Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001159.1 Hibiscus syriacus cultivar Beakdansim tig00002311_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: 73069
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2607 original size:15 final size:15
Alignment explanation
Indices: 2587--2621 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2577 AGACATTACT
2587 CGCCCCGCATCCGCC
1 CGCCCCGCATCCGCC
* *
2602 CGCCCCGTATCTGCC
1 CGCCCCGCATCCGCC
2617 CGCCC
1 CGCCC
2622 AGCTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.63, G:0.20, T:0.11
Consensus pattern (15 bp):
CGCCCCGCATCCGCC
Found at i:7997 original size:21 final size:22
Alignment explanation
Indices: 7961--8043 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 22
7951 AGTTAAAATC
* * *
7961 AATTTTATTATTTTTAGGATAT
1 AATTTTATAATATTTAGAATAT
*
7983 -ATTTTATAATATTTATAATAT
1 AATTTTATAATATTTAGAATAT
*
8004 AATTTTATAATACTTAGAAATATT
1 AATTTTATAATATTTAG-AATA-T
* *
8028 AATTTCATAAAATTTA
1 AATTTTATAATATTTA
8044 ATGGCGAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.35
22 14 0.29
23 4 0.08
24 14 0.29
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
AATTTTATAATATTTAGAATAT
Found at i:8012 original size:13 final size:14
Alignment explanation
Indices: 7987--8015 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7977 GGATATATTT
7987 TATAATATTTATAA
1 TATAATATTTATAA
8001 TATAAT-TTTATAA
1 TATAATATTTATAA
8014 TA
1 TA
8016 CTTAGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATAATATTTATAA
Found at i:9219 original size:23 final size:23
Alignment explanation
Indices: 9193--9276 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
9183 GACATATATA
9193 TGGTCCTTCGGGACAATTCTACG
1 TGGTCCTTCGGGACAATTCTACG
9216 TGGTCCTTCGGGACAATTCTACG
1 TGGTCCTTCGGGACAATTCTACG
*
9239 TGGTCATTCGGGACAATTCTACG
1 TGGTCCTTCGGGACAATTCTACG
* *
9262 CGGTTCTTCGGGACA
1 TGGTCCTTCGGGACA
9277 TTTTATATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATTCTACG
Found at i:13803 original size:416 final size:416
Alignment explanation
Indices: 13018--13850 Score: 1260
Period size: 416 Copynumber: 2.0 Consensus size: 416
13008 TAGAGCAAGT
* * ***
13018 CAAGTTGAGCCCCGACATGGCCTACAAAGAAGAGTCGATCCAAATTTTAGCTTTTGAGGTGAAAG
1 CAAGTTGAACCCCGACATGACCTACAAAGAAGAGTCGATCCAAATTTTAGCAAATGAGGTGAAAG
* *
13083 AGTTAAGAAATGAGAAAATTCATTTGGTAAAGGTGTTTTGGAGGAATCATGGAGTCGAGGAAGTT
66 AGTTAAGAAATAAGAAAATTCATTTGGTAAAGGTGTTTTGGAGGAATCATGGAGTCGAGGAAGCT
* * *
13148 ACTTGGGAAACCGAGGAAGACATGCAACTCTAGTATTCCCATCTTTTCTATCCAAGTAAAATTTT
131 ACTTGGGAAACCGAGGAAGACATGCAACTCCAATATTCCCATCTTTTCTATCCAAGTAAAATTTC
* *
13213 GATGAAGAAATTTTTATTAAAATGGGAGAGTTGTAATGCCCTGAATCTCAGGTTAGTAACTTGGG
196 GAGGAAGAAATTTTTATTAAAAGGGGAGAGTTGTAATGCCCTGAATCTCAGGTTAGTAACTTGGG
* *
13278 TCAACCCAAGAACTATATTTTAAGCCCAAATGACCTGTTAGAATAGCTTGGACCAAGTTTAGTTG
261 TCAACCCAAGAACCATATTTTAAGCCCAAATGACCTATTAGAATAGCTTGGACCAAGTTTAGTTG
* * * * * *
13343 AAATTAGGCTTGACTTGGGCCCAAGTGTTAGAATTGTGGGATGAGTTTTTGACAGAAAATAAAAG
326 AAATTAGGCCTGACTTGGGCCCAAATATTAGAATAGTAGGATGAGTTTTTAACAGAAAATAAAAG
13408 AGAAT-ATCCAAAAGAGTATTTTACCC
391 AGAATGA-CCAAAAGAGTATTTTACCC
13434 CAAGTTGAACCCCGACATGACCTACAAAGAAGAGTCGATCCAAATTTTAGCCAAAT-AGGTGAAA
1 CAAGTTGAACCCCGACATGACCTACAAAGAAGAGTCGATCCAAATTTTAG-CAAATGAGGTGAAA
* *
13498 TAGTTAAGAAATAAGAAAATTCCTTTGGTAAAGGTGTTTTGGAGGAATCATGGAGTCGAGGAAGC
65 GAGTTAAGAAATAAGAAAATTCATTTGGTAAAGGTGTTTTGGAGGAATCATGGAGTCGAGGAAGC
13563 TACTTGGGAAACCGAGGAAGACATGCAACTCCAATATTCCCATCTTTTCTATCCAAGTAAAATTT
130 TACTTGGGAAACCGAGGAAGACATGCAACTCCAATATTCCCATCTTTTCTATCCAAGTAAAATTT
* * * **
13628 CGAGGAATAAATTTTTATTAAGAGGGGAGAGTTGTAACT-CTCTGAATCTCAGGTTAGTAGTTTG
195 CGAGGAAGAAATTTTTATTAAAAGGGGAGAGTTGTAA-TGCCCTGAATCTCAGGTTAGTAACTTG
* * * * * *
13692 GGTTAACCCGAGACCCATATTTTGAGCCCAATTGTCCTATTAGAATAGCTTGGACCAAGTTTAGT
259 GGTCAACCCAAGAACCATATTTTAAGCCCAAATGACCTATTAGAATAGCTTGGACCAAGTTTAGT
* * **
13757 TGAAATT-GAGCCTGAGTTGGGCCCAAATATTGGAATAGTAGGATGAGTTTTTAAGGGAAAATAA
324 TGAAATTAG-GCCTGACTTGGGCCCAAATATTAGAATAGTAGGATGAGTTTTTAACAGAAAATAA
*
13821 AGGAGAATGACCAAAAGAGTATTTTACCC
388 AAGAGAATGACCAAAAGAGTATTTTACCC
13850 C
1 C
13851 TTTTAAATTT
Statistics
Matches: 375, Mismatches: 38, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
415 1 0.00
416 370 0.99
417 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (416 bp):
CAAGTTGAACCCCGACATGACCTACAAAGAAGAGTCGATCCAAATTTTAGCAAATGAGGTGAAAG
AGTTAAGAAATAAGAAAATTCATTTGGTAAAGGTGTTTTGGAGGAATCATGGAGTCGAGGAAGCT
ACTTGGGAAACCGAGGAAGACATGCAACTCCAATATTCCCATCTTTTCTATCCAAGTAAAATTTC
GAGGAAGAAATTTTTATTAAAAGGGGAGAGTTGTAATGCCCTGAATCTCAGGTTAGTAACTTGGG
TCAACCCAAGAACCATATTTTAAGCCCAAATGACCTATTAGAATAGCTTGGACCAAGTTTAGTTG
AAATTAGGCCTGACTTGGGCCCAAATATTAGAATAGTAGGATGAGTTTTTAACAGAAAATAAAAG
AGAATGACCAAAAGAGTATTTTACCC
Found at i:15165 original size:291 final size:291
Alignment explanation
Indices: 14641--15215 Score: 1141
Period size: 291 Copynumber: 2.0 Consensus size: 291
14631 TTACGACTGT
14641 GAAATTGAGTATCGCCTCGGTAAAGCTAATGTGGTTGCCGATGCGTTGAATCGCAATGTTATTAT
1 GAAATTGAGTATCGCCTCGGTAAAGCTAATGTGGTTGCCGATGCGTTGAATCGCAATGTTATTAT
14706 GGATTTGAGTGTTTTGTTTGCATGGATGAGTTTGTATGAGGATGGTAGTCTATTGGCTGAGTTAT
66 GGATTTGAGTGTTTTGTTTGCATGGATGAGTTTGTATGAGGATGGTAGTCTATTGGCTGAGTTAT
*
14771 ATATAGTTTCTACTCTTGTTTTGAAGATTTGTATGGAACAACATAACGATCCATTTTTGATCCAT
131 ATATAGTTTCTACTCTTGTTGTGAAGATTTGTATGGAACAACATAACGATCCATTTTTGATCCAT
14836 CAGATTAAAGAGGTTCAAAGTGTTGCATCTCAGGATTTTATAGTTGATCAGGATGGTGTTCTGTG
196 CAGATTAAAGAGGTTCAAAGTGTTGCATCTCAGGATTTTATAGTTGATCAGGATGGTGTTCTGTG
14901 TTTCAGAGGTTGGTACTGTATTTTTACAGGG
261 TTTCAGAGGTTGGTACTGTATTTTTACAGGG
14932 GAAATTGAGTATCGCCTCGGTAAAGCTAATGTGGTTGCCGATGCGTTGAATCGCAATGTTATTAT
1 GAAATTGAGTATCGCCTCGGTAAAGCTAATGTGGTTGCCGATGCGTTGAATCGCAATGTTATTAT
14997 GGATTTGAGTGTTTTGTTTGCATGGATGAGTTTGTATGAGGATGGTAGTCTATTGGCTGAGTTAT
66 GGATTTGAGTGTTTTGTTTGCATGGATGAGTTTGTATGAGGATGGTAGTCTATTGGCTGAGTTAT
15062 ATATAGTTTCTACTCTTGTTGTGAAGATTTGTATGGAACAACATAACGATCCATTTTTGATCCAT
131 ATATAGTTTCTACTCTTGTTGTGAAGATTTGTATGGAACAACATAACGATCCATTTTTGATCCAT
15127 CAGATTAAAGAGGTTCAAAGTGTTGCATCTCAGGATTTTATAGTTGATCAGGATGGTGTTCTGTG
196 CAGATTAAAGAGGTTCAAAGTGTTGCATCTCAGGATTTTATAGTTGATCAGGATGGTGTTCTGTG
15192 TTTCAGAGGTTGGTACTGTATTTT
261 TTTCAGAGGTTGGTACTGTATTTT
15216 GAGAAATTTT
Statistics
Matches: 283, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
291 283 1.00
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (291 bp):
GAAATTGAGTATCGCCTCGGTAAAGCTAATGTGGTTGCCGATGCGTTGAATCGCAATGTTATTAT
GGATTTGAGTGTTTTGTTTGCATGGATGAGTTTGTATGAGGATGGTAGTCTATTGGCTGAGTTAT
ATATAGTTTCTACTCTTGTTGTGAAGATTTGTATGGAACAACATAACGATCCATTTTTGATCCAT
CAGATTAAAGAGGTTCAAAGTGTTGCATCTCAGGATTTTATAGTTGATCAGGATGGTGTTCTGTG
TTTCAGAGGTTGGTACTGTATTTTTACAGGG
Found at i:17395 original size:36 final size:36
Alignment explanation
Indices: 17335--17437 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
17325 ATTTATCCAT
*
17335 TATCAGCTTTGGTACATTCTTGTATCAATGTTAGCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTAGCA
* * * *
17371 TATTAGCTTTGGTATATTAGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTAGCA
17407 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
17438 CCAGCACCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTAGCA
Found at i:18427 original size:227 final size:227
Alignment explanation
Indices: 18032--18489 Score: 853
Period size: 227 Copynumber: 2.0 Consensus size: 227
18022 AGTAAATTAG
* *
18032 AAAAAAATTAGTTTATTTTACTTAGTTTAGTTTTATCAGTATCTATGCATGAAAATAATATATTA
1 AAAAAAATTAGTTTATTTTACTTAGTTTAGTTTTATCAATATCTATGCATGAAAAGAATATATTA
18097 CATTATTATGTTTTTAAAACATTTCACGAAAAGACATGGTTTAGCAAAATTACTGATTAACAAAT
66 CATTATTATGTTTTTAAAACATTTCACGAAAAGACATGGTTTAGCAAAATTACTGATTAACAAAT
** *
18162 GAATTTATTTTCATCTTTCAAATAAATAAATTATAGTTGAGATATACTTTAAAATAGATTTTTTA
131 GAATTTATTTTCATCTGACAAAGAAATAAATTATAGTTGAGATATACTTTAAAATAGATTTTTTA
*
18227 AAAGTTAGAATAAGAGTGTTTTCAAATGAAAC
196 AAAGTTAGAATAAGAGGGTTTTCAAATGAAAC
18259 AAAAAAATTAGTTTATTTTACTTAGTTTAGTTTTATCAATATCTATGCATGAAAAGAATATATTA
1 AAAAAAATTAGTTTATTTTACTTAGTTTAGTTTTATCAATATCTATGCATGAAAAGAATATATTA
18324 CATTATTATGTTTTTAAAACATTTCACGAAAAGACATGGTTTAGCAAAATTACTGATTAACAAAT
66 CATTATTATGTTTTTAAAACATTTCACGAAAAGACATGGTTTAGCAAAATTACTGATTAACAAAT
*
18389 GAATTTATTTTCATGTGACAAAGAAATAAATTATAGTTGAGATATACTTTAAAATAGATTTTTTA
131 GAATTTATTTTCATCTGACAAAGAAATAAATTATAGTTGAGATATACTTTAAAATAGATTTTTTA
18454 AAAGTTAGAATAAGAGGGTTTTCAAATGAAAC
196 AAAGTTAGAATAAGAGGGTTTTCAAATGAAAC
18486 AAAA
1 AAAA
18490 TTTTTAGGCA
Statistics
Matches: 224, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
227 224 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (227 bp):
AAAAAAATTAGTTTATTTTACTTAGTTTAGTTTTATCAATATCTATGCATGAAAAGAATATATTA
CATTATTATGTTTTTAAAACATTTCACGAAAAGACATGGTTTAGCAAAATTACTGATTAACAAAT
GAATTTATTTTCATCTGACAAAGAAATAAATTATAGTTGAGATATACTTTAAAATAGATTTTTTA
AAAGTTAGAATAAGAGGGTTTTCAAATGAAAC
Found at i:25028 original size:36 final size:36
Alignment explanation
Indices: 24984--25086 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
24974 ATTTATCCAT
* *
24984 TATCAGCTTTGGTACATTCGTGTATTAATGTTATTA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
25020 TATTAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
25056 TATCAGCTTTGGTACATTTC-TGTATCAATGT
1 TATCAGCTTTGGTACA-TTCGTGTATCAATGT
25087 CCAGCACATT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 59 0.95
37 3 0.05
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:31426 original size:19 final size:17
Alignment explanation
Indices: 31398--31440 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
31388 ATAAATATTA
*
31398 AAATACTATTAAAATGAT
1 AAATATTATTAAAAT-AT
31416 AATATATTATTAAAATAT
1 AA-ATATTATTAAAATAT
31434 AAATATT
1 AAATATT
31441 TGTTCAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATATTATTAAAATAT
Found at i:31816 original size:30 final size:29
Alignment explanation
Indices: 31753--31821 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
31743 AATTTTTTGG
* * *
31753 AAAATGATTTACGTAAATTGAATTATCTG
1 AAAATAATTTACGTAAAATGAATTATCTA
31782 AAAATCAATTTACGTAAAATGAATTAT-TAA
1 AAAAT-AATTTACGTAAAATGAATTATCT-A
31812 AAAATAATTT
1 AAAATAATTT
31822 TTGAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (29 bp):
AAAATAATTTACGTAAAATGAATTATCTA
Found at i:32165 original size:16 final size:15
Alignment explanation
Indices: 32132--32174 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
32122 ATAAATATTA
*
32132 AATATTTTAATAATT
1 AATATTTTAATAAAT
*
32147 AATATTTTATTAAAAT
1 AATATTTTAAT-AAAT
*
32163 AATATGTTAATA
1 AATATTTTAATA
32175 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAAAT
Found at i:32353 original size:42 final size:42
Alignment explanation
Indices: 32292--32371 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
32282 TATATCGTGG
* * *
32292 AAAACCAATTATAGCTATCAGACATTGGAAAATATTTTCTGT
1 AAAACCAATTACAGCTATCAAACATTGGAAAACATTTTCTGT
*
32334 AAAACCAATTACAGGTATCAAACATTGGAAAACATTTT
1 AAAACCAATTACAGCTATCAAACATTGGAAAACATTTT
32372 TTCGAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (42 bp):
AAAACCAATTACAGCTATCAAACATTGGAAAACATTTTCTGT
Found at i:37644 original size:19 final size:19
Alignment explanation
Indices: 37616--37680 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 19
37606 AAAACCATAA
*
37616 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGAATCGATT
*
37634 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGATT
*
37653 CCCCTTCAAAGGGGGAATCGGTT
1 CCCC-T---AGGGGGAATCGATT
37676 CCCCT
1 CCCCT
37681 TCAAGGGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.10
19 16 0.40
20 1 0.03
22 1 0.03
23 18 0.45
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGATT
Found at i:37686 original size:22 final size:23
Alignment explanation
Indices: 37639--37689 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
37629 CGATTCCCCT
37639 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
37662 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
37684 AGGGGG
1 AGGGGG
37690 TATTGATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.20, C:0.24, G:0.37, T:0.20
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:43624 original size:11 final size:11
Alignment explanation
Indices: 43608--43637 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43598 AAATACTTTG
43608 TAAAATTATTT
1 TAAAATTATTT
43619 TAAAATTATTT
1 TAAAATTATTT
*
43630 TAATATTA
1 TAAAATTA
43638 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:44157 original size:35 final size:36
Alignment explanation
Indices: 44086--44157 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
44076 GGGGACGAGA
* * *
44086 AAAAATCGTTTATGCTAAACGGGGATGGGGATGGGG
1 AAAAATCGTTTATGCTAAACGGGGACGGCGACGGGG
*
44122 AAAAA-CGTTTATGTTAAACGGGGACGGCGACGGGG
1 AAAAATCGTTTATGCTAAACGGGGACGGCGACGGGG
44157 A
1 A
44158 CGAGTTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 27 0.84
36 5 0.16
ACGTcount: A:0.32, C:0.11, G:0.38, T:0.19
Consensus pattern (36 bp):
AAAAATCGTTTATGCTAAACGGGGACGGCGACGGGG
Found at i:44224 original size:2 final size:2
Alignment explanation
Indices: 44217--44319 Score: 76
Period size: 2 Copynumber: 55.0 Consensus size: 2
44207 ATAATTATTT
44217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
44256 TA AA TT TA -A TT TA AA T- TA AA TA TA TA TA TA TA TA -A TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
44295 TA TA TA TT TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
44320 CCCGGCCCGA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
1 7 0.09
2 69 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44291 original size:41 final size:41
Alignment explanation
Indices: 44234--44312 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
44224 ATATATATAT
44234 ATATATATATATATAATATTAATAAATTTAATTTAAATTAA
1 ATATATATATATATAATATTAATAAATTTAATTTAAATTAA
* *
44275 ATATATATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATATATATAATATTAATAAATTTAATTTAAAT
44313 ATATATACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
ATATATATATATATAATATTAATAAATTTAATTTAAATTAA
Found at i:44467 original size:25 final size:25
Alignment explanation
Indices: 44426--44476 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
44416 AATCCCCGCA
* *
44426 GTTTTTTAAGCGAGGACGGGTACGG
1 GTTTTTTAAACGAGGACGGGGACGG
*
44451 GTTTTTTAAACGGGGACGGGGACGG
1 GTTTTTTAAACGAGGACGGGGACGG
44476 G
1 G
44477 AGGACCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.43, T:0.25
Consensus pattern (25 bp):
GTTTTTTAAACGAGGACGGGGACGG
Found at i:45662 original size:60 final size:60
Alignment explanation
Indices: 45549--45662 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
45539 ATAACCTTCA
* * * *
45549 TTTTAAATTAGTCCTTAAACTTTAAAATACTTTAGTTTCATCCCTAAGTTATGACTCTCG
1 TTTTAAATCAATCCTTAAACTTTAAAATACTTTAATTTCATCCCTAAGCTATGACTCTCG
* **
45609 TTTTAAATCAATCCTTGAACTTTTGAATA-TTCTAATTTCATCCCTACA-CTATGA
1 TTTTAAATCAATCCTTAAACTTTAAAATACTT-TAATTTCATCCCTA-AGCTATGA
45663 AACTTTCTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 42 0.93
61 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (60 bp):
TTTTAAATCAATCCTTAAACTTTAAAATACTTTAATTTCATCCCTAAGCTATGACTCTCG
Found at i:45994 original size:60 final size:60
Alignment explanation
Indices: 45839--46007 Score: 164
Period size: 60 Copynumber: 2.8 Consensus size: 60
45829 GTATATACAT
* * * *
45839 ATAGTTTA-GGATGAAATTAGAATATTCAAAAAGTTTGGGGACCAATGTAGAATGAAGGTC
1 ATAGTTTAGGGATGAAATTGGAATATT-AAAAAGTTTGAGGACCAATTTAGAATGAAGATC
* * ** * * * *
45899 ATATTTTGGGGATGATGTTGAAATGTTCAAGAGTTTGAGGACCAATTTAGAATGATA-ATC
1 ATAGTTTAGGGATGAAATTGGAATATTAAAAAGTTTGAGGACCAATTTAGAATGA-AGATC
* *
45959 ATAGTTTAGGGATGAAATTGGAATATTTAAAAGTTT-ATGGATCAATTTA
1 ATAGTTTAGGGATGAAATTGGAATATTAAAAAGTTTGA-GGACCAATTTA
46008 AACCGAGAGT
Statistics
Matches: 85, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
59 1 0.01
60 70 0.82
61 14 0.16
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTGGAATATTAAAAAGTTTGAGGACCAATTTAGAATGAAGATC
Found at i:49946 original size:21 final size:21
Alignment explanation
Indices: 49920--49968 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
49910 GTTTAAAATT
*
49920 GATTAATTCATTGAATTAATC
1 GATTAATTCATCGAATTAATC
49941 GATTAATTCATCGAATTAATC
1 GATTAATTCATCGAATTAATC
49962 GATTAAT
1 GATTAAT
49969 CAAAAATATT
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:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (21 bp):
GATTAATTCATCGAATTAATC
Found at i:51747 original size:21 final size:20
Alignment explanation
Indices: 51701--51754 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
51691 GATTCTGACT
*
51701 ATCGCATTGCGATTTTCTAA
1 ATCGCATTGCGATTTTCGAA
*
51721 ATTCGCGTTGCGATTTTCCGAA
1 A-TCGCATTGCGATTTT-CGAA
*
51743 ATCGCAATGCGA
1 ATCGCATTGCGA
51755 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCGAA
Found at i:51789 original size:20 final size:20
Alignment explanation
Indices: 51766--51836 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
51756 TATGTAAATT
*
51766 GCAATGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
51786 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
51806 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
* *
51826 ACAATGCGATT
1 GCAACGCGATT
51837 TTCAAAGCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:52039 original size:22 final size:22
Alignment explanation
Indices: 52014--52056 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52004 GGCGACATCC
52014 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
52036 GTCCCCATCTCTGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
52057 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:52468 original size:20 final size:20
Alignment explanation
Indices: 52440--52492 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
52430 CGATTTTAGT
*
52440 TTCGCGTTGCAATAGTCAAA
1 TTCGTGTTGCAATAGTCAAA
* **
52460 TTCGTGTTGCGATAGTCATT
1 TTCGTGTTGCAATAGTCAAA
52480 TTCGTGTTGCAAT
1 TTCGTGTTGCAAT
52493 TTTCATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
TTCGTGTTGCAATAGTCAAA
Found at i:52498 original size:20 final size:20
Alignment explanation
Indices: 52460--52515 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
52450 AATAGTCAAA
**
52460 TTCGTGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
52480 TTCGTGTTGCAATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
52500 TTTGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
52516 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.54
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:54263 original size:18 final size:18
Alignment explanation
Indices: 54240--54285 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
54230 TTTACTCGTA
54240 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
54258 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
54276 ATTTCACTTA
1 ATTTCACTTA
54286 TATTGCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:54464 original size:20 final size:20
Alignment explanation
Indices: 54437--54504 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
54427 TAGTTTACTT
54437 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
54457 TTGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
54477 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
54497 TCGCAACG
1 TCGCAACG
54505 AGAGAATCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:54572 original size:18 final size:19
Alignment explanation
Indices: 54530--54576 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
54520 GCGATTCTCT
54530 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
54550 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
54568 TGTTGCGAT
1 CGTTGCGAT
54577 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:55093 original size:21 final size:21
Alignment explanation
Indices: 55067--55123 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
55057 CTCACATGTC
55067 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
55088 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
55109 ATCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
55124 CCTATCATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCCT
Found at i:55177 original size:21 final size:21
Alignment explanation
Indices: 55066--55193 Score: 107
Period size: 21 Copynumber: 6.1 Consensus size: 21
55056 ACTCACATGT
55066 CATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
*
55087 TATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
* **
55108 TATCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTCC
** *
55129 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
55150 CACCGTTCAAGAGGCCACTGT
1 CATCGTTCAAGAGGCCCCTCC
* *
55171 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
55192 CA
1 CA
55194 ACATTCTAGA
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 2 0.02
21 82 0.98
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:56763 original size:20 final size:20
Alignment explanation
Indices: 56738--56791 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
56728 AGGTACACTT
*
56738 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
56758 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
56778 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
56792 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:56807 original size:19 final size:20
Alignment explanation
Indices: 56785--56827 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
56775 AAATCGCAAC
*
56785 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
56804 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
56824 GCGA
1 GCGA
56828 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:56843 original size:34 final size:34
Alignment explanation
Indices: 56800--56970 Score: 146
Period size: 34 Copynumber: 4.9 Consensus size: 34
56790 AGTCAATTCG
* *
56800 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* * *
56834 CGTTGCGATAGTCGAATACCCGTTGCGATAATTAAATTCA
1 CGTTGCGATAGTCAAATACGCGTTGCG---ATT---TTCT
* * *
56874 CGCTGCGATAGTCAAATTCGCGTTGCGATTTTTT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
56908 CGTTGCGATAGTCAAATTCGCGTTGTGATTTT-T
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* * * *
56941 GAGTTGTGATAATCAAATTCGCGTTGCGAT
1 -CGTTGCGATAGTCAAATACGCGTTGCGAT
56971 AGTCAAATTC
Statistics
Matches: 114, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
33 1 0.01
34 81 0.71
37 6 0.05
40 26 0.23
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:56880 original size:20 final size:20
Alignment explanation
Indices: 56857--56902 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
56847 GAATACCCGT
*
56857 TGCGATAATTAAATTCACGC
1 TGCGATAATCAAATTCACGC
* * *
56877 TGCGATAGTCAAATTCGCGT
1 TGCGATAATCAAATTCACGC
56897 TGCGAT
1 TGCGAT
56903 TTTTTCGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
TGCGATAATCAAATTCACGC
Found at i:56971 original size:20 final size:20
Alignment explanation
Indices: 56943--56998 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
56933 TGATTTTTGA
* *
56943 GTTGTGATAATCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
56963 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
56983 GTTGCGATAGTCAAAT
1 GTTGCGATAGTCAAAT
56999 GAATGTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:57192 original size:18 final size:18
Alignment explanation
Indices: 57169--57203 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57159 AAGCCGGTTG
*
57169 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
57187 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
57204 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:60539 original size:21 final size:21
Alignment explanation
Indices: 60513--60586 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
60503 ATAGTTAGAA
60513 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
60534 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
* * **
60555 TAGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCTAAAT
*
60576 TCGCAATGCGA
1 TCGCATTGCGA
60587 ATATGTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCTAAAT
Found at i:60601 original size:20 final size:20
Alignment explanation
Indices: 60576--60626 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
60566 TTTTCCGAAT
60576 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
60596 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
60616 TCGCAATGCGA
1 TCGCAATGCGA
60627 TTCTAACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:60638 original size:20 final size:20
Alignment explanation
Indices: 60615--60688 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
60605 GAATATGTAA
* *
60615 ATCGCAATGCGATTCTAACT
1 ATCGCAACGCGATTCTGACT
*
60635 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
60655 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
60675 ATCGCAATGCGATT
1 ATCGCAACGCGATT
60689 TTCAAAGCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:60639 original size:40 final size:40
Alignment explanation
Indices: 60595--60686 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
60585 GAATATGTAA
*
60595 ATCGCAATGCGAATATGTA-AATCGCAATGCGATTCTAACT
1 ATCGCAATGCGAATATG-ACAATCGCAACGCGATTCTAACT
* * * * * *
60635 ATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATATGACAATCGCAACGCGATTCTAACT
60675 ATCGCAATGCGA
1 ATCGCAATGCGA
60687 TTTTCAAAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
ATCGCAATGCGAATATGACAATCGCAACGCGATTCTAACT
Found at i:60903 original size:22 final size:22
Alignment explanation
Indices: 60864--60905 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
60854 GGCGACATCT
*
60864 GTCCCCATCTCCGACGAAATTA
1 GTCCCCATCTCAGACGAAATTA
60886 GTCCCCATCTCTAG-CGAAAT
1 GTCCCCATCTC-AGACGAAAT
60906 CCGTCTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.26, C:0.36, G:0.14, T:0.24
Consensus pattern (22 bp):
GTCCCCATCTCAGACGAAATTA
Found at i:61351 original size:20 final size:20
Alignment explanation
Indices: 61300--61353 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
61290 GCGATTTTAG
* *
61300 TTTCGCGTTGCAATAGTCAA
1 TTTCGTGTTGCGATAGTCAA
* *
61320 ATTCGTGTTGCGATAGTCAT
1 TTTCGTGTTGCGATAGTCAA
61340 TTTCGTGTTGCGAT
1 TTTCGTGTTGCGAT
61354 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGTGTTGCGATAGTCAA
Found at i:61363 original size:20 final size:20
Alignment explanation
Indices: 61298--61363 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
61288 ATGCGATTTT
* *
61298 AGTTTCGCGTTGCAATAGTCA
1 AGTTTCGTGTTGCGATAGT-A
* *
61319 A-ATTCGTGTTGCGATAGTC
1 AGTTTCGTGTTGCGATAGTA
* **
61338 ATTTTCGTGTTGCGATTTTA
1 AGTTTCGTGTTGCGATAGTA
61358 AGTTTC
1 AGTTTC
61364 AGAAACTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
AGTTTCGTGTTGCGATAGTA
Found at i:63100 original size:18 final size:18
Alignment explanation
Indices: 63077--63126 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
63067 TTTACTCGTA
63077 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63095 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63113 ATTTCACTTAGATT
1 ATTTCACTTAGATT
63127 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:63405 original size:18 final size:18
Alignment explanation
Indices: 63343--63427 Score: 107
Period size: 18 Copynumber: 4.5 Consensus size: 18
63333 GCGATTCTCT
*
63343 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTC--ATTCG
63363 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA--TTCG
63383 CGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCATTCG
*
63401 TGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCATTCG
*
63419 TGTTGCGAT
1 CGTTGCGAT
63428 TTTAAGTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
18 31 0.51
20 30 0.49
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (18 bp):
CGTTGCGATAGTCATTCG
Found at i:64005 original size:21 final size:21
Alignment explanation
Indices: 63914--64018 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
63904 GACTCACCTG
*
63914 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
63936 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
63956 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
63977 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
63998 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
64019 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:64011 original size:42 final size:42
Alignment explanation
Indices: 63911--64021 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
63901 CCCGACTCAC
* * * *
63911 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
63953 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
63995 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
64022 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:65459 original size:14 final size:14
Alignment explanation
Indices: 65421--65482 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
65411 TTGCTTGTTT
*
65421 AATTGATTTGCAAA
1 AATTGATTTGTAAA
65435 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
65449 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
65464 TATTGATGTGTAAA
1 AATTGATTTGTAAA
65478 TAATT
1 -AATT
65483 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:65606 original size:20 final size:20
Alignment explanation
Indices: 65581--65634 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
65571 AGGTACACTT
*
65581 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
65601 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
65621 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
65635 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:65650 original size:19 final size:20
Alignment explanation
Indices: 65628--65670 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
65618 AAATCGCAAC
*
65628 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
65647 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
65667 GCGA
1 GCGA
65671 TTTTCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:65704 original size:20 final size:20
Alignment explanation
Indices: 65679--65841 Score: 89
Period size: 20 Copynumber: 8.8 Consensus size: 20
65669 GATTTTCTCA
* * *
65679 TTGCGATAGTCGAATACCCG
1 TTGCGATAGTCAAATTCACG
*
65699 TTGCGATAATCAAATTCACG
1 TTGCGATAGTCAAATTCACG
* *
65719 CTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCACG
**
65739 TTGCGAT--T----TTTTCG
1 TTGCGATAGTCAAATTCACG
*
65753 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCACG
* * *
65773 TTGTGAT--T---TTTGA-G
1 TTGCGATAGTCAAATTCACG
* * *
65787 TTGTGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCACG
*
65807 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCACG
*
65827 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
65842 GATGTGTAAT
Statistics
Matches: 109, Mismatches: 22, Indels: 24
0.70 0.14 0.15
Matches are distributed among these distances:
14 19 0.17
15 2 0.02
16 2 0.02
18 2 0.02
19 2 0.02
20 82 0.75
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCACG
Found at i:65763 original size:34 final size:34
Alignment explanation
Indices: 65643--65813 Score: 146
Period size: 34 Copynumber: 4.9 Consensus size: 34
65633 AGTCAATTCG
* * *
65643 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * * * *
65677 CATTGCGATAGTCGAATACCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* *
65717 CGCTGCGATAGTCAAATTCGCGTTGCGATTTTTT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
65751 CGTTGCGATAGTCAAATTCGCGTTGTGATTTT-T
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * *
65784 GAGTTGTGATAATCAAATTCGCGTTGCGAT
1 -CGTTGCGATAGTCAAATTCGCGTTGCGAT
65814 AGTCAAATTC
Statistics
Matches: 112, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
33 1 0.01
34 82 0.73
36 1 0.01
38 1 0.01
40 27 0.24
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:66032 original size:18 final size:18
Alignment explanation
Indices: 66009--66043 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65999 AAGCCGGTTG
*
66009 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
66027 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
66044 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:68270 original size:24 final size:23
Alignment explanation
Indices: 68204--68262 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
68194 TCGAAACATC
68204 ATCAAAATTCGAGTATGACCAAG
1 ATCAAAATTCGAGTATGACCAAG
* * *
68227 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTA-TGACCAAG
*
68251 ATCAAATTTCGA
1 ATCAAAATTCGA
68263 ATACTGACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (23 bp):
ATCAAAATTCGAGTATGACCAAG
Found at i:68810 original size:19 final size:20
Alignment explanation
Indices: 68781--68821 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
68771 AACATTTCCC
68781 ATGACCCCTCCAAAACACAA
1 ATGACCCCTCCAAAACACAA
68801 ATGA-CCCTCCAAAACACAA
1 ATGACCCCTCCAAAACACAA
68820 AT
1 AT
68822 TTATCCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.46, C:0.37, G:0.05, T:0.12
Consensus pattern (20 bp):
ATGACCCCTCCAAAACACAA
Found at i:69109 original size:20 final size:20
Alignment explanation
Indices: 69084--69186 Score: 134
Period size: 20 Copynumber: 5.2 Consensus size: 20
69074 AAATTCAGTG
*
69084 TTGCGACAATCAGAATCGCA
1 TTGCGATAATCAGAATCGCA
* *
69104 TTGCGATAGTCAGAATCGCG
1 TTGCGATAATCAGAATCGCA
*
69124 TTGCGATAATCAGAATCGCG
1 TTGCGATAATCAGAATCGCA
*
69144 TTGCGATAGTCAGAATCGCA
1 TTGCGATAATCAGAATCGCA
* * *
69164 TTGCGATAGTCATAATCGAA
1 TTGCGATAATCAGAATCGCA
69184 TTG
1 TTG
69187 TGATTTACAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (20 bp):
TTGCGATAATCAGAATCGCA
Found at i:69128 original size:40 final size:40
Alignment explanation
Indices: 69083--69250 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
69073 GAAATTCAGT
*
69083 GTTGCGACAATCAGAATCGCATTGCGATAGTCAGAATCGC
1 GTTGCGATAATCAGAATCGCATTGCGATAGTCAGAATCGC
*
69123 GTTGCGATAATCAGAATCGCGTTGCGATAGTCAGAATCGC
1 GTTGCGATAATCAGAATCGCATTGCGATAGTCAGAATCGC
* * * * * * * *
69163 ATTGCGATAGTCATAATCGAATTGTGAT-TTACATATTCGC
1 GTTGCGATAATCAGAATCGCATTGCGATAGT-CAGAATCGC
* * * * *
69203 ATTGCGA-ATTTGGAAAATCGCAATGCGATAGTCAGAATCGC
1 GTTGCGATA-AT-CAGAATCGCATTGCGATAGTCAGAATCGC
69244 GTTGCGA
1 GTTGCGA
69251 ATCTGAAACT
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
39 2 0.02
40 75 0.73
41 25 0.24
42 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (40 bp):
GTTGCGATAATCAGAATCGCATTGCGATAGTCAGAATCGC
Found at i:69597 original size:12 final size:12
Alignment explanation
Indices: 69580--69617 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
69570 CCGCCCTGAT
69580 TACCCGACCCGA
1 TACCCGACCCGA
*
69592 TACCCGACTCGA
1 TACCCGACCCGA
*
69604 TACCCGGCCCGA
1 TACCCGACCCGA
69616 TA
1 TA
69618 AATATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (12 bp):
TACCCGACCCGA
Found at i:69701 original size:15 final size:15
Alignment explanation
Indices: 69640--69720 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
69630 AATTATTATA
69640 TATATATATATAATAT
1 TATATATATATAAT-T
* *
69656 TA-ATAAATTTAATT
1 TATATATATATAATT
* * *
69670 TAAAT-TA-AAAATA
1 TATATATATATAATT
69683 TATATATA-AT-ATT
1 TATATATATATAATT
69696 TATATAT-T-TAATT
1 TATATATATATAATT
*
69709 TAAATATATATA
1 TATATATATATA
69721 CCCGGCCCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
12 1 0.02
13 25 0.51
14 8 0.16
15 13 0.27
16 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATAATT
Done.