTCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (15 bp):
ATCATTACCACCACT
Found at i:30235 original size:21 final size:21
Alignment explanation
Indices: 30191--30235 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30181 GTACATACTT
* *
30191 TCATTATCACCACTATGATCA
1 TCATTACCACCACTATCATCA
*
30212 TCATTACCACCACTATCATTA
1 TCATTACCACCACTATCATCA
30233 TCA
1 TCA
30236 CCACTTAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.33
Consensus pattern (21 bp):
TCATTACCACCACTATCATCA
Found at i:30238 original size:18 final size:18
Alignment explanation
Indices: 30191--30239 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
30181 GTACATACTT
*
30191 TCATTATCACCACTATGA
1 TCATTATCACCACCATGA
* *
30209 TCATCATTACCACCACT-A
1 TCATTATCACCACCA-TGA
30227 TCATTATCACCAC
1 TCATTATCACCAC
30240 TTAACGTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (18 bp):
TCATTATCACCACCATGA
Found at i:32050 original size:20 final size:20
Alignment explanation
Indices: 32025--32068 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
32015 CAAGTTGAGG
32025 ACACTTGAAGAAGGGTTAGA
1 ACACTTGAAGAAGGGTTAGA
32045 ACACTTGAAGAAGGGTTAGA
1 ACACTTGAAGAAGGGTTAGA
32065 ACAC
1 ACAC
32069 CTATCCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (20 bp):
ACACTTGAAGAAGGGTTAGA
Found at i:33175 original size:20 final size:20
Alignment explanation
Indices: 33147--33189 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
33137 TTTTCTTTTT
*
33147 AAAGAAAAAATG-GATTTTGA
1 AAAG-AAAAATGAAATTTTGA
*
33167 AAAGCAAAATGAAATTTTGA
1 AAAGAAAAATGAAATTTTGA
33187 AAA
1 AAA
33190 AGGATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.23
Consensus pattern (20 bp):
AAAGAAAAATGAAATTTTGA
Found at i:35091 original size:21 final size:21
Alignment explanation
Indices: 35052--35092 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35042 AGTAAAAGTT
* *
35052 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
35073 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
35093 TTTAACATTT
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:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:37268 original size:21 final size:22
Alignment explanation
Indices: 37214--37256 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
37204 ATTAATTAAC
*
37214 TTTATCAAATTTAAATTATAAG
1 TTTATCAAATTTAAAATATAAG
37236 TTTATCAAATTTAAAATATAA
1 TTTATCAAATTTAAAATATAA
37257 TGTTAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTATCAAATTTAAAATATAAG
Found at i:39700 original size:81 final size:80
Alignment explanation
Indices: 39503--39961 Score: 458
Period size: 81 Copynumber: 5.7 Consensus size: 80
39493 GGCGGTGGCC
* * * * * * *
39503 GACGCTCTGAAGATGATTCCTGTTGGTTCTGTCGATAAGCTAGCGCTGATGAACCTTCATTTTTG
1 GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCA-TTTTG
* *
39568 GAAGC--CGTCTTGTT
65 GAATCATGGTCTTGTT
* ** * *
39582 GATGCTCCAAAGAAGATTG-TCGTTTGCTCTCTTGAGAAGCTGGTGCTGATGAACCTTCGATTTT
1 GACGCTCTGAAGAAGATTGCT-GTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTC-ATTTT
* *
39646 GGAATCATTGTCTTGCT
64 GGAATCATGGTCTTGTT
* *
39663 GACGCTCTTAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATCTTTG
1 GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCAT-TTTG
*
39728 GAATCCAT-GTCTTGCT
65 GAAT-CATGGTCTTGTT
* * * * * *
39744 GACGTTCTGAGGACGATTGCTGTTGGTTCTCTTGAGAATCTGGTGCTAATGAATCTTCATTTTTG
1 GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCA-TTTTG
* *
39809 GAATCCTGGTCATGTT
65 GAATCATGGTCTTGTT
* * * * * * *
39825 GACACTCCGAATACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAATCTTCGTTTTTG
1 GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTC-ATTTTG
*
39890 GAATCCTGGTCTTGTT
65 GAATCATGGTCTTGTT
* * * * * *
39906 GACACTCTGAAGAAGATTGATGTTCGTTCTGTTGAGAAGCTGGGGCCGATGAACCT
1 GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCT
39962 GTCTTGCTGA
Statistics
Matches: 320, Mismatches: 50, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.00
79 53 0.17
80 5 0.02
81 256 0.80
82 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (80 bp):
GACGCTCTGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCATTTTGG
AATCATGGTCTTGTT
Found at i:39845 original size:162 final size:159
Alignment explanation
Indices: 39511--40293 Score: 690
Period size: 162 Copynumber: 4.9 Consensus size: 159
39501 CCGACGCTCT
* * * * * * *
39511 GAAGATGATTCCTGTTGGTTCTGTCGATAAGCTAGCGCTGATGAACCTTCATTTTTGGAAGCC-G
1 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCCTG
* ** * * *
39575 TCTTGTTGATGCTCCAAAGAAGATTGTCGTTTGCTCTCTTGAGAAGCTGGTGCTGATGAACCTTC
66 TCTTGCTGACACTCCGAAGAAGATTGT-GTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTC
* * *
39640 GATTTTGGAATCATTGTCTTGCTGACGCTCT
130 GATTTTGGAATC-CTGTCTTGCTGACACTCA
* * *
39671 TAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATCTTTGGAATCCAT
1 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCC-T
** * * * * * *
39736 GTCTTGCTGACGTTCTGAGGACGATTGCTGTTGGTTCTCTTGAGAATCTGGTGCTAATGAATCTT
65 GTCTTGCTGACACTCCGAAGAAGATTG-TGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTT
* * *
39801 C-ATTTTTGGAATCCTGGTCATGTTGACACTCC
129 CGA-TTTTGGAATCCT-GTCTTGCTGACACTCA
* * * * *
39833 GAATACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAATCTTCGTTTTTGGAATCCTG
1 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCCT-
* * * *
39898 GTCTTGTTGACACTCTGAAGAAGATTGATGTTCGTTCTGTTGAGAAGCT-G-G--G--G---C--
65 GTCTTGCTGACACTCCGAAGAAGATTG-TGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTT
*
39952 CGA---T-GAA-CCTGTCTTGCTGACATTCA
129 CGATTTTGGAATCCTGTCTTGCTGACACTCA
* * * ** *
39978 GAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCTTTGTTTATGGAATCCTT
1 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCC-T
* * *
40043 GTCATGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAGCCT-GCGCTGATGAACCT
65 GTCTTGCTGACACTCCGAAGAAGATTG-TGTTGGTTCTCTTGAGAAG-CTGGTGCTGATGAACCT
* * **
40107 TC-ATCTCTGGAATCCTCATCTTGCTGACGTTCA
128 TCGAT-TTTGGAATCCT-GTCTTGCTGACACTCA
* *
40140 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCATATTTGGAATCCTC
1 GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCCT-
* * * * * * *
40205 GTCTTGATGACACTCCGAAGAAGATTGTTGTCGATTATGTTGAGAA-TTGGGAGCTGATGAACCT
65 GTCTTGCTGACACTCCGAAGAAGATTG-TGTTGGTTCTCTTGAGAAGCT-GGTGCTGATGAACCT
**
40269 TCTTTTTTGGAATCCTTGTCTTGCT
128 TCGATTTTGGAATCC-TGTCTTGCT
40294 AACCCCCCAA
Statistics
Matches: 506, Mismatches: 86, Indels: 60
0.78 0.13 0.09
Matches are distributed among these distances:
145 106 0.21
146 7 0.01
147 4 0.01
148 1 0.00
149 1 0.00
151 2 0.00
152 1 0.00
153 1 0.00
154 1 0.00
155 1 0.00
156 2 0.00
159 1 0.00
160 59 0.12
161 8 0.02
162 308 0.61
163 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (159 bp):
GAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCCTG
TCTTGCTGACACTCCGAAGAAGATTGTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCG
ATTTTGGAATCCTGTCTTGCTGACACTCA
Found at i:40023 original size:64 final size:64
Alignment explanation
Indices: 39898--40025 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 64
39888 TGGAATCCTG
* * * * *
39898 GTCTTGTTGACACTCTGAAGAAGATTGATGTTCGTTCTGTTGAGAAGCTGGGGCCGATGAACCT
1 GTCTTGCTGACACTCAGAAGAAGATTGATGTTCGTTCTCTTGAGAAACTGGCGCCGATGAACCT
* * * * *
39962 GTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCT
1 GTCTTGCTGACACTCAGAAGAAGATTGATGTTCGTTCTCTTGAGAAACTGGCGCCGATGAACCT
40026 TTGTTTATGG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (64 bp):
GTCTTGCTGACACTCAGAAGAAGATTGATGTTCGTTCTCTTGAGAAACTGGCGCCGATGAACCT
Found at i:40102 original size:145 final size:145
Alignment explanation
Indices: 39837--40106 Score: 362
Period size: 145 Copynumber: 1.9 Consensus size: 145
39827 CACTCCGAAT
* * * * * *
39837 ACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAATCTTCGTTTTTGGAATCCTGGTCT
1 ACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCTTCGTTTATGGAATCCTGGTCA
* * * *
39902 TGTTGACACTCTGAAGAAGATTGATGTTCGTTCTGTTGAGAAGCTGGGGCCGATGAACCTGTCTT
66 TGCTGACACTCCGAAGAAGATTGATGTTCGTTCTCTTGAGAAGCTGGCGCCGATGAACCTGTCTT
39967 GCTGACATTCAGAAG
131 GCTGACATTCAGAAG
** * *
39982 ACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCTTTGTTTATGGAATCCTTGTCA
1 ACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCTTCGTTTATGGAATCCTGGTCA
* * * *
40047 TGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAGCCT-GCGCTGATGAACCT
66 TGCTGACACTCCGAAGAAGATTGATGTTCGTTCTCTTGAGAAG-CTGGCGCCGATGAACCT
40107 TCATCTCTGG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
145 104 0.98
146 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (145 bp):
ACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCTTCGTTTATGGAATCCTGGTCA
TGCTGACACTCCGAAGAAGATTGATGTTCGTTCTCTTGAGAAGCTGGCGCCGATGAACCTGTCTT
GCTGACATTCAGAAG
Found at i:40104 original size:81 final size:80
Alignment explanation
Indices: 39961--40364 Score: 352
Period size: 81 Copynumber: 5.0 Consensus size: 80
39951 CCGATGAACC
* * * * *
39961 TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCT
1 TGTCTTGCTGACACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCT
**
40026 TTGTTTATGGAATCCT
66 TCATTT-TGGAATCCT
* * *
40042 TGTCATGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAGCCT-GCGCTGATGAACC
1 TGTCTTGCTGACACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAG-CTGGCGCTGATGAACC
*
40106 TTCATCTCTGGAATCCT
65 TTCAT-TTTGGAATCCT
** ** * * *
40123 CATCTTGCTGACGTTCAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCT
1 TGTCTTGCTGACACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCT
40188 TCATATTTGGAATCCT
66 TCAT-TTTGGAATCCT
* * * * * * * * *
40204 CGTCTTGATGACACTCCGAAGAAGATTGTTGTCGATTATGTTGAGAA-TTGGGAGCTGATGAACC
1 TGTCTTGCTGACACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAGCT-GGCGCTGATGAACC
*
40268 TTCTTTTTTGGAATCCT
65 TTC-ATTTTGGAATCCT
* * * * * * * * *
40285 TGTCTTGCTAACCCCCCA-AAGAAGATTGATGTAGGTTATGTTGAGAAGTTGGC-C--CTGAACC
1 TGTCTTGCTGA-CACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACC
*
40346 TTCTTTCTTGGAATCCT
65 TTCATT-TTGGAATCCT
40363 TG
1 TG
40365 GCTCGTTGGG
Statistics
Matches: 267, Mismatches: 48, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
77 3 0.01
78 21 0.08
80 4 0.01
81 230 0.86
82 9 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (80 bp):
TGTCTTGCTGACACTCAGAAGAAGATTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCT
TCATTTTGGAATCCT
Found at i:40169 original size:226 final size:226
Alignment explanation
Indices: 39735--40187 Score: 566
Period size: 226 Copynumber: 2.0 Consensus size: 226
39725 TTGGAATCCA
* * * * * * *
39735 TGTCTTGCTGACGTTCTGAGGACGATTGCTGTTGGTTCTCTTGAGAATCTGGTGCTAATGAATCT
1 TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCT
* * * *
39800 TCATTTTTGGAATCCTGGTCATGTTGACACTCCGAATACGATTGCTGTTGGTTCTCTTGAGAAGC
66 TCATTTATGGAATCCTGGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGC
* * * * * ** * *
39865 TGGTGCTAATGAATCTTCGTTTTTGGAATCCTGGTCTTGTTGACACTCTGAAGAAGATTGATGTT
131 TGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCTTGCTGACACTCAGAAGAAGATTGATGTT
*
39930 CGTTCTGTTGAGAAGCTGGGGCCGATGAACC
196 CGTTCTCTTGAGAAGCTGGGGCCGATGAACC
**
39961 TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCT
1 TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCT
** * * *
40026 TTGTTTATGGAATCCTTGTCATGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAGC
66 TCATTTATGGAATCCTGGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAAG-
* ** * *
40091 CT-GCGCTGATGAACCTTCATCTCTGGAATCCTCATCTTGCTGACGTTCAGAAGACGATTGCTGT
130 CTGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCTTGCTGACACTCAGAAGAAGATTGATGT
* * *
40155 TGGTTCTCTTGAGAAGCTGGTGCTGATGAACC
195 TCGTTCTCTTGAGAAGCTGGGGCCGATGAACC
40187 T
1 T
40188 TCATATTTGG
Statistics
Matches: 190, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
226 188 0.99
227 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (226 bp):
TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTAATGAACCT
TCATTTATGGAATCCTGGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAAGC
TGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCTTGCTGACACTCAGAAGAAGATTGATGTT
CGTTCTCTTGAGAAGCTGGGGCCGATGAACC
Found at i:40218 original size:307 final size:307
Alignment explanation
Indices: 39654--40272 Score: 771
Period size: 307 Copynumber: 2.0 Consensus size: 307
39644 TTGGAATCAT
* ** * *
39654 TGTCTTGCTGACGCTCTTAAGAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCT
1 TGTCTTGCTGACACTCAGAAGAAGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGATGAACCT
* ** * * * *
39719 TCATCTTTGGAATCCATGTCTTGCTGACGTTCTGAGGACGATTGCTGTTGGTTCTCTTGAGAATC
66 TCATCTTTGGAATCCATGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAACC
* * * * ** * * *
39784 TGGTGCTAATGAATCTTCATTTTTGGAATCCTGGTCATGTTGACACTCCGAATACGATTGCTGTT
131 TGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCATGCTGACACTCAGAAGACGATTGCTGTT
* * * * * *
39849 GGTTCTCTTGAGAAGCTGGTGCTAATGAATCTTCGTTTTTGGAATCCTGGTCTTGTTGACACTCT
196 GGTTCTCTTGAGAAGCTGGTGCTAATGAACCTTCATATTTGGAATCCTCGTCTTGATGACACTCC
*
39914 GAAGAAGATTGATGTTCG-TTCTGTTGAGAAGCTGGG-GCCGATGAACC
261 GAAGAAGATTGATG-TCGATTATGTTGAGAA-CTGGGAGCCGATGAACC
* * *
39961 TGTCTTGCTGACATTCAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCT
1 TGTCTTGCTGACACTCAGAAGAAGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGATGAACCT
** * * *
40026 TTGT-TTATGGAATCCTTGTCATGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAG
66 TCATCTT-TGGAATCCATGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAA-
* * **
40090 CCT-GCGCTGATGAACCTTCATCTCTGGAATCCTCATCTTGCTGACGTTCAGAAGACGATTGCTG
129 CCTGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCATGCTGACACTCAGAAGACGATTGCTG
*
40154 TTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCATATTTGGAATCCTCGTCTTGATGACACT
194 TTGGTTCTCTTGAGAAGCTGGTGCTAATGAACCTTCATATTTGGAATCCTCGTCTTGATGACACT
* * *
40219 CCGAAGAAGATTGTTGTCGATTATGTTGAGAATTGGGAGCTGATGAACC
259 CCGAAGAAGATTGATGTCGATTATGTTGAGAACTGGGAGCCGATGAACC
40268 T-TCTT
1 TGTCTT
40273 TTTTGGAATC
Statistics
Matches: 264, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
306 13 0.05
307 249 0.94
308 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (307 bp):
TGTCTTGCTGACACTCAGAAGAAGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGATGAACCT
TCATCTTTGGAATCCATGTCATGCTGACACTCCGAAGAAGATTGCTGTTGGTTCTCTTGAGAACC
TGGCGCTAATGAACCTTCATCTCTGGAATCCTCATCATGCTGACACTCAGAAGACGATTGCTGTT
GGTTCTCTTGAGAAGCTGGTGCTAATGAACCTTCATATTTGGAATCCTCGTCTTGATGACACTCC
GAAGAAGATTGATGTCGATTATGTTGAGAACTGGGAGCCGATGAACC
Found at i:40329 original size:388 final size:388
Alignment explanation
Indices: 39609--40332 Score: 988
Period size: 388 Copynumber: 1.9 Consensus size: 388
39599 TGTCGTTTGC
* * * * **
39609 TCTCTTGAGAAGCTGGTGCTGATGAACCTTCGATTTTGGAATCATTGTCTTGCTGACGCTCTTAA
1 TCTCTTGAGAAACTGGCGCTGATGAACCTTCGATTTTGGAATCATTGTCATGCTGACACTCCGAA
* *
39674 GAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATCTTTGGAATCCATGTC
66 GAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATCTCTGGAATCCATATC
* * * *
39739 TTGCTGACGTTCTGAGGACGATTGCTGTTGGTTCTCTTGAGAATCTGGTGCTAATGAATCTTCAT
131 TTGCTGACGTTCAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAACCTTCAT
* * * * * * * * *
39804 TTTTGGAATCCTGGTCATGTTGACACTCCGAATACGATTGCTGTTGGTTCTCTTGAGAAGCTGGT
196 ATTTGGAATCCTCGTCATGATGACACTCCGAAGAAGATTGCTGTCGATTATCTTGAGAAGCTGGA
* * * * ** *
39869 GCTAATGAATCTTCGTTTTTGGAATCCTGGTCTTGTTGACACTCTGAAGAAGATTGATGTTCGTT
261 GCTAATGAACCTTCGTTTTTGGAATCCTGGTCTTGCTAACACCCCAAAGAAGATTGATGTACGTT
*
39934 CTGTTGAGAAGCTGGGGCCGATGAACCTGTCTTGCTGACATTCAGAAGACGATTGATGTTGGT
326 ATGTTGAGAAGCTGGGGCCGATGAACCTGTCTTGCTGACATTCAGAAGACGATTGATGTTGGT
* * *
39997 TCTCTTGAGAAACTGGCGCTGGTGAACCTTTG-TTTATGGAATCCTTGTCATGCTGACACTCCGA
1 TCTCTTGAGAAACTGGCGCTGATGAACCTTCGATTT-TGGAATCATTGTCATGCTGACACTCCGA
* *
40061 AGAAGGTTGTTGTTGGTTCTCTTGAGAAGCCT-GCGCTGATGAACCTTCATCTCTGGAATCC-TC
65 AGAAGATTGCTGTTGGTTCTCTTGAGAAG-CTGGCGCTGATGAACCTTCATCTCTGGAATCCAT-
*
40124 ATCTTGCTGACGTTCAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTT
128 ATCTTGCTGACGTTCAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAACCTT
* * * *
40189 CATATTTGGAATCCTCGTCTTGATGACACTCCGAAGAAGATTGTTGTCGATTATGTTGAGAA-TT
193 CATATTTGGAATCCTCGTCATGATGACACTCCGAAGAAGATTGCTGTCGATTATCTTGAGAAGCT
* * * *
40253 GGGAGCTGATGAACCTTCTTTTTTGGAATCCTTGTCTTGCTAACCCCCCAAAGAAGATTGATGTA
258 -GGAGCTAATGAACCTTCGTTTTTGGAATCCTGGTCTTGCTAACACCCCAAAGAAGATTGATGTA
*
40318 GGTTATGTTGAGAAG
322 CGTTATGTTGAGAAG
40333 TTGGCCCTGA
Statistics
Matches: 288, Mismatches: 44, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
387 5 0.02
388 281 0.98
389 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (388 bp):
TCTCTTGAGAAACTGGCGCTGATGAACCTTCGATTTTGGAATCATTGTCATGCTGACACTCCGAA
GAAGATTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATCTCTGGAATCCATATC
TTGCTGACGTTCAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTAATGAACCTTCAT
ATTTGGAATCCTCGTCATGATGACACTCCGAAGAAGATTGCTGTCGATTATCTTGAGAAGCTGGA
GCTAATGAACCTTCGTTTTTGGAATCCTGGTCTTGCTAACACCCCAAAGAAGATTGATGTACGTT
ATGTTGAGAAGCTGGGGCCGATGAACCTGTCTTGCTGACATTCAGAAGACGATTGATGTTGGT
Found at i:40331 original size:162 final size:162
Alignment explanation
Indices: 39976--40342 Score: 396
Period size: 162 Copynumber: 2.3 Consensus size: 162
39966 TGCTGACATT
* * **
39976 CAGAAGACGATTGATGTTGGTTCTCTTGAGAAACTGGCGCTGGTGAACCTTTGTTTATGGAATCC
1 CAGAAGACGATTGATGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTATGGAATCC
* * * * * * * *
40041 TTGTCATGCTGACACTCCGAAGAAGGTTGTTGTTGGTTCTCTTGAGAAGCCTGCGCTGATGAACC
66 TCGTCATGATGACACTCCGAAGAAGATTGTTGTCGATTATCTTGAGAAGCCGGAGCTGATGAACC
* ***
40106 TTCATCTCTGGAATCCTCATCTTGCTGACGTT
131 TTCATCTCTGGAATCCTCATCTTGCTAACCCC
* *
40138 CAGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGTGCTGATGAACCTTCATATT-TGGAATC
1 CAGAAGACGATTGATGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCAT-TTATGGAATC
* * ***
40202 CTCGTCTTGATGACACTCCGAAGAAGATTGTTGTCGATTATGTTGAGAATTGGGAGCTGATGAAC
65 CTCGTCATGATGACACTCCGAAGAAGATTGTTGTCGATTATCTTGAGAAGCCGGAGCTGATGAAC
* * * **
40267 CTTCTTTTTTGGAATCCTTGTCTTGCTAACCCCC
130 CTTCATCTCTGGAATCCTCATCTTGCTAA-CCCC
* * * * * *
40301 CA-AAGAAGATTGATGTAGGTTATGTTGAGAAGTTGGCCCTGA
1 CAGAAGACGATTGATGTTGGTTCTCTTGAGAAGCTGGCGCTGA
40343 ACCTTCTTTC
Statistics
Matches: 167, Mismatches: 36, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
162 162 0.97
163 5 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (162 bp):
CAGAAGACGATTGATGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTATGGAATCC
TCGTCATGATGACACTCCGAAGAAGATTGTTGTCGATTATCTTGAGAAGCCGGAGCTGATGAACC
TTCATCTCTGGAATCCTCATCTTGCTAACCCC
Found at i:46324 original size:20 final size:21
Alignment explanation
Indices: 46291--46329 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
46281 TTATAAAACT
* *
46291 CTAAAAATATTATTTATTTTA
1 CTAAAAATAATATTAATTTTA
46312 CTAAAAA-AATATTAATTT
1 CTAAAAATAATATTAATTT
46330 CGCTAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
CTAAAAATAATATTAATTTTA
Found at i:48331 original size:12 final size:10
Alignment explanation
Indices: 48291--48329 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
48281 TTATCACACC
48291 AAATTCTCTT
1 AAATTCTCTT
48301 AAATTCT-TT
1 AAATTCTCTT
48310 AAATTTCTCTT
1 AAA-TTCTCTT
*
48321 AAATACTCT
1 AAATTCTCT
48330 CTCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 16 0.62
11 5 0.19
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (10 bp):
AAATTCTCTT
Found at i:48409 original size:17 final size:18
Alignment explanation
Indices: 48372--48412 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48362 CTATTATGTA
*
48372 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
48390 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
48407 TTTACT
1 TTTACT
48413 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:48668 original size:111 final size:111
Alignment explanation
Indices: 48474--48806 Score: 596
Period size: 111 Copynumber: 3.0 Consensus size: 111
48464 TGGAAATCAT
*
48474 ATATCTCTACACTTTGCTGATAC-AGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGA-TAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
48538 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
48585 ATATCTCGACACTTTGCTGATACGATAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
48650 TAATTGGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
48696 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
48761 TAATTAGTTGATTTATTTAATACATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
48807 TTTTTGTAAT
Statistics
Matches: 213, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
111 212 1.00
112 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:53584 original size:24 final size:23
Alignment explanation
Indices: 53552--53639 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 23
53542 ATTTCCGACT
*
53552 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATAC-TGATC
*
53576 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGA-TACTGATC
* *
53600 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATA-CTGATC
*
53624 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
53640 TTATGATATC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.95
25 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATC
Found at i:53590 original size:12 final size:12
Alignment explanation
Indices: 53552--53634 Score: 80
Period size: 12 Copynumber: 6.9 Consensus size: 12
53542 ATTTCCGACT
53552 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
53564 TG-ATACATGACC
1 TGAATTC-TGTTC
53576 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
53588 TGATTTCTGATC
1 TGAATTCTGTTC
*
53600 TGGATTCTGTTC
1 TGAATTCTGTTC
53612 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
53624 TGAATTCTGTT
1 TGAATTCTGTT
53635 TTGATTTATG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
11 5 0.09
12 46 0.82
13 5 0.09
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:53607 original size:48 final size:48
Alignment explanation
Indices: 53555--53646 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
53545 TCCGACTTGA
*
53555 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATATC-TGACCTGAATTCTGTTCTGATTTATGATCTGG
** *
53603 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATTTATGAT
1 ATTCTGTTCTGATATCTGACCTGAATTCTGTTCTGATTTATGAT
53647 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTCTGTTCTGATTTATGATCTGG
Found at i:54761 original size:3 final size:3
Alignment explanation
Indices: 54753--54815 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
54743 ACCTGCTCAG
*
54753 GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC GAC -ACC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA-C GAC GAC GAC
54798 GAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC
54816 AGCAAAGAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 54 0.96
4 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.32, T:0.02
Consensus pattern (3 bp):
GAC
Found at i:55066 original size:35 final size:33
Alignment explanation
Indices: 55027--55111 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
55017 ATATTTCAGT
55027 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
55062 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
55097 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
55112 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:64695 original size:17 final size:17
Alignment explanation
Indices: 64673--64726 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
64663 AATGTTAATA
64673 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
64690 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
64707 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
64724 TTT
1 TTT
64727 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:66299 original size:21 final size:21
Alignment explanation
Indices: 66256--66300 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
66246 GCAGGGGTAC
* *
66256 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
66277 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
66298 ATG
1 ATG
66301 TCATCTCCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:66333 original size:21 final size:21
Alignment explanation
Indices: 66307--66379 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
66297 TATGTCATCT
*
66307 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
66328 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
66349 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
66370 CCGCAGGGTT
1 CCGCAGGGTT
66380 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:66961 original size:33 final size:34
Alignment explanation
Indices: 66902--66998 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
66892 AAATGTTTTT
*
66902 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
66936 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
66969 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
66999 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:67005 original size:34 final size:33
Alignment explanation
Indices: 66900--67005 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
66890 ATAAATGTTT
*
66900 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
66934 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
66966 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
67001 TTAAA
1 TTAAA
67006 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:67627 original size:128 final size:128
Alignment explanation
Indices: 67399--67899 Score: 993
Period size: 128 Copynumber: 3.9 Consensus size: 128
67389 TTACCTTATT
67399 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
67464 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
67527 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
67592 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTTAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
67655 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
67720 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
67783 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
67848 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
67900 ACTCCGATTA
Statistics
Matches: 371, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 371 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:67983 original size:8 final size:8
Alignment explanation
Indices: 67970--68010 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
67960 TCACAATCTT
67970 TCAAATTC
1 TCAAATTC
67978 TCAAATTC
1 TCAAATTC
* *
67986 CCAAACTC
1 TCAAATTC
67994 T-AAATTC
1 TCAAATTC
68001 TCAAATTC
1 TCAAATTC
68009 TC
1 TC
68011 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:74637 original size:13 final size:13
Alignment explanation
Indices: 74619--74647 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
74609 TTATGTCATT
74619 TTTTATTTTTTTA
1 TTTTATTTTTTTA
74632 TTTTATTTTTTTA
1 TTTTATTTTTTTA
74645 TTT
1 TTT
74648 CAAAATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:74676 original size:6 final size:6
Alignment explanation
Indices: 74665--74811 Score: 65
Period size: 6 Copynumber: 23.3 Consensus size: 6
74655 TAACCCTTTC
* * * *
74665 TTATTT TTATTT GT-TTT ATA-TT TTATTT CGTTTTTT TTATATAT ATATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT --TTATTT TTAT-T-T TTATTT
*
74715 TTATTCT CTTATTT TTATTAT TT-TTT TTATTCTT TTATAT TTATTTT
1 TTATT-T -TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTA-TTT
*
74762 TTCAATTTT TTATTT TT-TATT TTATTA TTATTT TTA--- TTATTT TTATTT
1 TT--A-TTT TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATTT
74810 TT
1 TT
74812 TAATTATTGG
Statistics
Matches: 110, Mismatches: 11, Indels: 40
0.68 0.07 0.25
Matches are distributed among these distances:
3 3 0.03
5 12 0.11
6 54 0.49
7 15 0.14
8 19 0.17
9 7 0.06
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:74688 original size:17 final size:17
Alignment explanation
Indices: 74665--74698 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
74655 TAACCCTTTC
74665 TTAT-TTTTATTT-GTT
1 TTATATTTTATTTCGTT
74680 TTATATTTTATTTCGTT
1 TTATATTTTATTTCGTT
74697 TT
1 TT
74699 TTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTATATTTTATTTCGTT
Found at i:74690 original size:16 final size:16
Alignment explanation
Indices: 74665--74702 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
74655 TAACCCTTTC
74665 TTATTTTTATTT-GTT
1 TTATTTTTATTTCGTT
74680 TTATATTTTATTTCGTT
1 TTAT-TTTTATTTCGTT
74697 TT-TTTT
1 TTATTTT
74703 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 9 0.43
17 5 0.24
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (16 bp):
TTATTTTTATTTCGTT
Found at i:74711 original size:27 final size:26
Alignment explanation
Indices: 74681--74759 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
74671 TTATTTGTTT
*
74681 TATATTTTATT-TCGTTTTTTTTATATA
1 TATATTTTATTCTC-TTATTTTTAT-TA
74708 TATATTTTTATTCTCTTATTTTTATTA
1 TATA-TTTTATTCTCTTATTTTTATTA
* * * *
74735 TTTTTTTTATTCTTTTATATTTATT
1 TATATTTTATTCTCTTATTTTTATT
74760 TTTTCAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 19 0.42
27 8 0.18
28 16 0.36
29 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (26 bp):
TATATTTTATTCTCTTATTTTTATTA
Found at i:74727 original size:14 final size:13
Alignment explanation
Indices: 74665--74799 Score: 71
Period size: 14 Copynumber: 9.8 Consensus size: 13
74655 TAACCCTTTC
*
74665 TTATTTTTATTTGTT
1 TTATTTTTA-TT-CT
74680 TTATATTTTATTTCGT
1 TTAT-TTTTA-TTC-T
*
74696 TT-TTTTTATATAT
1 TTATTTTTAT-TCT
*
74709 ATATTTTTATTCT
1 TTATTTTTATTCT
*
74722 CTTATTTTTATTAT
1 -TTATTTTTATTCT
74736 TT-TTTTTATTCTT
1 TTATTTTTATTC-T
* *
74749 TTATATTTATTTT
1 TTATTTTTATTCT
*
74762 TTCAATTTTTTATTTT
1 TT--A-TTTTTATTCT
*
74778 TTA-TTTTATT-A
1 TTATTTTTATTCT
74789 TTATTTTTATT
1 TTATTTTTATT
74800 ATTTTTATTT
Statistics
Matches: 98, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
11 3 0.03
12 22 0.22
13 13 0.13
14 32 0.33
15 6 0.06
16 22 0.22
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (13 bp):
TTATTTTTATTCT
Found at i:74737 original size:9 final size:9
Alignment explanation
Indices: 74723--74819 Score: 82
Period size: 9 Copynumber: 11.6 Consensus size: 9
74713 TTTTATTCTC
74723 TTATTTTTA
1 TTATTTTTA
*
74732 TTATTTTTT
1 TTATTTTTA
*
74741 TTATTCTT-
1 TTATTTTTA
*
74749 TTATATTTA
1 TTATTTTTA
*
74758 TT-TTTTCA
1 TTATTTTTA
*
74766 AT-TTTTTA
1 TTATTTTTA
74774 -T-TTTTTA
1 TTATTTTTA
*
74781 TT-TTATTA
1 TTATTTTTA
74789 TTATTTTTA
1 TTATTTTTA
74798 TTATTTTTA
1 TTATTTTTA
*
74807 TT-TTTTAA
1 TTATTTTTA
74815 TTATT
1 TTATT
74820 GGTTTTGATT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
7 7 0.10
8 31 0.42
9 35 0.48
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:74752 original size:34 final size:31
Alignment explanation
Indices: 74712--74863 Score: 105
Period size: 33 Copynumber: 4.7 Consensus size: 31
74702 TATATATATA
*
74712 TTTTTATTCTCTTATTTTTATTATTTTTTTTAT
1 TTTTTATTAT-TTATTTTT-TTATTTTTTTTAT
* *
74745 TCTTTTA-TATTTATTTTTTCA-ATTTTTTAT
1 T-TTTTATTATTTATTTTTTTATTTTTTTTAT
* *
74775 TTTTTATTTTATTATTATTTTTATTATTTTTAT
1 TTTTTATTAT-TTATT-TTTTTATTTTTTTTAT
** *
74808 TTTTTAATTATTGGTTTTGATTTA-TTATTTTAT
1 TTTTT-ATTATTTATTTT--TTTATTTTTTTTAT
*
74841 TATTCTATTATTT-TGTTTTTTAT
1 T-TTTTATTATTTAT-TTTTTTAT
74864 CTAATATTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
29 5 0.05
30 11 0.12
31 11 0.12
32 16 0.17
33 35 0.37
34 16 0.17
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTTTATTATTTATTTTTTTATTTTTTTTAT
Found at i:74805 original size:42 final size:41
Alignment explanation
Indices: 74666--74854 Score: 115
Period size: 40 Copynumber: 4.5 Consensus size: 41
74656 AACCCTTTCT
* *
74666 TATTTTTATT-TGTTTTATATTTT-ATTTCGTTTTTTTTATATAT
1 TATTTTTATTAT-TTTTATTTTTTAATTT--TTTATTTTAT-TAT
* * * *
74709 ATATTTTTATT-CTCTTATTTTTATTATTTTTT-TTATTCTT-T
1 -TATTTTTATTATTTTTATTTTT-TAATTTTTTATT-TTATTAT
* *
74750 TATATTTATT-TTTTCAATTTTTT-ATTTTTTATTTTATTAT
1 TATTTTTATTATTTT-TATTTTTTAATTTTTTATTTTATTAT
* **
74790 TATTTTTATTATTTTTATTTTTTAATTATTGGTTTTGATTTAT
1 TATTTTTATTATTTTTATTTTTTAATTTTTTATTTT-A-TTAT
74833 TA-TTTTATTATTCTATTATTTT
1 TATTTTTATTATT-T-TTATTTT
74855 GTTTTTTATC
Statistics
Matches: 119, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
39 11 0.09
40 31 0.26
41 20 0.17
42 14 0.12
43 21 0.18
44 18 0.15
45 4 0.03
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (41 bp):
TATTTTTATTATTTTTATTTTTTAATTTTTTATTTTATTAT
Found at i:74836 original size:54 final size:48
Alignment explanation
Indices: 74728--74844 Score: 130
Period size: 54 Copynumber: 2.4 Consensus size: 48
74718 TTCTCTTATT
*
74728 TTTATTATTTT-TT-TTATTCTTTTATATTTATTTTTTCAATTTTTTA
1 TTTATTATTTTATTATTATTCTTTTATATTTATTTTTTAAATTTTTTA
* * *
74774 TTTTTTATTTTATTATTATTTTTATTATTTTTATTTTTTAATTATTGGTTTTGA
1 TTTATTATTTTATTATTATTCTT-TTATATTTATTTTTTAA--ATT--TTTT-A
74828 TTTATTATTTTATTATT
1 TTTATTATTTTATTATT
74845 CTATTATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
46 10 0.17
47 2 0.03
48 7 0.12
49 15 0.26
51 3 0.05
53 4 0.07
54 17 0.29
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.75
Consensus pattern (48 bp):
TTTATTATTTTATTATTATTCTTTTATATTTATTTTTTAAATTTTTTA
Found at i:79893 original size:84 final size:84
Alignment explanation
Indices: 79745--80568 Score: 879
Period size: 84 Copynumber: 9.8 Consensus size: 84
79735 GCTATCTGCC
* * * * * * * * ** *
79745 AAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAGCTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAACATAACTCAAGGCT
* *
79810 AGAAGGGTTATTTGTGACCA
65 AGAAGGGTTATCTGCGACCA
*
79830 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCATCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
* * *
79895 TAAGGGTTATCTGCCAAC-
66 GAAGGGTTATCTGCGACCA
* * * * * * *
79913 AAAGACCTTCGATTTTGACTACGCTCAGCTCTAAGGCAAATCATTTGCAAAATATCTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
* * *
79978 GAAGGGTTATTTGCCATCA
66 GAAGGGTTATCTGCGACCA
* * * *
79997 AAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
* **
80062 GAACGGTTATCTATGACCA
66 GAAGGGTTATCTGCGACCA
* * * * *
80081 AAAAACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATAATTTGCAACATAACTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
* * *
80146 GAAGGGTTATTTGCCAACA
66 GAAGGGTTATCTGCGACCA
* * * * * *
80165 AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATTATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
* *
80230 GAAAGGTTATCTGCCAACC-
66 GAAGGGTTATCTG-CGACCA
* * * * *
80249 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
*
80314 GAAGGGCTATCT--G-CC-
66 GAAGGGTTATCTGCGACCA
* * * * * * *
80329 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAACATAACTCAAGGCT
*
80394 AGAAGGGTTATCTGTGACCA
65 AGAAGGGTTATCTGCGACCA
* * * * * *
80414 AAAGTCTTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAACATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
*
80479 GAAGGGTTATCTGCCAACC-
66 GAAGGGTTATCTG-CGACCA
* * * * *
80498 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
80563 GAAGGG
66 GAAGGG
80569 CTATATATCA
Statistics
Matches: 620, Mismatches: 111, Indels: 17
0.83 0.15 0.02
Matches are distributed among these distances:
80 28 0.05
81 38 0.06
83 73 0.12
84 426 0.69
85 55 0.09
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTCAAGGCTA
GAAGGGTTATCTGCGACCA
Found at i:81965 original size:8 final size:8
Alignment explanation
Indices: 81952--82056 Score: 65
Period size: 8 Copynumber: 12.8 Consensus size: 8
81942 TCTATTTCGT
81952 TTTTTTTA
1 TTTTTTTA
81960 -TTTTTTA
1 TTTTTTTA
* *
81967 -TATAT-A
1 TTTTTTTA
81973 TTTTTTTA
1 TTTTTTTA
* *
81981 TTCTCTTA
1 TTTTTTTA
81989 TTTTTTTA
1 TTTTTTTA
81997 TTTATTCTT-
1 TTT-TT-TTA
*
82006 TTATATTTA
1 TT-TTTTTA
*
82015 TTTTTTCAATT
1 TTTTTT---TA
82026 TTTTTTTA
1 TTTTTTTA
82034 TTTTTTTTA
1 -TTTTTTTA
82043 TTTTTTTA
1 TTTTTTTA
82051 TTTTTT
1 TTTTTT
82057 AATTATTGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.01
7 13 0.17
8 36 0.48
9 15 0.20
10 3 0.04
11 7 0.09
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:81976 original size:20 final size:20
Alignment explanation
Indices: 81953--82048 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 20
81943 CTATTTCGTT
81953 TTTTTTATTTTTTATATATA
1 TTTTTTATTTTTTATATATA
* *
81973 TTTTTTTATTCTCTTAT-T-TT
1 -TTTTTTATT-TTTTATATATA
*
81993 TTTATTTATTCTTTTATATTTA
1 TTT-TTTATT-TTTTATATATA
* *
82015 TTTTTTCAATTTTTT-TTTATT
1 TTTTTT--ATTTTTTATATATA
82036 TTTTTTATTTTTT
1 TTTTTTATTTTTT
82049 TATTTTTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 10 0.16
20 13 0.21
21 23 0.37
22 13 0.21
23 3 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTTTTATATATA
Found at i:81977 original size:14 final size:14
Alignment explanation
Indices: 81921--82051 Score: 85
Period size: 14 Copynumber: 9.3 Consensus size: 14
81911 TAACCCTTTC
*
81921 TTATTTTTATTTGTT
1 TTATATTTATTT-TT
81936 TTATATTCTATTTCGTT
1 TTATATT-TATTT--TT
81953 TT-T-TTTA-TTTT
1 TTATATTTATTTTT
*
81964 TTATATATATTTTT
1 TTATATTTATTTTT
*
81978 TTATTCTCTTA-TTTT
1 TTA-TAT-TTATTTTT
*
81993 TT-TATTTATTCTT
1 TTATATTTATTTTT
82006 TTATATTTATTTTT
1 TTATATTTATTTTT
* *
82020 TCA-ATTTTTTTTT
1 TTATATTTATTTTT
* *
82033 ATTTTTTTTATTTTT
1 -TTATATTTATTTTT
82048 TTAT
1 TTAT
82052 TTTTTAATTA
Statistics
Matches: 91, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
11 4 0.04
12 4 0.04
13 21 0.23
14 25 0.27
15 24 0.26
16 8 0.09
17 5 0.05
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (14 bp):
TTATATTTATTTTT
Found at i:81980 original size:42 final size:40
Alignment explanation
Indices: 81928--82048 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 40
81918 TTCTTATTTT
81928 TATTTGTTTTATATTCTATTTCGTTTTTTTTATTTTTTATATA
1 TATTT-TTTTATATTCTATTT--TTTTTTTTATTTTTTATATA
* *
81971 TATTTTTTTAT-TCTCTTATTTTTTTATTTATTCTTTTATATT
1 TATTTTTTTATAT-TC-TATTTTTTTTTTTATT-TTTTATATA
* * *
82013 TATTTTTTCA-ATTTTTTTTTATTTTTTTTATTTTTT
1 TATTTTTTTATA-TTCTATTT-TTTTTTTTATTTTTT
82049 TATTTTTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
41 19 0.29
42 36 0.55
43 11 0.17
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (40 bp):
TATTTTTTTATATTCTATTTTTTTTTTTATTTTTTATATA
Found at i:82019 original size:12 final size:11
Alignment explanation
Indices: 81951--82063 Score: 63
Period size: 11 Copynumber: 10.1 Consensus size: 11
81941 TTCTATTTCG
81951 TTTTT-TTTAT
1 TTTTTATTTAT
*
81961 TTTTTATATAT
1 TTTTTATTTAT
*
81972 ATTTT-TTTAT
1 TTTTTATTTAT
* *
81982 TCTCTTATTTTT
1 T-TTTTATTTAT
*
81994 TTATTTA-TTCT
1 TT-TTTATTTAT
*
82005 TTTATATTTAT
1 TTTTTATTTAT
82016 TTTTTCAATTT-T
1 TTTTT--ATTTAT
*
82028 TTTTTATTTTTT
1 TTTTTA-TTTAT
*
82040 TTATTTTTTTAT
1 TT-TTTATTTAT
*
82052 TTTTTAATTAT
1 TTTTTATTTAT
82063 T
1 T
82064 GGTTTTGGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
10 13 0.17
11 35 0.45
12 23 0.29
13 7 0.09
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:82028 original size:10 final size:9
Alignment explanation
Indices: 81951--82056 Score: 76
Period size: 9 Copynumber: 11.7 Consensus size: 9
81941 TTCTATTTCG
81951 TTTTTTTTA
1 TTTTTTTTA
81960 TTTTTTATATA
1 TTTTTT-T-TA
81971 TATTTTTTTA
1 T-TTTTTTTA
* *
81981 -TTCTCTTA
1 TTTTTTTTA
81989 -TTTTTTTA
1 TTTTTTTTA
*
81997 TTTATTCTT-
1 TTT-TTTTTA
* *
82006 TTATATTTA
1 TTTTTTTTA
**
82015 TTTTTTCAA
1 TTTTTTTTA
82024 TTTTTTTTTA
1 -TTTTTTTTA
82034 TTTTTTTTA
1 TTTTTTTTA
82043 -TTTTTTTA
1 TTTTTTTTA
82051 TTTTTT
1 TTTTTT
82057 AATTATTGGT
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
8 23 0.31
9 29 0.39
10 14 0.19
11 4 0.05
12 5 0.07
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:82050 original size:42 final size:42
Alignment explanation
Indices: 81951--82051 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
81941 TTCTATTTCG
*
81951 TTTTTTTTA-TTTTTTATATATATTTTTTTATTCTCTTATTT
1 TTTTTTTTATTTTTTTATATATATTTTTTAATTCTCTTATTT
* * * *
81992 TTTTATTTATTCTTTTATATTTATTTTTTCAATT-T-TTTTTT
1 TTTTTTTTATTTTTTTATATATATTTTTT-AATTCTCTTATTT
82033 ATTTTTTTTATTTTTTTAT
1 -TTTTTTTTATTTTTTTAT
82052 TTTTTAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 13 0.26
42 34 0.68
43 3 0.06
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (42 bp):
TTTTTTTTATTTTTTTATATATATTTTTTAATTCTCTTATTT
Found at i:82069 original size:28 final size:28
Alignment explanation
Indices: 82011--82069 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
82001 TTCTTTTATA
* **
82011 TTTATTTTTTCAATTTTTTTTTATTTTT
1 TTTATTTTTTCAATTTTTTATTATTGGT
*
82039 TTTATTTTTT-TATTTTTTAATTATTGGT
1 TTTATTTTTTCAATTTTTT-ATTATTGGT
82067 TTT
1 TTT
82070 GGTTTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (28 bp):
TTTATTTTTTCAATTTTTTATTATTGGT
Found at i:82103 original size:20 final size:21
Alignment explanation
Indices: 82066--82109 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
82056 TAATTATTGG
*
82066 TTTTGGTTTATTATTCTATTA
1 TTTTGGTTTATTATTCTAATA
* *
82087 TTTTGTTTTTTTA-TCTAATA
1 TTTTGGTTTATTATTCTAATA
82107 TTT
1 TTT
82110 ATTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTGGTTTATTATTCTAATA
Found at i:83352 original size:60 final size:60
Alignment explanation
Indices: 83259--83372 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
83249 GTATATACAT
* *** *
83259 ATAGTTTGGGATGAACTTGAAATATTCTAAAAGTTTGGGGACTAGTTTAGAATGAAGGTC
1 ATAGTTTGGGATGAAATTGAAATATTCTAAAAGTTTCACGACTAATTTAGAATGAAGGTC
*
83319 ATAGTTTGGGGATGAAATTGAAATGTTC-AAAAGTTTCACGACTAATTTAGAATG
1 ATAGTTT-GGGATGAAATTGAAATATTCTAAAAGTTTCACGACTAATTTAGAATG
83373 CCCATAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 29 0.62
61 18 0.38
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTCTAAAAGTTTCACGACTAATTTAGAATGAAGGTC
Found at i:94222 original size:35 final size:35
Alignment explanation
Indices: 94182--94259 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 35
94172 CATGTATTCT
* *
94182 ATGTGATATGATACGATCTACATGATTACATGCAC
1 ATGTGATATGAAACGATATACATGATTACATGCAC
* *
94217 ATGTGATATATGAAATGATATACGTGATTACATGCAC
1 ATGTG--ATATGAAACGATATACATGATTACATGCAC
*
94254 TTGTGA
1 ATGTGA
94260 CATATATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 6 0.17
37 30 0.83
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (35 bp):
ATGTGATATGAAACGATATACATGATTACATGCAC
Found at i:94571 original size:32 final size:31
Alignment explanation
Indices: 94530--94649 Score: 147
Period size: 30 Copynumber: 3.9 Consensus size: 31
94520 GAGTCGAGGG
*
94530 TTACCTATGTCTTTCGGGACATATGGGCAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
94562 TTACCTATGTCCTTT-GGGACATATGGACAGA
1 TTACCTATGT-CTTTCGGGACATATGGACAGA
* *
94593 TTTCCTATGTCTTTCGGGACATATGGATAG-
1 TTACCTATGTCTTTCGGGACATATGGACAGA
* *
94623 TTACCTATAT-TCTTCGGAACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
94650 TAGGTCCTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.01
30 26 0.33
31 25 0.32
32 23 0.29
33 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Done.