Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000983.1 Hibiscus syriacus cultivar Beakdansim tig00001967_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: 94240
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2997 original size:54 final size:53
Alignment explanation
Indices: 2933--3246 Score: 387
Period size: 54 Copynumber: 5.8 Consensus size: 53
2923 GTAGCCGATA
* *
2933 CATAAACTTATTATGAATTGTGTGGGTTGCACACTTAGTGCCTATACGATCGTT
1 CATAAACTTATTATGAATT-TGTGGGTTGCACACTTAGTGCCGATACGGTCGTT
** * *
2987 CATAAACTTATTATGAATTTCGTGGGTTGCACACTTAGTGATGATATGGTCATT
1 CATAAACTTATTATGAATTT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTT
* ** * * *
3041 CATAAA-ATATTATGAATTCCATGGGGTGCACACTTAGTCCCGATACGGTCATT
1 CATAAACTTATTATGAATT-TGTGGGTTGCACACTTAGTGCCGATACGGTCGTT
* *
3094 CATAAACTTATTATGAATTTCGTGGGTTGCACACTTAGTGTCGATATGGTCGTT
1 CATAAACTTATTATGAATTT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTT
* * ** * *
3148 CATAAACTTATTATGAATCTATTTGTTGCATACTTAGTGCCAATACGGTCGTT
1 CATAAACTTATTATGAATTTGTGGGTTGCACACTTAGTGCCGATACGGTCGTT
*
3201 CATAAACTTATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATA
1 CATAAACTTATTATGAA-TTTGTGGGTTGCACACTTAGTGCCGATA
3247 GTACACATAG
Statistics
Matches: 218, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
53 88 0.40
54 130 0.60
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (53 bp):
CATAAACTTATTATGAATTTGTGGGTTGCACACTTAGTGCCGATACGGTCGTT
Found at i:3127 original size:107 final size:108
Alignment explanation
Indices: 2933--3246 Score: 454
Period size: 107 Copynumber: 2.9 Consensus size: 108
2923 GTAGCCGATA
* * * * *
2933 CATAAACTTATTATGAATTGTGTGGGTTGCACACTTAGTGCCTATACGATCGTTCATAAACTTAT
1 CATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGCCAATACGGTCGTTCATAAACTTAT
2998 TATGAATTTCGTGGGTTGCACACTTAGTGAT-GATATGGTCATT
66 TATGAATTTCGTGGGTTGCACACTTAGTG-TCGATATGGTCATT
* * * * *
3041 CATAAA-ATATTATGAATTCCATGGGGTGCACACTTAGTCCCGATACGGTCATTCATAAACTTAT
1 CATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGCCAATACGGTCGTTCATAAACTTAT
*
3105 TATGAATTTCGTGGGTTGCACACTTAGTGTCGATATGGTCGTT
66 TATGAATTTCGTGGGTTGCACACTTAGTGTCGATATGGTCATT
* ** *
3148 CATAAACTTATTATGAA-TCTATTTGTTGCATACTTAGTGCCAATACGGTCGTTCATAAACTTAT
1 CATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGCCAATACGGTCGTTCATAAACTTAT
*
3212 TATGAATTTTGTGGGTTGCACACTTAGTGTCGATA
66 TATGAATTTCGTGGGTTGCACACTTAGTGTCGATA
3247 GTACACATAG
Statistics
Matches: 184, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
106 1 0.01
107 168 0.91
108 15 0.08
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (108 bp):
CATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGCCAATACGGTCGTTCATAAACTTAT
TATGAATTTCGTGGGTTGCACACTTAGTGTCGATATGGTCATT
Found at i:3215 original size:161 final size:161
Alignment explanation
Indices: 2933--3239 Score: 411
Period size: 161 Copynumber: 1.9 Consensus size: 161
2923 GTAGCCGATA
*
2933 CATAAACTTATTATGAATTGTGTGGGTTGCACACTTAGTGCCTATACGATCGTTCATAAACTTAT
1 CATAAACTTATTATGAATTGTGTGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACTTAT
* * ** *
2998 TATGAATTTCGTGGGTTGCACACTTAGTGATGATATGGTCATTCATAAAATATTATGAATTCCAT
66 TATGAATCTCATGGGTTGCACACTTAGTGACAATACGGTCATTCATAAAATATTATGAATTCCAT
3063 GGGGTGCACACTTAGTCCCGATACGGTCATT
131 GGGGTGCACACTTAGTCCCGATACGGTCATT
* * *
3094 CATAAACTTATTATGAATT-TCGTGGGTTGCACACTTAGTGTCGATATGGTCGTTCATAAACTTA
1 CATAAACTTATTATGAATTGT-GTGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACTTA
** * * * * **
3158 TTATGAATCT-ATTTGTTGCATACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTTT
65 TTATGAATCTCATGGGTTGCACACTTAGTGACAATACGGTCATTCATAAA-ATATTATGAATTCC
* *
3222 GTGGGTTGCACACTTAGT
129 ATGGGGTGCACACTTAGT
3240 GTCGATAGTA
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
160 31 0.25
161 94 0.75
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (161 bp):
CATAAACTTATTATGAATTGTGTGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACTTAT
TATGAATCTCATGGGTTGCACACTTAGTGACAATACGGTCATTCATAAAATATTATGAATTCCAT
GGGGTGCACACTTAGTCCCGATACGGTCATT
Found at i:5722 original size:93 final size:93
Alignment explanation
Indices: 5555--5757 Score: 257
Period size: 93 Copynumber: 2.2 Consensus size: 93
5545 CTGTCAAATG
* * * * **
5555 AGTTC-TCATTATGAACTTTCCATTGGAAATGTTAATCTCTCAAATGAGGTGTTGCTGATTAGAA
1 AGTTCTTCATTATGAACTCTCCACTGGAAATATTAATCCCTCAAATGAGGTGTCACTGATTAGAA
5619 ATGTCATAAATCTAGAAAAGGTTGAACA
66 ATGTCATAAATCTAGAAAAGGTTGAACA
* ** **
5647 AGTTCTTCATTATGAACTCTCTACTGGAAATATTGGTCCCTCATGTGAGGTGTCACTGATTCA-A
1 AGTTCTTCATTATGAACTCTCCACTGGAAATATTAATCCCTCAAATGAGGTGTCACTGATT-AGA
* *
5711 AATGTCGTAAATCTAGCAAAGGTTGAACA
65 AATGTCATAAATCTAGAAAAGGTTGAACA
*
5740 AGTTCTTCATTACGAACT
1 AGTTCTTCATTATGAACT
5758 TTTTCTCCAT
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
92 5 0.05
93 89 0.94
94 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (93 bp):
AGTTCTTCATTATGAACTCTCCACTGGAAATATTAATCCCTCAAATGAGGTGTCACTGATTAGAA
ATGTCATAAATCTAGAAAAGGTTGAACA
Found at i:5883 original size:21 final size:21
Alignment explanation
Indices: 5857--5903 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
5847 TATGGATTGA
5857 TTCTTTGCTAAAATCATATTC
1 TTCTTTGCTAAAATCATATTC
5878 TTCTTTGCTAAAATCATATTC
1 TTCTTTGCTAAAATCATATTC
5899 TTCTT
1 TTCTT
5904 CATGCAGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (21 bp):
TTCTTTGCTAAAATCATATTC
Found at i:6331 original size:74 final size:74
Alignment explanation
Indices: 6162--6720 Score: 629
Period size: 74 Copynumber: 7.5 Consensus size: 74
6152 TGAATTGAAA
* * * *
6162 TTTGTTTTAAGAAATACAATCTCGAGTGAGATAAAATTTCTTGTTTC-AGGTAAAAATTGTCTCA
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTC--GTTTCGA-GTGAAAACTGTCTCA
* *
6226 AGTGAGACAGAG
63 AGCGAGACAAAG
* * * * * * *
6238 TTT-TTTTAAGAAAAACAATCCCTTGTTAGATAAAATTTGGTTTAGAGTGAAAACTGTATCAAGT
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
6302 GAGACGAAG
66 GAGACAAAG
* * *
6311 TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAAATTGTCTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
* * *
6376 AATACAAAT
66 GAGACAAAG
* * * * **
6385 TTTGTTTTAATAAAAACTATCTCGATTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTTGAGC
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
6450 GAGACAAAG
66 GAGACAAAG
* * * *
6459 TTTGTTTTAAGAAAAATAAACTCAAGTGAGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
6524 GAGACGAAG
66 GAGACAAAG
* * * * * * *
6533 TTTATTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTCGTTTTGGGTGAAAACTATTTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
**
6598 GAGATGAAG
66 GAGACAAAG
* * * *
6607 TTTGTTTTAAGAAAAACTATCT-TGAGTGAGATAAAATTTCATTTCGAGTTAAAACTGTTTCAAG
1 TTTGTTTTAAGAAAAACAATCTCT-AGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAG
*
6671 TGAGACAAAG
65 CGAGACAAAG
* * *
6681 TTTGTTTTAGGAAAAACTATCTCGAGTGAGATAAAATTTC
1 TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTC
6721 TGATCTTTGC
Statistics
Matches: 410, Mismatches: 69, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
73 29 0.07
74 348 0.85
75 30 0.07
76 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (74 bp):
TTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
GAGACAAAG
Found at i:6374 original size:38 final size:38
Alignment explanation
Indices: 6265--6719 Score: 213
Period size: 36 Copynumber: 12.3 Consensus size: 38
6255 ATCCCTTGTT
* * *
6265 AGATAAAATTTGGTTTAGAGTGAAAACTGTATCAAGTG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
** * ** * **
6303 AGA-CGAAGTTTGTTTTAAG-AAAAACAATCTCAAGTG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* *
6339 AGATAAAATTTTGTTTCGAGTGAAAATTGTCTCAAG-C
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* * * * * *
6376 A-ATACAAATTTTGTTT-TAATAAAAACTATCTCGATTG
1 AGATA-AAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* ** *
6413 AGATAAAATTTCGTTTCGAGTGAAAACTGTCTTGAGCG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* * * * * **
6451 AGA-CAAAGTTTGTTT-TA-AGAAAAATAAACTCAAGTG
1 AGATAAAATTTTGTTTCGAGTGAAAACT-GTCTCAAGTG
*
6487 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGCG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
** * * * * *
6525 AGACGAAGTTTAT-TTT-AAG-AAAAACTATCTCGAGTG
1 AGATAAAATTT-TGTTTCGAGTGAAAACTGTCTCAAGTG
* * * * * *
6561 AGATAAAATTTCGTTTTGGGTGAAAACTATTTCAAGCG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* * ** * * **
6599 AGAT-GAAGTTTGTTTTAAG-AAAAACTATCTTGAGTG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
** * *
6635 AGATAAAATTTCATTTCGAGTTAAAACTGTTTCAAGTG
1 AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
* * * * *
6673 AGA-CAAAGTTTGTTT-TAG-GAAAAACTATCTCGAGTG
1 AGATAAAATTTTGTTTCGAGTG-AAAACTGTCTCAAGTG
6709 AGATAAAATTT
1 AGATAAAATTT
6720 CTGATCTTTG
Statistics
Matches: 294, Mismatches: 105, Indels: 37
0.67 0.24 0.08
Matches are distributed among these distances:
35 6 0.02
36 98 0.33
37 98 0.33
38 85 0.29
39 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (38 bp):
AGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGTG
Found at i:6511 original size:222 final size:222
Alignment explanation
Indices: 6162--6719 Score: 692
Period size: 222 Copynumber: 2.5 Consensus size: 222
6152 TGAATTGAAA
* * * *
6162 TTTGTTTTAAGAAATACAATCTCGAGTGAGATAAAATTTCTTGTTTC-AGGTAAAAATTGTCTCA
1 TTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTC--GTTTCGA-GTAAAAACTGTCTTA
* * * ** *
6226 AGTGAGACAGAGTTT-TTTTAAGAAAAACAATCCCTTGTTAGATAAAATTTGGTTTAGAGTGAAA
63 AGTGAGACAAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTGGTTTAGAGTGAAA
* * *
6290 ACTGTATCAAGTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTT
128 ACTGTATCAAGCGAGACGAAGTTTATTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCGTTT
* * * *
6355 CGAGTGAAAATTGTCTCAAGCAATACAAAT
193 CGAGTGAAAACTATCTCAAGCAAGACAAAG
* * * * *
6385 TTTGTTTTAATAAAAACTATCTCGATTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTTGAGC
1 TTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTCGTTTCGAGTAAAAACTGTCTTAAGT
* * *
6450 GAGACAAAGTTTGTTTTAAGAAAAATAAACTCAAGTGAGATAAAATTTTGTTTCGAGTGAAAACT
66 GAGACAAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTGGTTTAGAGTGAAAACT
* * * * *
6515 GTCTCAAGCGAGACGAAGTTTATTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTCGTTTTGG
131 GTATCAAGCGAGACGAAGTTTATTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCGTTTCGA
* * **
6580 GTGAAAACTATTTCAAGCGAGATGAAG
196 GTGAAAACTATCTCAAGCAAGACAAAG
* * *
6607 TTTGTTTTAAGAAAAACTATCTTGAGTGAGATAAAATTTCATTTCGAGTTAAAACTGT-TTCAAG
1 TTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTCGTTTCGAGTAAAAACTGTCTT-AAG
* *
6671 TGAGACAAAGTTTGTTTTAGGAAAAACT-ATCTCGAGTGAGATAAAATTT
65 TGAGACAAAGTTTGTTTTAAGAAAAA-TAATCTCAAGTGAGATAAAATTT
6720 CTGATCTTTG
Statistics
Matches: 287, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
221 31 0.11
222 219 0.76
223 37 0.13
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (222 bp):
TTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTCGTTTCGAGTAAAAACTGTCTTAAGT
GAGACAAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTGGTTTAGAGTGAAAACT
GTATCAAGCGAGACGAAGTTTATTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCGTTTCGA
GTGAAAACTATCTCAAGCAAGACAAAG
Found at i:8890 original size:29 final size:30
Alignment explanation
Indices: 8839--8899 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
8829 CAAAGCGCAC
8839 AACAAGACAAAAAGAAATCAAGTTAGTAGA
1 AACAAGACAAAAAGAAATCAAGTTAGTAGA
*
8869 AACAAGACAAAAAG-AATCAAGTTAGTTGA
1 AACAAGACAAAAAGAAATCAAGTTAGTAGA
8898 AA
1 AA
8900 TGATTAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.15
Consensus pattern (30 bp):
AACAAGACAAAAAGAAATCAAGTTAGTAGA
Found at i:13501 original size:39 final size:39
Alignment explanation
Indices: 13457--13569 Score: 108
Period size: 39 Copynumber: 2.9 Consensus size: 39
13447 AGTTAAAAGA
* * *
13457 AATAATTTGGATTGATATAGTGAAATAATTTTAA-AAATT
1 AATAATTTAGAATGATATAGTGAAACAA-TTTAAGAAATT
*
13496 AATAATTTAGAATGTTATAGTGAAACAATTTAAGAAATT
1 AATAATTTAGAATGATATAGTGAAACAATTTAAGAAATT
* * *
13535 AGA-AATTTAAAAT-ATCAT-GTGAAATAATTTGAGAA
1 A-ATAATTTAGAATGAT-ATAGTGAAACAATTTAAGAA
13570 TTAGGAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 21 0.33
39 41 0.65
40 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (39 bp):
AATAATTTAGAATGATATAGTGAAACAATTTAAGAAATT
Found at i:13557 original size:38 final size:40
Alignment explanation
Indices: 13473--13573 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 40
13463 TTGGATTGAT
* * *
13473 ATAGTGAAATAATTTTAA-AAATTA-ATAATTTAGAATGTT
1 ATAGTGAAATAA-TTTAAGAAATTAGATAATTTAAAATATC
*
13512 ATAGTGAAACAATTTAAGAAATTAGA-AATTTAAAATATC
1 ATAGTGAAATAATTTAAGAAATTAGATAATTTAAAATATC
*
13551 AT-GTGAAATAATTTGAG-AATTAG
1 ATAGTGAAATAATTTAAGAAATTAG
13574 GAATAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.11
38 18 0.33
39 29 0.54
40 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.36
Consensus pattern (40 bp):
ATAGTGAAATAATTTAAGAAATTAGATAATTTAAAATATC
Found at i:18234 original size:21 final size:20
Alignment explanation
Indices: 18204--18242 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18194 ACTTCAAATC
18204 CAAGCATCTAGA-AACACAAT
1 CAAGCATCTA-ATAACACAAT
18224 CAAGCATTCTAATAACACA
1 CAAGCA-TCTAATAACACA
18243 TTTAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (20 bp):
CAAGCATCTAATAACACAAT
Found at i:27786 original size:3 final size:3
Alignment explanation
Indices: 27778--28021 Score: 269
Period size: 3 Copynumber: 78.7 Consensus size: 3
27768 ATCACCATTT
* *
27778 TTA TTA TTA TTTA TTTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TCA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
27824 TTA TTTA TTTA TTA TTA TTT TTG TTA TTA TT- TTA TTA TTA TTA TCTGA
1 TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-T-A
* *
27872 CTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * *
27918 TTA TTTA GTTA TTA TTA TTG TTG TTA TTA TT- TTA TTA TTA TTA TCCGA
1 TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA
* *
27966 TTA TTA TTA TTA TTT TTA TTT 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
28014 TTA TTA TT
1 TTA TTA TT
28022 TCACTCATAT
Statistics
Matches: 212, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
2 6 0.03
3 178 0.84
4 25 0.12
5 3 0.01
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:27942 original size:94 final size:94
Alignment explanation
Indices: 27779--28015 Score: 372
Period size: 94 Copynumber: 2.5 Consensus size: 94
27769 TCACCATTTT
* *
27779 TATTATTATTTATTTATT-TTA-TTATTATTATTATTATTATCATCATTATTTATTTATTATTAT
1 TATTATTA-TTA-TTATTATTATTTATTATTATTATTATTATTATCATTATTTAGTTATTATTAT
* *
27842 TTTTGTTATTATTTTATTATTATTATCTGAC
64 TGTTGTTATTATTTTATTATTATTATCCGAC
27873 TATTATTATTATTATTATTATTTATTATTATTATTATTATTATCATTATTTAGTTATTATTATTG
1 TATTATTATTATTATTATTATTTATTATTATTATTATTATTATCATTATTTAGTTATTATTATTG
*
27938 TTGTTATTATTTTATTATTATTATCCGAT
66 TTGTTATTATTTTATTATTATTATCCGAC
* *
27967 TATTATTATTATTTTTATT-TTTATTATTATTATTATTATTATTATTATT
1 TATTATTATTATTATTATTATTTATTATTATTATTATTATTATCATTATT
28016 ATTATTTCAC
Statistics
Matches: 134, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
92 5 0.04
93 35 0.26
94 94 0.70
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (94 bp):
TATTATTATTATTATTATTATTTATTATTATTATTATTATTATCATTATTTAGTTATTATTATTG
TTGTTATTATTTTATTATTATTATCCGAC
Found at i:30619 original size:21 final size:21
Alignment explanation
Indices: 30595--30637 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
30585 CACTTTTAAC
30595 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
30616 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
30637 A
1 A
30638 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:33741 original size:16 final size:15
Alignment explanation
Indices: 33722--33771 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
33712 GCAAAAACCA
33722 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAA-C
33738 AAAAAAGAAGAA-AAC
1 AAAAAAGAA-AAGAAC
33753 AAAAAAG-AAAGAAC
1 AAAAAAGAAAAGAAC
33767 AAAAA
1 AAAAA
33772 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 8 0.25
16 11 0.34
17 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAC
Found at i:33748 original size:14 final size:14
Alignment explanation
Indices: 33722--33771 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
33712 GCAAAAACCA
33722 AAAAAAGAAAAGAAGC
1 AAAAAAG-AAAGAA-C
*
33738 AAAAAAGAAGAAAAC
1 AAAAAAGAA-AGAAC
33753 AAAAAAGAAAGAAC
1 AAAAAAGAAAGAAC
33767 AAAAA
1 AAAAA
33772 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 9 0.29
15 12 0.39
16 10 0.32
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAAC
Found at i:35451 original size:106 final size:106
Alignment explanation
Indices: 35326--36066 Score: 1257
Period size: 106 Copynumber: 7.0 Consensus size: 106
35316 GTTCCACTTG
* * * * *
35326 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
35391 CAGAGCCAATTTCAACTTCACAGGGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
35432 AGACAACACAAGTTTAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
35497 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
35538 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTTAATAAACAACTTCACAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* * *
35603 CAGAACCAATTTCAACTTCACAACGAAGGATATTTGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
35644 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
35709 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
35750 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTTGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
35815 CAGAGCCAATTTAAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
35856 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
35921 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
35962 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
36027 CAGAGCCAATTTCAATTTCACAGCGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
36067 GGAACAATAT
Statistics
Matches: 598, Mismatches: 37, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 598 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:36718 original size:254 final size:259
Alignment explanation
Indices: 36264--36778 Score: 970
Period size: 254 Copynumber: 2.0 Consensus size: 259
36254 CTTAAGACAG
36264 AAGACGATTCAGAGGCCACTCACCAAAAGCTTTAAGTCGGGTTTCAACTTCACGACGAAGGATAT
1 AAGACGATTCAGAGGCCACTCACCAAAAGCTTTAAGTCGGGTTTCAACTTCACGACGAAGGATAT
36329 CGTGCTCATAAGCTTTCAGTTCAACTCGACCTTACGATGAGGGAGTCATTTCATATTACACTCCA
66 CGTGCTCATAAGCTTTCAGTTCAACTCGACCTTACGATGAGGGAGTCATTTCA-ATTACACTCCA
36394 CGTCAGAGGATATTCAATAAGGACGAAATCTGTGTCTTTTAATCTTTGAACTATTTTCGTTACAC
130 CGTCAGAGGATATTCAATAAGGACGAAATCTGTGTCTTTTAATCTTTGAACTATTTTCGTTACAC
36459 GATAATGAGCAAAGAGGGGCAGCTGTAGACACCAAATTTCATCCCATTATAATA-TTAATATAAA
195 GATAATGAGCAAAGAGGGGCAGCTGTAGACACCAAATTTCATCCCATTATAATATTTAATATAAA
36523 AAGACGATTCAGAGGCCACTCACC-AAAGCTTTAAGTTC-GGTTTCAACTTCACGACGAAGGATA
1 AAGACGATTCAGAGGCCACTCACCAAAAGCTTTAAG-TCGGGTTTCAACTTCACGACGAAGGATA
36586 TCGTGCTCATAAGCTTTCAGTTCAACTCGACCTTACG-TGAGGGAGTCATTTC-A-TACACTCCA
65 TCGTGCTCATAAGCTTTCAGTTCAACTCGACCTTACGATGAGGGAGTCATTTCAATTACACTCCA
36648 CGTCAGAGGATATTCAATAAGGACGAAATCTGTGTCTTTTAATCTTTGAACTATTTTCGTTACAC
130 CGTCAGAGGATATTCAATAAGGACGAAATCTGTGTCTTTTAATCTTTGAACTATTTTCGTTACAC
36713 GATAATGAGCAAAGAGGGGCAGCTGTAGACACCAAATTTCATCCCATTATAATATTTAATATAAA
195 GATAATGAGCAAAGAGGGGCAGCTGTAGACACCAAATTTCATCCCATTATAATATTTAATATAAA
36778 A
1 A
36779 CATATTATAT
Statistics
Matches: 254, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
254 128 0.50
255 12 0.05
257 15 0.06
258 73 0.29
259 26 0.10
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (259 bp):
AAGACGATTCAGAGGCCACTCACCAAAAGCTTTAAGTCGGGTTTCAACTTCACGACGAAGGATAT
CGTGCTCATAAGCTTTCAGTTCAACTCGACCTTACGATGAGGGAGTCATTTCAATTACACTCCAC
GTCAGAGGATATTCAATAAGGACGAAATCTGTGTCTTTTAATCTTTGAACTATTTTCGTTACACG
ATAATGAGCAAAGAGGGGCAGCTGTAGACACCAAATTTCATCCCATTATAATATTTAATATAAA
Found at i:36791 original size:2 final size:2
Alignment explanation
Indices: 36780--36811 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
36770 AATATAAAAC
36780 AT AT -T AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36812 TATGTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36801 original size:13 final size:13
Alignment explanation
Indices: 36780--36810 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
36770 AATATAAAAC
*
36780 ATATTATATATAT
1 ATATAATATATAT
36793 ATATAATATATAT
1 ATATAATATATAT
36806 ATATA
1 ATATA
36811 TTATGTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:42634 original size:19 final size:19
Alignment explanation
Indices: 42607--42658 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
42597 ATGGTTTAAG
42607 CCTTCGAGAAGAGAACAAAA
1 CCTT-GAGAAGAGAACAAAA
42627 CCTTGAGAAGAGAACAAAA
1 CCTTGAGAAGAGAACAAAA
*
42646 CCTTTAGAA-AGAA
1 CCTTGAGAAGAGAA
42659 AATAGTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.13
Consensus pattern (19 bp):
CCTTGAGAAGAGAACAAAA
Found at i:47298 original size:24 final size:24
Alignment explanation
Indices: 47266--47316 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
47256 CTAGCCCAAA
47266 AGATAATTTTCCACTGCCTCATAT
1 AGATAATTTTCCACTGCCTCATAT
47290 AGATAATTTTCCACTGCCTCATAT
1 AGATAATTTTCCACTGCCTCATAT
47314 AGA
1 AGA
47317 CACTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (24 bp):
AGATAATTTTCCACTGCCTCATAT
Found at i:50635 original size:119 final size:119
Alignment explanation
Indices: 50388--50763 Score: 424
Period size: 119 Copynumber: 3.2 Consensus size: 119
50378 TTATAGATTC
* * * * * * * *
50388 AATCCATCACATAATGACGTGGATCGACATTTTCAATGGAATGGTTCAAAATGATAAGAACTCAT
1 AATCCATCACAAAAGGAGGTTGATCGACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCAT
* * * *
50453 CCGAAGAGGAA-AGAATAAGTTCATAATGAGAAGAACTAGTTCGACTTTTTGCTTA
66 CTGAA-A-GAAGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTCA
* **
50508 TATCCATCACAAAAGGAGGTTGATCGACATTTCCAATGGAAGGGTTCATAGAT-AGAAGAACTTG
1 AATCCATCACAAAAGGAGGTTGATCGACATTTCCAATGGAAGGGTTCATA-ATGAGAAGAACTCA
*
50572 TCTGAACA-AAGAGAATAAGTTAATAATGAGAAGAACTTGTTCGACCTTTTGCTCA
65 TCTGAA-AGAAGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTCA
50627 AATCCATCACAGAAA-GAGG-TGAATCGACATTTCCAATGG-AGGGTTCATAATGAGAAGAACTC
1 AATCCATCACA-AAAGGAGGTTG-ATCGACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTC
** * * * * *
50689 ATCTGAAAGGGGAAAATAAGTTCATAATGAGAAGAACTTATTCAACC-TTTCCTGA
64 ATCTGAAAGAAGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTCA
* *
50744 AAACCATCACAGAAGGAGGT
1 AATCCATCACAAAAGGAGGT
50764 GGTTCAACAC
Statistics
Matches: 218, Mismatches: 30, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
116 2 0.01
117 23 0.11
118 61 0.28
119 71 0.33
120 59 0.27
121 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (119 bp):
AATCCATCACAAAAGGAGGTTGATCGACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCAT
CTGAAAGAAGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTCA
Found at i:50870 original size:3 final size:3
Alignment explanation
Indices: 50864--50973 Score: 91
Period size: 3 Copynumber: 37.0 Consensus size: 3
50854 TTTTTATCAT
50864 TTA TTA TTA TTA GTTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * * ** *
50910 TT- TTA TTA TCA TCA TCA TTA TTA GTA TTA TT- TTA TTG TTA TCG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
50956 TTG TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
50974 ATTCACTCTT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
2 6 0.07
3 80 0.87
4 6 0.07
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:58359 original size:7 final size:6
Alignment explanation
Indices: 58344--58417 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
58334 AAATTTTTAA
* * * *
58344 CTTTTT C-TTTT CTCTTT CTTTATT AATTTTT CTCTTT CTCTTT CATTTTAT
1 CTTTTT CTTTTT CTTTTT CTTT-TT -CTTTTT CTTTTT CTTTTT C-TTTT-T
* *
58395 CTTTTA CTTTTT CTCTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTT
58418 ACTCATCTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
5 5 0.09
6 32 0.60
7 11 0.21
8 5 0.09
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:58369 original size:26 final size:25
Alignment explanation
Indices: 58337--58417 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 25
58327 CCCTCTTAAA
58337 TTTTTAACTTTTTCTTTTCTCTTTC
1 TTTTTAACTTTTTCTTTTCTCTTTC
58362 TTTATTAA-TTTTTCTCTTTCTCTTTC
1 TTT-TTAACTTTTTCT-TTTCTCTTTC
* * *
58388 ATTTTATCTTTTACTTTTTCTCTTTC
1 TTTTTAACTTTTTC-TTTTCTCTTTC
58414 TTTT
1 TTTT
58418 ACTCATCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 13 0.27
26 34 0.71
27 1 0.02
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTAACTTTTTCTTTTCTCTTTC
Found at i:59518 original size:26 final size:26
Alignment explanation
Indices: 59480--59533 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
59470 ACTAAGTGTG
*
59480 TATGGTGGGCACGACCTTATGTATAT
1 TATGGTGGACACGACCTTATGTATAT
*
59506 TATGGTGGACACGACCTTATGTGTAT
1 TATGGTGGACACGACCTTATGTATAT
59532 TA
1 TA
59534 GCACTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (26 bp):
TATGGTGGACACGACCTTATGTATAT
Found at i:63442 original size:26 final size:26
Alignment explanation
Indices: 63402--63460 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
63392 AAGGCACTAA
*
63402 GTGTA-TATAGTGGGCACGACCTTAT
1 GTGTATTATAGTGGGCACGACATTAT
*
63427 GTGTATTATGGTGGGCACGACATTAT
1 GTGTATTATAGTGGGCACGACATTAT
*
63453 ATGTATTA
1 GTGTATTA
63461 GCACTTCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (26 bp):
GTGTATTATAGTGGGCACGACATTAT
Found at i:65312 original size:17 final size:17
Alignment explanation
Indices: 65271--65334 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
65261 TGTTTATGAG
*
65271 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-CA
* *
65289 TGAATTGAAATCTGTCA
1 GGAATTGGAATCTGTCA
65306 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
65323 GGAATTGGAATC
1 GGAATTGGAATC
65335 CAATTCCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
17 28 0.68
18 13 0.32
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTCA
Found at i:68143 original size:13 final size:13
Alignment explanation
Indices: 68125--68149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68115 ACTATTTATT
68125 AAAATTTTAATTA
1 AAAATTTTAATTA
68138 AAAATTTTAATT
1 AAAATTTTAATT
68150 TTAATTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTTTAATTA
Found at i:74453 original size:105 final size:105
Alignment explanation
Indices: 74271--74623 Score: 517
Period size: 105 Copynumber: 3.4 Consensus size: 105
74261 TTTTTCGGAT
* * * * *
74271 GAGTTCTTCTCATTATGAACTCTTCTAGAAATATTGATTCACCTCTTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
* * * **
74336 GGAACAAGCTCTTTTTATTACAAACCTTCTCCTTTAAAAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
74376 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGATA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
74441 GGAACATGCTCTTCTCATTATGAACCTTCTCATTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
74481 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTTACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
74546 GGAACAAGTTCTTCTCATTGCGAACTTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
74586 GAGTTTTTCTCATTATGAACTCTTATGGAAATGTTGAT
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGAT
74624 CGGTTTAACC
Statistics
Matches: 222, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 222 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:75727 original size:52 final size:52
Alignment explanation
Indices: 75667--75861 Score: 198
Period size: 52 Copynumber: 3.8 Consensus size: 52
75657 TGAAAATCAT
75667 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* * * * * ** * *
75719 TATCAAGAAATCTCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTC-TAAAAACTCATTTGAAAA
* * * * * *
75772 CATTAAGAAACCCCT-AAAATTAGGTTTAGCTTCTTTCAAGAC-CATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAG-TT-TCTAAAAACTCATTTGAAAA
*
75824 CA-CGAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAA
75862 GTGTTCTTTT
Statistics
Matches: 111, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
50 4 0.04
51 12 0.11
52 64 0.58
53 30 0.27
54 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (52 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:76126 original size:36 final size:35
Alignment explanation
Indices: 76078--76191 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 35
76068 GAAAAAAATG
* *
76078 TCTCAAGCGAGACAAAGTCTGTTTTAAGGGAAACTA
1 TCTCAAGGGAGACAAA-TTTGTTTTAAGGGAAACTA
* * * *
76114 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTG
1 TCTCAAGGGAGAC-AAATTTGTTTTAAGGGAAACTA
*
76150 TCTCAAGGGAGACAAATTTTTTTTCAAGGGAAACATA
1 TCTCAAGGGAGACAAATTTGTTTT-AAGGGAAAC-TA
76187 T-TCAA
1 TCTCAA
76192 AGATTTTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
35 9 0.14
36 50 0.78
37 5 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (35 bp):
TCTCAAGGGAGACAAATTTGTTTTAAGGGAAACTA
Found at i:76361 original size:37 final size:37
Alignment explanation
Indices: 76320--76693 Score: 203
Period size: 37 Copynumber: 10.8 Consensus size: 37
76310 GAGATGATGC
*
76320 TTGTTTTGAGAGAAAAATATCTCAAGTGAAACAAAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
* * *
76357 TTGTTTTAAGAGAAAAATGTCTCAAGCGAGACAAAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
* * * * **
76394 TTGTTTTTA-AGAAAAACAACT---TTG-AA-ATTA-
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
*** *
76424 TTGTTCCGA-AGAAAAATGTCTCAAGTGAAACAAAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
76460 TTGTTTTAAGAGAAAAATGA-CTCAAGTGAAACAAAAT
1 TTGTTTTAAGAGAAAAAT-ATCTCAAGTGAAACAAAAT
* * *
76497 TTGTTTTAA-AGAAAAACAACT---TTG-----AAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
* **
76525 TTGTGTTCTGA-AGAAAAATGA-CTCAAGTGAAATGAAAT
1 TTGT-TT-TAAGAGAAAAAT-ATCTCAAGTGAAACAAAAT
* * *
76563 TTGTTTTAAGATAAAAATGTCTCAAGTGAGACAAAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
* * * *
76600 TTGTTTTTA-AGAAAAACAACT---TTG-----AAAT
1 TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
* ** *
76628 TTGTGTTCCGACGAAAAATGTCTCAAGTGAAACAAAAT
1 TTGTTTTAAGA-GAAAAATATCTCAAGTGAAACAAAAT
* *
76666 TAGTTTTAAGAGAAAAATGTCTCAAGTG
1 TTGTTTTAAGAGAAAAATATCTCAAGTG
76694 GGACGACATT
Statistics
Matches: 251, Mismatches: 54, Indels: 64
0.68 0.15 0.17
Matches are distributed among these distances:
28 18 0.07
29 3 0.01
30 34 0.14
31 3 0.01
32 1 0.00
33 11 0.04
34 2 0.01
35 3 0.01
36 34 0.14
37 123 0.49
38 19 0.08
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (37 bp):
TTGTTTTAAGAGAAAAATATCTCAAGTGAAACAAAAT
Found at i:76464 original size:103 final size:103
Alignment explanation
Indices: 76330--76693 Score: 604
Period size: 103 Copynumber: 3.5 Consensus size: 103
76320 TTGTTTTGAG
* *
76330 AGAAAAATATCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGCGAGACAAAATT
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATT
76395 TGTTTTTAAGAAAAACAACTTTGAAATTAT-TGTTCCGA
66 TGTTTTTAAGAAAAACAACTTTGAAATT-TGTGTTCCGA
* *
76433 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGACTCAAGTGAAACAAAATT
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATT
* *
76498 TGTTTTAAAGAAAAACAACTTTGAAATTTGTGTTCTGA
66 TGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGA
* ** *
76536 AGAAAAATGACTCAAGTGAAATGAAATTTGTTTTAAGATAAAAATGTCTCAAGTGAGACAAAATT
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATT
76601 TGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGA
66 TGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGA
* *
76639 CGAAAAATGTCTCAAGTGAAACAAAATTAGTTTTAAGAGAAAAATGTCTCAAGTG
1 AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGTG
76694 GGACGACATT
Statistics
Matches: 240, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
102 1 0.00
103 239 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (103 bp):
AGAAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATT
TGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGA
Found at i:80556 original size:6 final size:6
Alignment explanation
Indices: 80529--80600 Score: 90
Period size: 6 Copynumber: 12.0 Consensus size: 6
80519 AAATGTAATG
* * * * * *
80529 ATGCAA ATGCAG ATACAA ATGCAG ATGCAA ATACAT ATGCAA ATGCAG
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
80577 ATGCAA ATGCAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGCAA ATGCAA
80601 TGAAGGTGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:80600 original size:12 final size:12
Alignment explanation
Indices: 80528--80599 Score: 108
Period size: 12 Copynumber: 6.0 Consensus size: 12
80518 AAAATGTAAT
80528 GATGCAAATGCA
1 GATGCAAATGCA
*
80540 GATACAAATGCA
1 GATGCAAATGCA
*
80552 GATGCAAATACA
1 GATGCAAATGCA
*
80564 TATGCAAATGCA
1 GATGCAAATGCA
80576 GATGCAAATGCA
1 GATGCAAATGCA
*
80588 AATGCAAATGCA
1 GATGCAAATGCA
80600 ATGAAGGTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (12 bp):
GATGCAAATGCA
Found at i:82188 original size:20 final size:20
Alignment explanation
Indices: 82158--82199 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
82148 CATGGATATA
*
82158 AGTTGGTTTAA-GTAATGGT
1 AGTTGGTTTAATGAAATGGT
82177 AGTTGAGTTTAATGAAATGGT
1 AGTTG-GTTTAATGAAATGGT
82198 AG
1 AG
82200 GGGTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (20 bp):
AGTTGGTTTAATGAAATGGT
Found at i:88096 original size:21 final size:22
Alignment explanation
Indices: 88071--88111 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
88061 AGTATGTCCA
88071 GGGGGTATCGA-TTCCCCCTGG
1 GGGGGTATCGATTTCCCCCTGG
88092 GGGGGTATCGATTTCCCCCT
1 GGGGGTATCGATTTCCCCCT
88112 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.10, C:0.29, G:0.34, T:0.27
Consensus pattern (22 bp):
GGGGGTATCGATTTCCCCCTGG
Found at i:88772 original size:15 final size:15
Alignment explanation
Indices: 88754--88803 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
88744 CGAGGGTATT
88754 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
88769 GTAGTCCTTCGGGAT
1 GTAGTCCTTCGGGAC
88784 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
88799 GTAGT
1 GTAGT
88804 GGTTCTACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.30
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:92403 original size:15 final size:16
Alignment explanation
Indices: 92385--92418 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
92375 TTTGAATCTT
*
92385 TGAGGTTTA-GGGTTA
1 TGAGATTTAGGGGTTA
92400 TGAGATTTAGGGGTTA
1 TGAGATTTAGGGGTTA
92416 TGA
1 TGA
92419 AAAATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGAGATTTAGGGGTTA
Done.