Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000719.1 Hibiscus syriacus cultivar Beakdansim tig00001397_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: 74876
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:149 original size:16 final size:16
Alignment explanation
Indices: 128--159 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
118 TACAAAATCT
128 AATAATCCATAATATA
1 AATAATCCATAATATA
*
144 AATAATCCATTATATA
1 AATAATCCATAATATA
160 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:161 original size:2 final size:2
Alignment explanation
Indices: 154--211 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
144 AATAATCCAT
154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
195 TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA T
212 TACAAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1250 original size:36 final size:37
Alignment explanation
Indices: 1188--1262 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
1178 CTACGAGGAA
1188 AGAAAGTGTAATTTGGGGGATTATTAATTG-GAAAATT
1 AGAAAGTGTAATTTGGGGGATTATTAATTGAG-AAATT
1225 AGAAAGTGTAATTT-GGGGATTATTAATTGAGAAATT
1 AGAAAGTGTAATTTGGGGGATTATTAATTGAGAAATT
1261 AG
1 AG
1263 TCAAATCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
36 22 0.59
37 15 0.41
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (37 bp):
AGAAAGTGTAATTTGGGGGATTATTAATTGAGAAATT
Found at i:4214 original size:23 final size:22
Alignment explanation
Indices: 4187--4239 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
4177 TCAATTTTCA
*
4187 TTATTTTTTGAAATATTTGAT-TT
1 TTATTATTT-AAA-ATTTGATATT
4210 TTATTATTTAAAATTTGATAATT
1 TTATTATTTAAAATTTGAT-ATT
4233 TTATTAT
1 TTATTAT
4240 ATTTGATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 7 0.26
22 3 0.11
23 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (22 bp):
TTATTATTTAAAATTTGATATT
Found at i:4574 original size:23 final size:24
Alignment explanation
Indices: 4547--4592 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4537 TTGTTCTATT
4547 TTCTATAATA-TA-AATTTTATTTC
1 TTCTA-AATACTATAATTTTATTTC
*
4570 TTCTAAATACTATATTTTTATTT
1 TTCTAAATACTATAATTTTATTT
4593 TTAAAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTAAATACTATAATTTTATTTC
Found at i:8494 original size:52 final size:54
Alignment explanation
Indices: 8416--8523 Score: 175
Period size: 52 Copynumber: 2.0 Consensus size: 54
8406 ATTATAATAT
*
8416 CCTTGTGATTAGTTATAATCCCCTAACTCTAGGCTAGTCTCCTA-TT-TATGTG
1 CCTTGTAATTAGTTATAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
* *
8468 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATGTG
1 CCTTGTAATTAGTTATAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
8522 CC
1 CC
8524 CCTTCTTGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 41 0.80
53 2 0.04
54 8 0.16
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (54 bp):
CCTTGTAATTAGTTATAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTG
Found at i:9899 original size:40 final size:35
Alignment explanation
Indices: 9813--9896 Score: 159
Period size: 35 Copynumber: 2.4 Consensus size: 35
9803 CTCCACCCGT
*
9813 GACCCGACTCGACCGACAAAATTAATGTTTCACCC
1 GACCCGACCCGACCGACAAAATTAATGTTTCACCC
9848 GACCCGACCCGACCGACAAAATTAATGTTTCACCC
1 GACCCGACCCGACCGACAAAATTAATGTTTCACCC
9883 GACCCGACCCGACC
1 GACCCGACCCGACC
9897 CGAATATATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.15
Consensus pattern (35 bp):
GACCCGACCCGACCGACAAAATTAATGTTTCACCC
Found at i:9942 original size:26 final size:29
Alignment explanation
Indices: 9886--9942 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 29
9876 TTCACCCGAC
*
9886 CCGACCCGACCCGAATATATGACTTAGAAAA
1 CCGACCCGACCCGAATATA-GAC-TAAAAAA
9917 CCGACCCGACCCGAA-ATA-A-TAAAAAA
1 CCGACCCGACCCGAATATAGACTAAAAAA
9943 AAAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 6 0.24
28 1 0.04
30 3 0.12
31 15 0.60
ACGTcount: A:0.44, C:0.30, G:0.14, T:0.12
Consensus pattern (29 bp):
CCGACCCGACCCGAATATAGACTAAAAAA
Found at i:13560 original size:52 final size:52
Alignment explanation
Indices: 13482--13634 Score: 234
Period size: 52 Copynumber: 2.9 Consensus size: 52
13472 TATCCTTGTG
*
13482 ATTAGTTGTAATCTCCTAACTCTAGGCTAGTCTCCTATTTATGTGCCATGTA
1 ATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTGCCATGTA
*
13534 ATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTGCCTTGTA
1 ATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTGCCATGTA
* * * *
13586 ATTAGTTTTAATCCACTAACTCTAGGCTAGTTTCTTATTTCTATGTGCC
1 ATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTA-TT-TATGTGCC
13635 CCATCTTGTG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 83 0.89
53 2 0.02
54 8 0.09
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (52 bp):
ATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTGCCATGTA
Found at i:25854 original size:3 final size:3
Alignment explanation
Indices: 25846--25897 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
25836 TTCATTTTAA
* *
25846 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT AAT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
25892 ATT ATT
1 ATT ATT
25898 TAAATATTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:30307 original size:20 final size:21
Alignment explanation
Indices: 30223--30305 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
30213 AACAGAACCC
*
30223 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
30244 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* * *
30266 CAAAGGAGGAATCGGTT-CCCT
1 C-AGGGGGGAATCGATTCCCCT
30287 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
30306 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:36970 original size:54 final size:53
Alignment explanation
Indices: 36867--36971 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
36857 ATAATTTTAC
* * * * *
36867 ATTTATTATTATTTTATTTATTTATAGTCATTGTTTAGTTATTTTTTTACTTA
1 ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTGTTTTACTTA
36920 ATTT-TTATTATTTTAATATATTT-TAAATCATTACTTTAATTATTGTTTTACT
1 ATTTATTATTATTTT-ATATATTTAT-AATCATT-CTTTAATTATTGTTTTACT
36972 ATATTATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
52 11 0.25
53 17 0.39
54 16 0.36
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.64
Consensus pattern (53 bp):
ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTGTTTTACTTA
Found at i:36998 original size:35 final size:35
Alignment explanation
Indices: 36923--36998 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
36913 TTACTTAATT
*
36923 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
36958 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
36993 TTTATT
1 TTTATT
36999 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:38437 original size:94 final size:91
Alignment explanation
Indices: 38243--38552 Score: 410
Period size: 94 Copynumber: 3.5 Consensus size: 91
38233 TTTTTCTTTA
* *
38243 ACCGTTAATAGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAATCGATTTTTTTCT
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAAT-AATC-ATTTTTTTCT
38308 TTAACATTAATCGAACCAAAATTATTTG
64 TTAACATTAATCGAACCAAAATTATTTG
*
38336 ACCGTTAATCGAACCTAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCAAATTTTTTTC
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAA-TAATC--ATTTTTTTC
* *
38401 TTTAATATTAATCGAACCGAAATTATTTG
63 TTTAACATTAATCGAACCAAAATTATTTG
*
38430 ACCGTTAATCGAACCAAAATTTATTTAAAAATTATT-----AACC----AA--A-TTTTTTCTTT
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATAATCATTTTTTTCTTT
38483 AACCATTAATCGAACCAAAATTATTTG
66 AA-CATTAATCGAACCAAAATTATTTG
* *
38510 ACCGTTAATCGAACCCAAATTTATTTGAAAAATATTAACCGAA
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAA
38553 TTAACAGAAT
Statistics
Matches: 197, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
79 12 0.06
80 56 0.28
84 2 0.01
85 2 0.01
89 4 0.02
93 50 0.25
94 71 0.36
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (91 bp):
ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATAATCATTTTTTTCTTT
AACATTAATCGAACCAAAATTATTTG
Found at i:38444 original size:26 final size:27
Alignment explanation
Indices: 38407--38537 Score: 117
Period size: 26 Copynumber: 4.9 Consensus size: 27
38397 TTTCTTTAAT
*
38407 ATTAATCGAACCGAAA-TTATTTGACC
1 ATTAATCGAACCAAAATTTATTTGACC
* * **
38433 GTTAATCGAACCAAAATTTATTTAAAA
1 ATTAATCGAACCAAAATTTATTTGACC
* * * *
38460 ATT-AT-TAACCAAATTTTTTCTTTAACC
1 ATTAATCGAACCAAA--ATTTATTTGACC
38487 ATTAATCGAACCAAAA-TTATTTGACC
1 ATTAATCGAACCAAAATTTATTTGACC
* *
38513 GTTAATCGAACCCAAATTTATTTGA
1 ATTAATCGAACCAAAATTTATTTGA
38538 AAAATATTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
25 7 0.09
26 38 0.46
27 28 0.34
28 2 0.02
29 7 0.09
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (27 bp):
ATTAATCGAACCAAAATTTATTTGACC
Found at i:38516 original size:80 final size:79
Alignment explanation
Indices: 38383--38554 Score: 265
Period size: 80 Copynumber: 2.2 Consensus size: 79
38373 ACCGAACCAA
* * *
38383 ATTAATCAAATTTTTTTCTTTAATATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAA
1 ATTAACCAAA-TTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
38448 ATTTATTT-AAAAATT
65 ATTTATTTGAAAAA-T
*
38463 ATTAACCAAATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAA
1 ATTAACCAAATTTTTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
38528 ATTTATTTGAAAAAT
65 ATTTATTTGAAAAAT
*
38543 ATTAACCGAATT
1 ATTAACCAAATT
38555 AACAGAATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
79 12 0.14
80 68 0.80
81 5 0.06
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (79 bp):
ATTAACCAAATTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAAA
TTTATTTGAAAAAT
Found at i:38604 original size:74 final size:67
Alignment explanation
Indices: 38510--38681 Score: 200
Period size: 67 Copynumber: 2.5 Consensus size: 67
38500 AAATTATTTG
38510 ACCGTTAATCGAACCCAAATTTATTTGAAAAATATTAACCGAATTAACAGAATAAAATAAATTAT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAAATATTAACCG-A--AACA-AAT-AAATAAA-T-T
38575 TTTTCTTTA
59 TTTTCTTTA
* * * * * * **
38584 ACCGTTAATCGAACCGAAATTTATATGGAAATTATTAACCGAACCAAATCAATCGATTTTTTCTT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAAATATTAACCGAAACAAATAAATAAATTTTTTCTT
38649 TA
66 TA
*
38651 ACCATTAATCGAACCCAAATTTATTTGAAAA
1 ACCGTTAATCGAACCCAAATTTATTTGAAAA
38682 TTCAATTCAG
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
67 37 0.43
68 1 0.01
69 4 0.05
70 3 0.03
71 3 0.03
73 1 0.01
74 37 0.43
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (67 bp):
ACCGTTAATCGAACCCAAATTTATTTGAAAAATATTAACCGAAACAAATAAATAAATTTTTTCTT
TA
Found at i:39028 original size:67 final size:71
Alignment explanation
Indices: 38952--39121 Score: 197
Period size: 74 Copynumber: 2.4 Consensus size: 71
38942 ATTAACTGTT
* * *
38952 AAAT-AATTTCGGTTCGATTAATGGTTAAAG-AAAA-AA-TCAGTTGATTTGG-TTCGGTTAATA
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTCAGTTGATTCGGATTCAGTTAATA
*
39012 CTTTTC
66 ATTTTC
* * * *
39018 AAATAAATTTCGGTTCGATTAACGATTAAAGAAAAATAATTTATTTTATTCGGTTAATTCAGTTA
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTCAGTTGATTCGG---ATTCAGTTA
39083 ATAATTTTC
63 ATAATTTTC
*
39092 AAATAAATTTGGGTTCGATTAACGGTTAAA
1 AAATAAATTTCGGTTCGATTAACGGTTAAA
39122 TAATTTTGGT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
66 4 0.05
67 24 0.28
68 4 0.05
69 2 0.02
70 9 0.10
74 43 0.50
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (71 bp):
AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTCAGTTGATTCGGATTCAGTTAATA
ATTTTC
Found at i:39049 original size:167 final size:167
Alignment explanation
Indices: 38759--39154 Score: 650
Period size: 167 Copynumber: 2.4 Consensus size: 167
38749 TTATTTAGTT
* * * *
38759 AATAATTTTCGATTCGATTAACGGCCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAATCC
1 AATAAATTTGGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAATCA
*
38824 GTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC-AGTTAAAGAAAAAT
66 GTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGA-TTAAAGAAAAAT
38888 AATTTATTTTATTCGGTTAATTCGGTTAATAATTTTCA
130 AATTTATTTTATTCGGTTAATTCGGTTAATAATTTTCA
* * *
38926 AATAAATTTGCATTCGATTAACTGTTAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAATCA
1 AATAAATTTGGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAATCA
*
38991 GTTGATTTGGTTCGGTTAATACTTTTCAAATAAATTTCGGTTCGATTAACGATTAAAGAAAAATA
66 GTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATTAAAGAAAAATA
*
39056 ATTTATTTTATTCGGTTAATTCAGTTAATAATTTTCA
131 ATTTATTTTATTCGGTTAATTCGGTTAATAATTTTCA
* * * *
39093 AATAAATTTGGGTTCGATTAACGGTTAAATAATTTTGGTTTGATTAATGGTTAAAGAAAAAA
1 AATAAATTTGGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAA
39155 ATTTGGTTAA
Statistics
Matches: 213, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
167 212 1.00
168 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (167 bp):
AATAAATTTGGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAATCA
GTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGATTAAAGAAAAATA
ATTTATTTTATTCGGTTAATTCGGTTAATAATTTTCA
Found at i:39211 original size:26 final size:27
Alignment explanation
Indices: 39090--39222 Score: 105
Period size: 26 Copynumber: 5.0 Consensus size: 27
39080 TTAATAATTT
* *
39090 TCAAATAAATTTGGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAATGG
* * *
39117 TTAAAT-AATTTTGGTTTGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAATGG
* * * * *
39143 TTAAAGAAAAAAATTT-GGTT-AATAAAT-T
1 -T---CAAATAAATTTCGGTTCGATTAATGG
39171 TCAAATAAATTTCGGTTCGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAATGG
39198 TCAAAT-AATTTCGGTTCGATTAATG
1 TCAAATAAATTTCGGTTCGATTAATG
39223 TTAAAGAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
24 9 0.11
25 4 0.05
26 41 0.49
27 13 0.15
29 5 0.06
30 7 0.08
31 5 0.06
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCGATTAATGG
Found at i:39219 original size:81 final size:80
Alignment explanation
Indices: 39073--39245 Score: 265
Period size: 81 Copynumber: 2.1 Consensus size: 80
39063 TTATTCGGTT
* * * * * *
39073 AATTCAGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTTAAATAATTTTGGTTTGATT
1 AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
39138 AATGGTTAAAGAAAAA
66 AAT-GTTAAAGAAAAA
* *
39154 AATTTGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAATGGTCAAATAATTTCGGTTCGATT
1 AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
39219 AATGTTAAAGAAAAA
66 AATGTTAAAGAAAAA
39234 AATTCGGTTAAT
1 AATTCGGTTAAT
39246 TTGGTTCGGT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 23 0.28
81 60 0.72
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (80 bp):
AATTCGGTTAATAAATTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATT
AATGTTAAAGAAAAA
Found at i:39267 original size:94 final size:94
Alignment explanation
Indices: 39159--39386 Score: 366
Period size: 94 Copynumber: 2.4 Consensus size: 94
39149 AAAAAAATTT
* *
39159 GGTTAATAAATTTCAAATAAATTTCGGTTCGATTAATGGTCAAATAATTTCGGTTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
* **
39224 TAAAGAAAAAAATTCGGTTAATTTGGTTC
66 TAAAGAAAAAAAATCAATTAATTTGGTTC
*
39253 GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
*
39318 TAAAGAAAAAAAATCAATTGATTTGGTTC
66 TAAAGAAAAAAAATCAATTAATTTGGTTC
* **
39347 GGCTAATAATTTTCAAATAAATTTTAGTTCGATTAACGGT
1 GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
39387 GAAAGAAAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 124 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (94 bp):
GGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGT
TAAAGAAAAAAAATCAATTAATTTGGTTC
Found at i:45919 original size:3 final size:3
Alignment explanation
Indices: 45911--45958 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
45901 ATGCTGGAAG
* *
45911 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TGT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45958 T
1 T
45959 TCATTGGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:45964 original size:23 final size:23
Alignment explanation
Indices: 45914--45958 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
45904 CTGGAAGTAT
*
45914 TATTATTATTATTATTATTATTA
1 TATTGTTATTATTATTATTATTA
*
45937 TATTGTTATTGTTATTATTATT
1 TATTGTTATTATTATTATTATT
45959 TCATTGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TATTGTTATTATTATTATTATTA
Found at i:47748 original size:21 final size:21
Alignment explanation
Indices: 47718--47766 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
47708 TTTTGCCAAG
*
47718 TCATTGCTGATGATTCATGAT
1 TCATTACTGATGATTCATGAT
47739 TCATTACTGATGATTCATGAT
1 TCATTACTGATGATTCATGAT
47760 TCATTAC
1 TCATTAC
47767 CATTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (21 bp):
TCATTACTGATGATTCATGAT
Found at i:48118 original size:21 final size:22
Alignment explanation
Indices: 48077--48135 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
48067 CGATCTAAAA
*
48077 TAATAAAAAATAATATTTTTATT
1 TAAT-AAAAATAATATTTTAATT
48100 TAATAAAAATAATGA-TTTAATT
1 TAATAAAAATAAT-ATTTTAATT
*
48122 GAA-AAAAATAATAT
1 TAATAAAAATAATAT
48136 AACGAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 9 0.28
22 17 0.53
23 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
TAATAAAAATAATATTTTAATT
Found at i:58131 original size:26 final size:26
Alignment explanation
Indices: 58102--58152 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
58092 TTGTCTGTAG
*
58102 GTATTGAAACATTGCAAAGAAGTATT
1 GTATCGAAACATTGCAAAGAAGTATT
*
58128 GTATCGATACATTGCAAAGAAGTAT
1 GTATCGAAACATTGCAAAGAAGTAT
58153 CAATACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (26 bp):
GTATCGAAACATTGCAAAGAAGTATT
Found at i:59269 original size:38 final size:38
Alignment explanation
Indices: 59197--59276 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
59187 TTAGAAAGTG
59197 ATATTATAGATAGAAAATAAATATCGATACTTGTATATA
1 ATATTATAGATAGAAAATAAATATCGATACTTGTATA-A
* * *
59236 ATATTATAGGTAGAAAAT-AATATTG-TAGGTTGTATAA
1 ATATTATAGATAGAAAATAAATATCGATA-CTTGTATAA
59273 ATAT
1 ATAT
59277 ACCAAATACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 7 0.19
38 13 0.35
39 17 0.46
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.38
Consensus pattern (38 bp):
ATATTATAGATAGAAAATAAATATCGATACTTGTATAA
Found at i:60860 original size:12 final size:12
Alignment explanation
Indices: 60840--60892 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
60830 TAGAGGAGGC
*
60840 AGAGGAGGAAGA
1 AGAGAAGGAAGA
*
60852 TGAGAAGG-A-A
1 AGAGAAGGAAGA
*
60862 A-AGAAGGAATA
1 AGAGAAGGAAGA
60873 AGAGAAGGAAGA
1 AGAGAAGGAAGA
60885 AGAGAAGG
1 AGAGAAGG
60893 TAGTAAGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.18
10 2 0.06
11 3 0.09
12 23 0.68
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (12 bp):
AGAGAAGGAAGA
Found at i:60869 original size:21 final size:22
Alignment explanation
Indices: 60845--60887 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
60835 GAGGCAGAGG
*
60845 AGGAAGATGAGAAGGAA-AAGA
1 AGGAAGAAGAGAAGGAAGAAGA
*
60866 AGGAATAAGAGAAGGAAGAAGA
1 AGGAAGAAGAGAAGGAAGAAGA
60888 GAAGGTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (22 bp):
AGGAAGAAGAGAAGGAAGAAGA
Found at i:64670 original size:17 final size:17
Alignment explanation
Indices: 64648--64686 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 17
64638 AGGTTTTGAG
64648 AAGCAAGAAGAGGAGTA
1 AAGCAAGAAGAGGAGTA
64665 AAGC---AAGAGGAGTA
1 AAGCAAGAAGAGGAGTA
64679 AAGCAAGA
1 AAGCAAGA
64687 GTAGGCAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.74
17 5 0.26
ACGTcount: A:0.54, C:0.08, G:0.33, T:0.05
Consensus pattern (17 bp):
AAGCAAGAAGAGGAGTA
Found at i:64674 original size:14 final size:14
Alignment explanation
Indices: 64655--64687 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
64645 GAGAAGCAAG
64655 AAGAGGAGTAAAGC
1 AAGAGGAGTAAAGC
64669 AAGAGGAGTAAAGC
1 AAGAGGAGTAAAGC
64683 AAGAG
1 AAGAG
64688 TAGGCAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.36, T:0.06
Consensus pattern (14 bp):
AAGAGGAGTAAAGC
Found at i:66406 original size:199 final size:189
Alignment explanation
Indices: 66066--66632 Score: 658
Period size: 178 Copynumber: 3.0 Consensus size: 189
66056 ATAAAGTATT
* * * *
66066 GATACTTTTTGTCCAATATGCATCCCAAATGAGATGCATACATAAAATATCGATACATGTATG-A
1 GATACTTTTT-TCC--TAT-CATCCCAAACGAGATGCACACATAAAGTATCGATACACGTATGAA
* *
66130 AAGTATCGATTCTTAAAACTACGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATATAGG
62 AAGTATCGATTCTTAAAACTTCGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATGTAGG
* * *
66195 CGGTAAAAATATACCGATTTAATGACAAGATACGTAAACGTAAATTATCGATACTTTTTGTAAGA
127 CGGTAAAAATATACCG-TTTAATGACAAAATACGTAAACATAAAATATCGATACTTTTT-T----
66260 GTACC
186 GT-CC
66265 GATACTTTTTTCCTGTATACATCCCAAACGAGATGCACACATAAAGTATCGATACACGTATGAAA
1 GATACTTTTTTCC--TAT-CATCCCAAACGAGATGCACACATAAAGTATCGATACACGTATGAAA
*
66330 AATATCGATTCTTAAAACTTCGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATGTAGGC
63 AGTATCGATTCTTAAAACTTCGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATGTAGGC
* * *
66395 GGTAAAAATATACCGTTTAATGACAAAATATGTAAACATAAAGTATCAATAC-TTTTTGTCC
128 GGTAAAAATATACCGTTTAATGACAAAATACGTAAACATAAAATATCGATACTTTTTTGTCC
* * * * * *
66456 -AGTA------TGCT-T--T-CCAAACTAGATGCACGCAGAAAGTATCGATACACGTGTGAGAAG
1 GA-TACTTTTTTCCTATCATCCCAAACGAGATGCACACATAAAGTATCGATACACGTATGAAAAG
* * * *
66510 TATCGATTCTTAAAATTTC-AAAATGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGCGG
65 TATCGATTCTTAAAACTTCGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATGTAGGCGG
* * *
66574 TAAACATATACTGGCTTAATGACAAAATACGTAAACATAAAATATCGATACTTTTTTGT
130 TAAAAATATAC-CGTTTAATGACAAAATACGTAAACATAAAATATCGATACTTTTTTGT
66633 ATTTGTATCG
Statistics
Matches: 332, Mismatches: 32, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
177 52 0.16
178 90 0.27
179 8 0.02
182 1 0.00
183 1 0.00
185 2 0.01
190 1 0.00
191 4 0.01
192 2 0.01
196 1 0.00
197 4 0.01
198 77 0.23
199 89 0.27
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (189 bp):
GATACTTTTTTCCTATCATCCCAAACGAGATGCACACATAAAGTATCGATACACGTATGAAAAGT
ATCGATTCTTAAAACTTCGAAACTGATTAGTATAAAGTAATAGGTAAATTTACAATGTAGGCGGT
AAAAATATACCGTTTAATGACAAAATACGTAAACATAAAATATCGATACTTTTTTGTCC
Found at i:66624 original size:376 final size:374
Alignment explanation
Indices: 65607--66653 Score: 1246
Period size: 381 Copynumber: 2.8 Consensus size: 374
65597 TTTATTACTT
* * * *
65607 TAAAGTAATAGGTAAATTTACAATGTAAGAGGTAAAAATATACATGTTTAATGAAAAAATGTGTA
1 TAAAGTAATAGGTAAATTTACAATGT-AGCGGTAAAAATATAC-CGTTTAATGACAAAATATGTA
* * * * * *
65672 AACATAAAGTTTCGATCCTTTTTATCCAATATG-ATTCCTAAACTAGAAGTAAAAAGAAAGTATC
64 AACATAAAGTATCGATACTTTTTGTCCAATATGCATTCC-AAACTAGATGCAAACAGAAAGTATC
* *
65736 GATACAAGTATGAAAAGTATCAATTCTTAAAACTTCGAAATCGATTAACT-TAAAGTAATAGGTA
128 GATACAAGTATG-AAAGTATCGATTCTTAAAACTTCAAAAT-GATTAA-TATAAAGTAATAGGTA
* * * * * *
65800 AATTTACAATGTTAGCGGTAAAAAACTACCAGTTTATGATAAAATACGTTAACATAAAATAGT-G
190 AATTTACAATGTAAGCGGTAAAATA-TACCGGTTAATGACAAAATACGTAAACATAAAATA-TCG
* * ** * * *
65864 ATACTTTTTGTATGTGTATTGATACTTTTTGTCCAGTATGCTTCCCAAACTTAAGTAAGTAAAAT
253 ATACTTTTTGTAAGAGTACCGATACTTTTTGTCCAGTATACATCCCAAAC-TAAGTAAGCAAAAT
* * *
65929 GAAAGTATCGATACATGTATGAAAAGTATCGATTCTTAAAACTTCGAAACCGATTATT
317 GAAAGTATCGATACACGTATGAAAAATATCGATTCTTAAAACTTCGAAACCGATTATA
* * * *
65987 TGAAGGTAATAAGTAAATTTACAATGTTAGCGGTAATAATATACCGGTTTAATGACAAGATATGT
1 T-AAAGTAATAGGTAAATTTACAATG-TAGCGGTAAAAATATACC-GTTTAATGACAAAATATGT
* * * * *
66052 AAACATAAAGTATTGATACTTTTTGTCCAATATGCATCCCAAA-TGAGATGCATACATAAAATAT
63 AAACATAAAGTATCGATACTTTTTGTCCAATATGCATTCCAAACT-AGATGCAAACAGAAAGTAT
* * * *
66116 CGATACATGTATGAAAGTATCGATTCTTAAAACTACGAAACTGATTAGTATAAAGTAATAGGTAA
127 CGATACAAGTATGAAAGTATCGATTCTTAAAACTTC-AAAATGATTAATATAAAGTAATAGGTAA
* * * * * *
66181 ATTTACAATATAGGCGGTAAAAATATACCGATTTAATGACAAGATACGTAAACGTAAATTATCGA
191 ATTTACAATGTAAGCGGT-AAAATATACCG-GTTAATGACAAAATACGTAAACATAAAATATCGA
* * * *
66246 TACTTTTTGTAAGAGTACCGATACTTTTT-TCCTGTATACATCCCAAAC-GAG-ATGCACACAT-
254 TACTTTTTGTAAGAGTACCGATACTTTTTGTCCAGTATACATCCCAAACTAAGTAAGCA-AAATG
*
66307 AAAGTATCGATACACGTATGAAAAATATCGATTCTTAAAACTTCGAAACTGATTAGTA
318 AAAGTATCGATACACGTATGAAAAATATCGATTCTTAAAACTTCGAAACCGATTA-TA
66365 TAAAGTAATAGGTAAATTTACAATGTAGGCGGTAAAAATATACCGTTTAATGACAAAATATGTAA
1 TAAAGTAATAGGTAAATTTACAATGTA-GCGGTAAAAATATACCGTTTAATGACAAAATATGTAA
* * * **
66430 ACATAAAGTATCAATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCGA
65 ACATAAAGTATCGATACTTTTTGTCCAATATGCATTCCAAACTAGATGCAAACAGAAAGTATCGA
* * *
66495 TACACGTGTGAGAAGTATCGATTCTTAAAATTTCAAAATGATTAATATAAAGTAATAGGTAAATT
130 TACAAGTATGA-AAGTATCGATTCTTAAAACTTCAAAATGATTAATATAAAGTAATAGGTAAATT
*
66560 TACAATGTAAGCGGTAAACATATACTGGCTTAATGACAAAATACGTAAACATAAAATATCGATAC
194 TACAATGTAAGCGGTAAA-ATATACCGG-TTAATGACAAAATACGTAAACATAAAATATCGATAC
*** *
66625 TTTTTTGTATTTGTATCGATACTTTTTGT
257 -TTTTTGTAAGAGTACCGATACTTTTTGT
66654 TTAGTATGAA
Statistics
Matches: 566, Mismatches: 82, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
375 3 0.01
376 167 0.30
377 135 0.24
378 8 0.01
379 1 0.00
380 79 0.14
381 168 0.30
382 5 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (374 bp):
TAAAGTAATAGGTAAATTTACAATGTAGCGGTAAAAATATACCGTTTAATGACAAAATATGTAAA
CATAAAGTATCGATACTTTTTGTCCAATATGCATTCCAAACTAGATGCAAACAGAAAGTATCGAT
ACAAGTATGAAAGTATCGATTCTTAAAACTTCAAAATGATTAATATAAAGTAATAGGTAAATTTA
CAATGTAAGCGGTAAAATATACCGGTTAATGACAAAATACGTAAACATAAAATATCGATACTTTT
TGTAAGAGTACCGATACTTTTTGTCCAGTATACATCCCAAACTAAGTAAGCAAAATGAAAGTATC
GATACACGTATGAAAAATATCGATTCTTAAAACTTCGAAACCGATTATA
Found at i:66660 original size:20 final size:22
Alignment explanation
Indices: 66616--66660 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
66606 AAACATAAAA
*
66616 TATCGATACTTTTTTGTATTTG
1 TATCGATACTTTTTTGTATTAG
66638 TATCGATAC-TTTTTGT-TTAG
1 TATCGATACTTTTTTGTATTAG
66658 TAT
1 TAT
66661 GAAAACACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (22 bp):
TATCGATACTTTTTTGTATTAG
Found at i:68744 original size:15 final size:15
Alignment explanation
Indices: 68724--68753 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68714 AGACTATTTA
68724 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
68739 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
68754 GCATGTTTGA
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:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:69134 original size:6 final size:6
Alignment explanation
Indices: 69107--69166 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
69097 TTTCATACTG
* * * *
69107 AATTTC -ATTTA AATTTC AAATTTC AATTTC AATTTG AGTTTC AATTTG
1 AATTTC AATTTC AATTTC -AATTTC AATTTC AATTTC AATTTC AATTTC
*
69155 AGTTTC AATTTC
1 AATTTC AATTTC
69167 GGCTCCACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
5 4 0.10
6 32 0.76
7 6 0.14
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.50
Consensus pattern (6 bp):
AATTTC
Found at i:69148 original size:12 final size:12
Alignment explanation
Indices: 69133--69165 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
69123 CAAATTTCAA
69133 TTTCAATTTGAG
1 TTTCAATTTGAG
69145 TTTCAATTTGAG
1 TTTCAATTTGAG
69157 TTTCAATTT
1 TTTCAATTT
69166 CGGCTCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (12 bp):
TTTCAATTTGAG
Found at i:71447 original size:445 final size:443
Alignment explanation
Indices: 70638--72122 Score: 2048
Period size: 449 Copynumber: 3.3 Consensus size: 443
70628 CACCTAAGAA
* * * * * * *
70638 ACATGTAACGATACAAGGCAATATAACATGTTGAAAATTGACAAAACCGATTTCAATAGGCCAAT
1 ACATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAACCGATTTCAATATGACAAA
** * * * * * *
70703 ACCGGTAAAGAGATATCAGATTACACAAAAACAAAACGTCTCGAAAGTATTGATACCTTACAAAA
66 ACAAGTAAAAAGATACCAGTTTACAAAAAAACGAAACGTCTCGAAAGTATCGATACCTTACAAAA
*
70768 AAGTATCGATACTTAAGTAAGGGTAATGGTATCGATTAAATATAAATAACTTAACAGGTTCAAAA
131 AAGTATCGATACTTAAGTAA-GGTAATGGTATCGATTAAATATAAATAACTTAACATGTTCAAAA
* * *
70833 TTGACAAAACATGTTTCCATAATTGCGCCTATAAAGTATCAATACACGTATAAGAAGTATC-AGT
195 TTGACAAAAC-TGTTTCCATAATTGCGCCTATAAAGTATCGATACACGTATGAGAATTATCGA-T
*
70897 TCTTAAAACTTCGAAAC-AGATTAATTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAA
258 TCTTAAAACTTCGAAACGA-ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAA
* *
70961 TATA-CCGATTTAATGACAAAATACGTTAACATAAAGTATCGATACTTTTTTTATGTGTCGATAC
322 TATATCAG-TTTAATGACAAAATACGTTAACATAAAGTATCGATACTTTTTTTATGTATCGATAC
*
71025 TTTTTGTCCAGTATGCTTCCCAAACTAGATGCACGCAGAAAGTATCGATATC-TAATAC
386 TTTTTGTCCAGTATGCTTCCCAAACTAGATGCACGCAGAAAGTATTGATA-CATAATAC
* * *
71083 ATATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAATCGGTTTCAATATGACAAA
1 ACATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAACCGATTTCAATATGACAAA
* * * * *
71148 ATAGGTAAAAAGATACCGGTTTACAAAAAAACGAAACGTCTCGAAAGTATCGATACTTTACACAA
66 ACAAGTAAAAAGATACCAGTTTACAAAAAAACGAAACGTCTCGAAAGTATCGATACCTTACAAAA
* * * *
71213 AAGTATTGATATTTAAGTAAGTTTAATGGTATCTATTAAATATAAATAACTTAACATGTTCAAAA
131 AAGTATCGATACTTAAGTAAG-GTAATGGTATCGATTAAATATAAATAACTTAACATGTTCAAAA
* * * *
71278 TTTACAAAACTGTTTTCTATAATTGTGCCTATAAAGTATCGATACATGTATGAGAATTATCGATT
195 TTGACAAAACTG-TTTCCATAATTGCGCCTATAAAGTATCGATACACGTATGAGAATTATCGATT
* * * *
71343 TTTAAAACTTCGAAACGAATTACTTTAAAGTAATAGGTTAATTTAAAATGTAAGTAGTAAAAATA
259 CTTAAAACTTCGAAACGAATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATA
* * *
71408 TATCAGTTTAATGACAAAATACGTTAACATAAAGTATCGATACTTTTTGTACATGTATCAATACC
324 TATCAGTTTAATGACAAAATACGTTAACATAAAGTATCGATACTTTTT-T-TATGTATCGATACT
* * * *
71473 TTTTGTTCAGTATACTTCCCAAACTATATGCACGCAGAAAATATTGATACATAATAC
387 TTTTGTCCAGTATGCTTCCCAAACTAGATGCACGCAGAAAGTATTGATACATAATAC
* *
71530 ACATGTATCGATACATGACAATATAACATGTTAAAAATTGATAAAACCAATTTCAATATGACAAA
1 ACATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAACCGATTTCAATATGACAAA
* * *
71595 ACAAGTAAAAAGATACCAATTTACAAAAAAAAAATGAAATGTCTCGAAAGTATCGATA-CTT-CA
66 ACAAGTAAAAAGATACCAGTTTAC---AAAAAAACGAAACGTCTCGAAAGTATCGATACCTTACA
* * *
71658 ACAAAAGTATCGATACTTCATTAACGGTAATGGTATCGATTAAATATAAATAACATAACATGTTC
128 A-AAAAGTATCGATACTTAAGTAA-GGTAATGGTATCGATTAAATATAAATAACTTAACATGTTC
*
71723 AAAATTGACAAAACTGGTTTCCATAATTGCACCTATAAAGTATCGATACACGTATGAG-ATGTAT
191 AAAATTGACAAAACT-GTTTCCATAATTGCGCCTATAAAGTATCGATACACGTATGAGAAT-TAT
* *
71787 CGATTCTTAAAACTTCGAAACGGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGCGGTAA
254 CGATTCTTAAAACTTCGAAACGAATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAA
* * * * *
71852 AAATATATCGGTTTAATGAAAAAATATGTTAACATAAAGTATCAATACTTGTTGTGTATGTATCG
319 AAATATATCAGTTTAATGACAAAATACGTTAACATAAAGTATCGATACTT-TT-TTTATGTATCG
** * *
71917 ATACTTTTTGTCCAGTATGCTTTTCAAACCAGATGCACACAGAAAGTATTGATACATAATAC
382 ATACTTTTTGTCCAGTATGCTTCCCAAACTAGATGCACGCAGAAAGTATTGATACATAATAC
* * * *
71979 ACATGTATCGATATATGACAATATAACAGGTTGAAAATTGATAAATCCGGTTTCAATATGACAAA
1 ACATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAACCGATTTCAATATGACAAA
** * *
72044 ACAAGTAAAAAGATACTGGTTTACACAAAAACGAAACGTCTCGAAAGTATCGATACCATACAAAA
66 ACAAGTAAAAAGATACCAGTTTACAAAAAAACGAAACGTCTCGAAAGTATCGATACCTTACAAAA
72109 AAGTATCGATACTT
131 AAGTATCGATACTT
72123 CAATAAGAGT
Statistics
Matches: 913, Mismatches: 108, Indels: 36
0.86 0.10 0.03
Matches are distributed among these distances:
444 3 0.00
445 322 0.35
446 34 0.04
447 158 0.17
448 7 0.01
449 355 0.39
450 33 0.04
451 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (443 bp):
ACATGTATCGATACATGACAATATAACATGTTGAAAATTGATAAAACCGATTTCAATATGACAAA
ACAAGTAAAAAGATACCAGTTTACAAAAAAACGAAACGTCTCGAAAGTATCGATACCTTACAAAA
AAGTATCGATACTTAAGTAAGGTAATGGTATCGATTAAATATAAATAACTTAACATGTTCAAAAT
TGACAAAACTGTTTCCATAATTGCGCCTATAAAGTATCGATACACGTATGAGAATTATCGATTCT
TAAAACTTCGAAACGAATTACTTTAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATA
TCAGTTTAATGACAAAATACGTTAACATAAAGTATCGATACTTTTTTTATGTATCGATACTTTTT
GTCCAGTATGCTTCCCAAACTAGATGCACGCAGAAAGTATTGATACATAATAC
Found at i:74006 original size:18 final size:19
Alignment explanation
Indices: 73971--74006 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
73961 CACGGAATGT
73971 AAGATTACCAGTGGAATAA
1 AAGATTACCAGTGGAATAA
*
73990 AAGATTATCAG-GGAATA
1 AAGATTACCAGTGGAATA
74007 GGATTACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCAGTGGAATAA
Found at i:74226 original size:36 final size:36
Alignment explanation
Indices: 74155--74227 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
74145 GTTGGAAAAT
* *
74155 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
74191 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
74227 A
1 A
74228 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Done.