Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003695.1 Hibiscus syriacus cultivar Beakdansim tig00007900_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: 59557
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1094 original size:3 final size:3
Alignment explanation
Indices: 1086--1128 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1076 ATCATGACAA
1086 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1129 CCTAAGAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1115 original size:20 final size:20
Alignment explanation
Indices: 1090--1128 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1080 TGACAAAATA
1090 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
1110 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
1129 CCTAAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:4291 original size:39 final size:39
Alignment explanation
Indices: 4236--4352 Score: 127
Period size: 39 Copynumber: 3.0 Consensus size: 39
4226 TTAAATGTTT
*
4236 ATTTATAATTT-TTAAATTATTTCACTC-TAATATTGT-AA
1 ATTT-TAATTTCTTAAATTATTTCAC-CATAATATTCTAAA
*
4274 ATTCTTAATTTCTTAAATT-TTGCTACCATAATATTCTAAA
1 ATT-TTAATTTCTTAAATTATTTC-ACCATAATATTCTAAA
*
4314 ATTTTAATTTCTTAAATTATTTCA-CATTAACATTCTAAA
1 ATTTTAATTTCTTAAATTATTTCACCA-TAATATTCTAAA
4353 TAATTTTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
38 15 0.22
39 45 0.66
40 8 0.12
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (39 bp):
ATTTTAATTTCTTAAATTATTTCACCATAATATTCTAAA
Found at i:4508 original size:2 final size:2
Alignment explanation
Indices: 4501--4527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4491 ATTTTAGAAT
4501 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4528 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5527 original size:31 final size:31
Alignment explanation
Indices: 5492--5554 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5482 CAGGACATTT
*
5492 CGAGTTTTTTCATCCTAAACCGAATTTCAAC
1 CGAGTTTTTTCATCATAAACCGAATTTCAAC
5523 CGAGTTTTTTCATCATAAACCGAATTTCAAC
1 CGAGTTTTTTCATCATAAACCGAATTTCAAC
5554 C
1 C
5555 TAATCTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (31 bp):
CGAGTTTTTTCATCATAAACCGAATTTCAAC
Found at i:7020 original size:14 final size:14
Alignment explanation
Indices: 7001--7043 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
6991 ACTCAAAACC
7001 CATCTTTACTCTTT
1 CATCTTTACTCTTT
7015 CATCTTTACTCTTT
1 CATCTTTACTCTTT
7029 CATCTTTACTCTTT
1 CATCTTTACTCTTT
7043 C
1 C
7044 CATGTCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.56
Consensus pattern (14 bp):
CATCTTTACTCTTT
Found at i:7687 original size:71 final size:71
Alignment explanation
Indices: 7571--7713 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
7561 AATTTATTAT
7571 AAATCGAAAACGTTAGTGATCAATTTTTTATTTTTAAAATTTTAGCGAGGAAAACGAAAACTTAC
1 AAATCGAAAACGTTAGTGATCAATTTTTTATTTTTAAAATTTTAGCGAGGAAAACGAAAACTTAC
7636 TCAAAG
66 TCAAAG
*
7642 AAATCGAAAATGTTAGTGATCAATTTTTTATTTTTAAAATTTTAGCGAGGAAAACGAAAACTTAC
1 AAATCGAAAACGTTAGTGATCAATTTTTTATTTTTAAAATTTTAGCGAGGAAAACGAAAACTTAC
7707 TCAAAG
66 TCAAAG
7713 A
1 A
7714 TGTGACCGTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (71 bp):
AAATCGAAAACGTTAGTGATCAATTTTTTATTTTTAAAATTTTAGCGAGGAAAACGAAAACTTAC
TCAAAG
Found at i:17037 original size:21 final size:23
Alignment explanation
Indices: 17002--17062 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
16992 TTGGTGCAGA
*
17002 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
17022 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
17045 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
17063 CAGGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:17069 original size:21 final size:21
Alignment explanation
Indices: 17043--17082 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17033 CCCCCTTTGA
*
17043 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
17064 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
17083 TGGGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:17496 original size:25 final size:27
Alignment explanation
Indices: 17449--17498 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17439 AGAATTTTCC
*
17449 AAAAAATTTTAAATTTTCGAAATTAAA
1 AAAAAATGTTAAATTTTCGAAATTAAA
17476 AAAAAATGTT-AATTTTC-AAATTA
1 AAAAAATGTTAAATTTTCGAAATTA
17499 TTGTGTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 9 0.41
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAAAATGTTAAATTTTCGAAATTAAA
Found at i:23065 original size:26 final size:25
Alignment explanation
Indices: 23036--23087 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
23026 TAAATTTATG
23036 TATTCAAA-GAATAATTATCTTGTTAA
1 TATTCAAATGAA-AATTATCTT-TTAA
*
23062 TATTCAAATTAAAATTATCTTTTAA
1 TATTCAAATGAAAATTATCTTTTAA
23087 T
1 T
23088 TTACTACAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 17 0.71
27 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (25 bp):
TATTCAAATGAAAATTATCTTTTAA
Found at i:29744 original size:87 final size:87
Alignment explanation
Indices: 29590--29752 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
29580 TATGTTATAT
** * * *
29590 CATTTAACCGTTAATATTATCAAGCACAATAACATATTAAGTAACACTTATATAATGTAGTATGT
1 CATTTAACCGGAAATATTATCAAACACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
29655 AACACTTATATAATAAAATAGG
66 AACACTTATATAATAAAATAGG
* ** *
29677 CATTTAACCGGAAATATTATCAAATACAATAACATATTTGGTAGCACTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAACACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
*
29742 AACGCTTATAT
66 AACACTTATAT
29753 TAACATATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAACACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
AACACTTATATAATAAAATAGG
Found at i:30627 original size:182 final size:182
Alignment explanation
Indices: 30131--31800 Score: 2259
Period size: 182 Copynumber: 9.3 Consensus size: 182
30121 TGTTGACCTA
* * * *
30131 TTTTCTCATATTTTTAGCTGTTATAATGTTATCGATCGATATATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* *
30196 TTTAGGCGCTATAACTTCTTCTCTTTAAAATTCAGAAAGTGTCGATACTTATATTAAATTATTGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* **
30261 CACTTTCAACATAT-TCGGTAGAGTTTTACCGGTTTTGTCATTTTGAGATTGG
131 CACTTTCAACATATCT-GGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* *
30313 TTTTGTCATATTTTTA-CATGTTATATTGTTATAGATCGATACATTTT-TTAAAGTATCGACACT
1 TTTTGTCATATTTTTAGC-TGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACT
* *
30376 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTCA-AAAGTGTCGATACTTATATTAAAGTATC
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAA-TTCAGAAAGTGTCGATACTTATATTAAATTATC
* *
30440 GACACTTTCAACATATCTGGTAG-TTATTTACCTGTTTTGTCATTTTGAGACCGG
129 GACACTTTCAACATATCTGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACCGG
*
30494 TTTTATCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
30559 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
30624 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * * * *
30676 TTTTGTCATATTTTTACCTGTTATATTATTATTGATCGATACATTTT-TTAAAGTATCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * * * * *
30740 TATAAGCGCTATAACTTCTTCTCTTTTTATTTCTA-AAAGTGTCTATACTTATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTC-AGAAAGTGTCGATACTTATATTAAATTATCG
* * * * * *
30804 ACACTGTCAACATATCCT-ATAG-TTATTTGCCTGTTTTGTCATTTTGAGACCGA
130 ACACTTTCAACATAT-CTGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACCGG
* *
30857 TTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * *
30922 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTATAGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
30987 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * * * ** *
31039 TTTTGTCATATTTTTACCTTTTATATTGTTATGGATCAATACATTTTTTTAAAGTATCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * * *
31104 TATAGACGCTATAACTTCTTCTCTTTTAAATTCCA-AAA-AGT-G----------TAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCG
* *
31156 ACACTTTCAACATAT-TCGGTAG-TTATTTACCTGTTTTGTCATTTTGAGACCGG
130 ACACTTTCAACATATCT-GGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACCGG
*
31209 TTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
31274 TTTAGGCGCTATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
31339 CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * * *
31391 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-TTAAAGTATCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * * * *
31455 TATAGGCGCTATAACTTCTTCTCTTTTTATTTCTA-AAAGTGTCTATACTTATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTC-AGAAAGTGTCGATACTTATATTAAATTATCG
* * * * * *
31519 ACACTGTCAACATATCCT-ATAG-TTATTTGCCTGTTTTGTTATTTTGAGACCGG
130 ACACTTTCAACATAT-CTGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACCGG
* * *
31572 TTTTTTCATATTTTTAACTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCAACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
31637 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * *
31702 CACTATCAACATAT-TCGGTAGCGTTTTACCGGTTTTGTCATTTTAAGATCGG
131 CACTTTCAACATATCT-GGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * *
31754 TTTTGTCATATTTTTA-CTTGTAATATTGCTATGGAGT-GATACATTTT
1 TTTTGTCATATTTTTAGC-TGTTATATTGTTATAGA-TCGATACATTTT
31801 TCATTTGTAT
Statistics
Matches: 1311, Mismatches: 134, Indels: 86
0.86 0.09 0.06
Matches are distributed among these distances:
169 3 0.00
170 145 0.11
171 2 0.00
172 1 0.00
180 5 0.00
181 482 0.37
182 665 0.51
183 8 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
Found at i:30801 original size:363 final size:364
Alignment explanation
Indices: 30131--31801 Score: 2696
Period size: 363 Copynumber: 4.6 Consensus size: 364
30121 TGTTGACCTA
* * * *
30131 TTTTCTCATATTTTTAGCTGTTATAATGTTATCGATCGATATATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * *
30196 TTTAGGCGCTATAACTTCTTCTCTTTAAAATTCAGAAAGTGTCGATACTTATATTAAATTATTGA
66 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * **
30261 CACTTTCAACATATTCGGTAGAGTTTTACCGGTTTTGTCATTTTGAGATTGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* * *
30326 TTACATGTTATATTGTTATAGATCGATACATTTTTTAAAGTATCGACACTTTATAGGCGCTATAA
196 TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAA
* *
30391 CTTCTTCTCTTTTAAATTTC-AAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATA
261 CTTCTTCTCTTTTAAATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
*
30455 T-CTGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
326 TCCT-ATAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
*
30494 TTTTATCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
30559 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
30624 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* *
30689 TTACCTGTTATATTATTATTGATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAA
196 TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAA
*
30754 CTTCTTCTCTTTT-TATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
261 CTTCTTCTCTTTTAAATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
* *
30818 TCCTATAGTTATTTGCCTGTTTTGTCATTTTGAGACCGA
326 TCCTATAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
* *
30857 TTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* *
30922 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTATAGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
30987 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* *
31052 TTACCTTTTATATTGTTATGGATCAATACATTTTTTTAAAGTATCGACACTTTAT-AGACGCTAT
196 TTACCTGTTATATTGTTATGGATCGATACA-TTTTTTAAAGTATCGACACTTTATAAG-CGCTAT
* * *
31116 AACTTCTTCTCTTTTAAATTCCAAAAAGTG-------------TAAAGTATCGACACTTTCAACA
259 AACTTCTTCTCTTTTAAATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACA
* **
31168 TATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
324 TATCCTATAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
*
31209 TTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
31274 TTTAGGCGCTATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
31339 CACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
*
31404 TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAGGCGCTATAA
196 TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAA
*
31469 CTTCTTCTCTTTT-TATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
261 CTTCTTCTCTTTTAAATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
* *
31533 TCCTATAGTTATTTGCCTGTTTTGTTATTTTGAGACCGG
326 TCCTATAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
* * *
31572 TTTTTTCATATTTTTAACTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCAACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
31637 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * * *
31702 CACTATCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTAAGATCGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* * *
31767 TTACTTGTAATATTGCTATGGAGT-GATACATTTTT
196 TTACCTGTTATATTGTTATGGA-TCGATACATTTTT
31802 CATTTGTATC
Statistics
Matches: 1217, Mismatches: 71, Indels: 40
0.92 0.05 0.03
Matches are distributed among these distances:
350 11 0.01
351 45 0.04
352 274 0.23
362 5 0.00
363 823 0.68
364 48 0.04
365 11 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (364 bp):
TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
TTACCTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAA
CTTCTTCTCTTTTAAATTTCTAAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATA
TCCTATAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
Found at i:31430 original size:715 final size:718
Alignment explanation
Indices: 30125--31801 Score: 2846
Period size: 715 Copynumber: 2.3 Consensus size: 718
30115 ACTTTATGTT
* * * *
30125 GACCTATTTTCTCATATTTTTAGCTGTTATAATGTTATCGATCGATATATTTTCATAAAGTGTCG
1 GACCGATTTTCTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
* *
30190 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTAAAATTCAGAAAGTGTCGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* * *
30255 TATTGACACTTTCAACATATTCGGTAGAGTTTTACCGGTTTTGTCATTTTGAGATTGGTTTTGTC
131 TATCGACACTTTCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGATCGGTTTTGTC
* * * *
30320 ATATTTTTACATGTTATATTGTTATAGATCGATACA-TTTTTTAAAGTATCGACACTTTATAGGC
196 ATATTTTTACCTTTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGAC
* *
30384 GCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTC
261 GCTATAACTTCTTCTCTTTTAAATTCCAAAAGAGTCG---------TTAAAGTATCGACACTTTC
30449 AACATATCTGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTAGCTG
317 AACATATCTGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTAGCTG
*
30514 TTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTT
382 TTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTT
30579 CTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTA
447 CTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTA
*
30644 GCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTATTATT
512 GCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTATTATG
30709 GATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAACTTCTTCTCTTTTTATTTCT
577 GATCGATACATTTTTTAAAGTATCGACACTTTATAAGCGCTATAACTTCTTCTCTTTTTATTTCT
30774 AAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATATCCTATAGTTATTTGCCTGTT
642 AAAAGTGTCTATACTTATATTAAAGTATCGACACTGTCAACATATCCTATAGTTATTTGCCTGTT
30839 TTGTCATTTTGA
707 TTGTCATTTTGA
* * *
30851 GACCGATTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTCATAAAGTGTCG
1 GACCGATTTTCTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
* *
30916 ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTATAGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* *
30981 TATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTC
131 TATCGACACTTTCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGATCGGTTTTGTC
*
31046 ATATTTTTACCTTTTATATTGTTATGGATCAATACATTTTTTTAAAGTATCGACACTTTATAGAC
196 ATATTTTTACCTTTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGAC
31111 GCTATAACTTCTTCTCTTTTAAATTCCAAAA-AGT-G-TAAAGTATCGACACTTTCAACATAT-T
261 GCTATAACTTCTTCTCTTTTAAATTCCAAAAGAGTCGTTAAAGTATCGACACTTTCAACATATCT
*
31172 CGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTAGCTGTTATATTA
326 -GGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTAGCTGTTATATTA
*
31237 TTATAGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTTTTCTCTTTTA
390 TTATAGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTA
*
31302 AATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCTGGTAGCGTTTTA
455 AATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTA
*
31367 CCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
520 CCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATA
*
31432 CATTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTTATTTCTAAAAGTGT
585 CATTTTTTAAAGTATCGACACTTTATAAGCGCTATAACTTCTTCTCTTTTTATTTCTAAAAGTGT
*
31497 CTATACTTATATTAAAGTATCGACACTGTCAACATATCCTATAGTTATTTGCCTGTTTTGTTATT
650 CTATACTTATATTAAAGTATCGACACTGTCAACATATCCTATAGTTATTTGCCTGTTTTGTCATT
31562 TTGA
715 TTGA
* * * *
31566 GACCGGTTTTTTCATATTTTTAACTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCA
1 GACCGATTTTCTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
31631 ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* *
31696 TATCGACACTATCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTAAGATCGGTTTTGTC
131 TATCGACACTTTCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGATCGGTTTTGTC
* *
31761 ATATTTTTA-CTTGTAATATTGCTATGGAGT-GATACATTTTT
196 ATATTTTTACCTT-TTATATTGTTATGGA-TCGATACATTTTT
31802 CATTTGTATC
Statistics
Matches: 902, Mismatches: 45, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
714 4 0.00
715 625 0.69
716 1 0.00
725 1 0.00
726 214 0.24
727 57 0.06
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (718 bp):
GACCGATTTTCTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
ACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
TATCGACACTTTCAACATATTCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGATCGGTTTTGTC
ATATTTTTACCTTTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGAC
GCTATAACTTCTTCTCTTTTAAATTCCAAAAGAGTCGTTAAAGTATCGACACTTTCAACATATCT
GGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTAGCTGTTATATTAT
TATAGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAA
ATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATAC
ATTTTTTAAAGTATCGACACTTTATAAGCGCTATAACTTCTTCTCTTTTTATTTCTAAAAGTGTC
TATACTTATATTAAAGTATCGACACTGTCAACATATCCTATAGTTATTTGCCTGTTTTGTCATTT
TGA
Found at i:31974 original size:20 final size:20
Alignment explanation
Indices: 31951--31989 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31941 ATGTATCTGG
*
31951 TAATATCGTATATTAACTGA
1 TAATACCGTATATTAACTGA
31971 TAATACCGTATATTAACTG
1 TAATACCGTATATTAACTG
31990 TATATTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
TAATACCGTATATTAACTGA
Found at i:33242 original size:36 final size:36
Alignment explanation
Indices: 33127--33268 Score: 223
Period size: 36 Copynumber: 3.9 Consensus size: 36
33117 ACCAATTTAG
33127 GTTTCATAAGAAATTTGAGTATTTTTTTCTTATTAAAT
1 GTTTCATAAGAAATTTGAGTA--TTTTTCTTATTAAAT
* *
33165 GTTTCATAAGAAATTTGGGTATTTTTCTTAATTAAAG
1 GTTTCATAAGAAATTTGAGTATTTTTCTT-ATTAAAT
*
33202 GTTTCATAAGAAATTTGAGCATTTTTCTTATTAAAT
1 GTTTCATAAGAAATTTGAGTATTTTTCTTATTAAAT
33238 GTTTCATAAGAAATTTGAGTA-TTTTCTTATT
1 GTTTCATAAGAAATTTGAGTATTTTTCTTATT
33269 GAATATTAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
35 10 0.10
36 34 0.35
37 33 0.34
38 20 0.21
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (36 bp):
GTTTCATAAGAAATTTGAGTATTTTTCTTATTAAAT
Found at i:33249 original size:73 final size:73
Alignment explanation
Indices: 33125--33266 Score: 241
Period size: 73 Copynumber: 1.9 Consensus size: 73
33115 TCACCAATTT
* *
33125 AGGTTTCATAAGAAATTTGAGTATTTTTTTCTTATTAAATGTTTCATAAGAAATTTGGGTATTTT
1 AGGTTTCATAAGAAATTTGAGCA-TTTTTTCTTATTAAATGTTTCATAAGAAATTTGAGTA-TTT
33190 TCTTAATTAA
64 TCTTAATTAA
33200 AGGTTTCATAAGAAATTTGAGCA-TTTTTCTTATTAAATGTTTCATAAGAAATTTGAGTATTTTC
1 AGGTTTCATAAGAAATTTGAGCATTTTTTCTTATTAAATGTTTCATAAGAAATTTGAGTATTTTC
33264 TTA
66 TTA
33267 TTGAATATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 8 0.12
73 35 0.54
75 22 0.34
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (73 bp):
AGGTTTCATAAGAAATTTGAGCATTTTTTCTTATTAAATGTTTCATAAGAAATTTGAGTATTTTC
TTAATTAA
Found at i:34348 original size:574 final size:575
Alignment explanation
Indices: 33253--34393 Score: 2016
Period size: 574 Copynumber: 2.0 Consensus size: 575
33243 ATAAGAAATT
*
33253 TGAGTATTTTCTTATTGAATATTAATTGAAGTTGTAAATTGACAATTGATTATAATATTGATGAT
1 TGAGTATTTTCTTATTGAAGATTAATTGAAGTTGTAAATTGACAATTGATTATAATATTGATGAT
* * *
33318 ATATTGATTGTTAATTGATAAAGAACAATGATATGATCCCGGTTTGATGGTGAATGACGTTGCCT
66 AGATTGATTGTTAATTGATAAAGAACAATGATATGATCCCAGTTTGATGGTGAATGACGTTGCCG
* *
33383 TGGACAAGTGAAGTAGCCAAGGCAAGTAAAGTTAATGACGTTACCGTGACAAGTGAAGTTGTCAT
131 TGGACAAGTGAAGTAGCCAAGGAAAGTAAAGTTAATAACGTTACCGTGACAAGTGAAGTTGTCAT
*
33448 GGAAAGTGTAGGATCACATCAAACAATTTTGGATCATGATTTAAATCTTTAATATTTTAGTGAGT
196 GGAAAGTGTAGGATCACATCAAACAATTTTGGATCATGATTTAAATATTTAATATTTTAGTGAGT
*
33513 GTGTTAGTCACCAAAGCGACCCACTCAAAATTCATTAAATAATTTATATTATATTTATAAATGTT
261 GTGTTAGTCACCAAAGCGACCCACTCAAAATTCATCAAATAATTTATATTATATTTATAAATGTT
*
33578 TATTTGATGTAGCATCATAAATTACATTTAAAAATAATAAACATTTATAGTTATTAAAATGTAGT
326 TATTTGATGTAGCATCATAAATGACATTTAAAAATAATAAACATTTATAGTTATTAAAATGTAGT
* *
33643 AATTCGATTACCCAAATGTAGGTCTTACTCATGGTTAATAATAATTGAAGTAGGTTATGAACTTT
391 AATACGATTACCCAAAGGTAGGTCTTACTCATGGTTAATAATAATTGAAGTAGGTTATGAACTTT
*
33708 GTTTAATTAATATATAAGTTACATCCAAAGATGACTTGTATGTTAAAGTAAATTTAATGGTTGAC
456 GTTTAATTAATATATAAGTTACATCCAAAGATGACTTGTATGTTAAAGTAAATTTAATGATTGAC
*
33773 CTTATATATTTTATAAGAATGATACATGTTTGATGATTATTGGTTGTAAATTTAA
521 CTTATATATGTTATAAGAATGATACATGTTTGATGATTATTGGTTGTAAATTTAA
* *
33828 TGAGTGTTTTCTTATTGAAGATTAATTGAAGTTGTAAATTGACAATTTATTATAATATTGATGAT
1 TGAGTATTTTCTTATTGAAGATTAATTGAAGTTGTAAATTGACAATTGATTATAATATTGATGAT
* * *
33893 AGATTGATTGTTAATTGATAAGGAACAATGATATGATCCCAGTTTGATGGTTAATGGCGTTGCCG
66 AGATTGATTGTTAATTGATAAAGAACAATGATATGATCCCAGTTTGATGGTGAATGACGTTGCCG
* *
33958 T-GACAAGTGAAGTTGCCAAGGAAAGTAAAGTTAATAACGTTACCGTGACAAGTGAAGTTGTCGT
131 TGGACAAGTGAAGTAGCCAAGGAAAGTAAAGTTAATAACGTTACCGTGACAAGTGAAGTTGTCAT
*
34022 GGCAAGTGTAGGATCACAT-AAACCAATTTTGGATCATGATTTAAATATTTAATATTTTAGTGAG
196 GGAAAGTGTAGGATCACATCAAA-CAATTTTGGATCATGATTTAAATATTTAATATTTTAGTGAG
* * *
34086 TGTGTTAGTCACCAAAGCGACCCACTCGAAATTCATCAAATGATTTATATTATGTTTATAAATGT
260 TGTGTTAGTCACCAAAGCGACCCACTCAAAATTCATCAAATAATTTATATTATATTTATAAATGT
34151 TTATTTGATGTAGCATCATAAATGACATTTAAAAATAATAAACATTTATAGTTATTAAAATGTAG
325 TTATTTGATGTAGCATCATAAATGACATTTAAAAATAATAAACATTTATAGTTATTAAAATGTAG
*
34216 TAATACGATTACCCAAAGGTAGGTCTTATTCATGGTTAATAATAATTGAAGTAGGTTATGAACTT
390 TAATACGATTACCCAAAGGTAGGTCTTACTCATGGTTAATAATAATTGAAGTAGGTTATGAACTT
*
34281 TGTTTGATTAATATATAAGTTACATCCAAAGATGACTTGTATGTTAAAGTAAATTTAATGATTGA
455 TGTTTAATTAATATATAAGTTACATCCAAAGATGACTTGTATGTTAAAGTAAATTTAATGATTGA
*
34346 CCTTATATATGTTATAAGAATGATGCATGTTTGATGATTATTGGTTGT
520 CCTTATATATGTTATAAGAATGATACATGTTTGATGATTATTGGTTGT
34394 GTTTAGATTT
Statistics
Matches: 538, Mismatches: 27, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
573 3 0.01
574 413 0.77
575 122 0.23
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (575 bp):
TGAGTATTTTCTTATTGAAGATTAATTGAAGTTGTAAATTGACAATTGATTATAATATTGATGAT
AGATTGATTGTTAATTGATAAAGAACAATGATATGATCCCAGTTTGATGGTGAATGACGTTGCCG
TGGACAAGTGAAGTAGCCAAGGAAAGTAAAGTTAATAACGTTACCGTGACAAGTGAAGTTGTCAT
GGAAAGTGTAGGATCACATCAAACAATTTTGGATCATGATTTAAATATTTAATATTTTAGTGAGT
GTGTTAGTCACCAAAGCGACCCACTCAAAATTCATCAAATAATTTATATTATATTTATAAATGTT
TATTTGATGTAGCATCATAAATGACATTTAAAAATAATAAACATTTATAGTTATTAAAATGTAGT
AATACGATTACCCAAAGGTAGGTCTTACTCATGGTTAATAATAATTGAAGTAGGTTATGAACTTT
GTTTAATTAATATATAAGTTACATCCAAAGATGACTTGTATGTTAAAGTAAATTTAATGATTGAC
CTTATATATGTTATAAGAATGATACATGTTTGATGATTATTGGTTGTAAATTTAA
Found at i:36757 original size:15 final size:15
Alignment explanation
Indices: 36737--36765 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36727 ATATGTTGCG
36737 AGTGGTCAATTGCTA
1 AGTGGTCAATTGCTA
36752 AGTGGTCAATTGCT
1 AGTGGTCAATTGCT
36766 GAGGGAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (15 bp):
AGTGGTCAATTGCTA
Found at i:37090 original size:21 final size:21
Alignment explanation
Indices: 37061--37101 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37051 TATAAGAGGA
*
37061 TGAAGAAGAAAGAGATGAAGG
1 TGAAGAAGAAAGAAATGAAGG
* *
37082 TGAATAAGAACGAAATGAAG
1 TGAAGAAGAAAGAAATGAAG
37102 TATCAACACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.32, T:0.12
Consensus pattern (21 bp):
TGAAGAAGAAAGAAATGAAGG
Found at i:37203 original size:71 final size:71
Alignment explanation
Indices: 37087--37227 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 71
37077 GAAGGTGAAT
* * * *
37087 AAGAACGAAATGAAGTATCAACACTTTCGATTCAAGTGAACAGAAGGAAGCATCG-GCACTTTTG
1 AAGAACGAAAGGAAGCATCAACACTTTCGATTCAAATGAACAGAAGGAAGCAT-GAGCACTTTCG
37151 ATTCAAG
65 ATTCAAG
**
37158 AAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAATGAACAGAAGGAAGCATGAGCACTTTCGA
1 AAGAACGAAAGGAAGCATCAACACTTTCGATTCAAATGAACAGAAGGAAGCATGAGCACTTTCGA
37223 TTCAA
66 TTCAA
37228 ATGTTCATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 1 0.02
71 62 0.98
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.21
Consensus pattern (71 bp):
AAGAACGAAAGGAAGCATCAACACTTTCGATTCAAATGAACAGAAGGAAGCATGAGCACTTTCGA
TTCAAG
Found at i:37228 original size:35 final size:35
Alignment explanation
Indices: 37108--37230 Score: 178
Period size: 35 Copynumber: 3.5 Consensus size: 35
37098 GAAGTATCAA
*
37108 CACTTTCGATTCAAGTGAACAGAAGGAAGCATCGG
1 CACTTTCGATTCAAATGAACAGAAGGAAGCATCGG
* *
37143 CACTTTTGATTCAAGAAGAAC-GAAAGGAAGCATCGG
1 CACTTTCGATTCAA-ATGAACAG-AAGGAAGCATCGG
37179 CACTTTCGATTCAAATGAACAGAAGGAAGCAT-GAG
1 CACTTTCGATTCAAATGAACAGAAGGAAGCATCG-G
37214 CACTTTCGATTCAAATG
1 CACTTTCGATTCAAATG
37231 TTCATCTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
34 1 0.01
35 47 0.59
36 31 0.39
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (35 bp):
CACTTTCGATTCAAATGAACAGAAGGAAGCATCGG
Found at i:41180 original size:117 final size:117
Alignment explanation
Indices: 41011--41303 Score: 419
Period size: 117 Copynumber: 2.5 Consensus size: 117
41001 TCCCCGAAAC
** *
41011 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAAT
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGAGCCTGAAGTAAT
* * * *
41075 AACGTCTCCATCCAGTCGCTTCC-ATAACTACAATGTGTAGGTTCCCCAGTACA
65 AACGTCCCCATCCAGCCAC-TCCAATAACTACAATGTGTAGGTTCCCCAGAACA
* *
41128 ATACACCTACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGTCTGAAGTAATA
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGAAGTAATA
* * * *
41193 ACTTCCCCATCCAGCCACTCCAATCACTATAATGTGTAGGTTCCCCAGAACC
66 ACGTCCCCATCCAGCCACTCCAATAACTACAATGTGTAGGTTCCCCAGAACA
* *
41245 ATACACCCACCTGCACACCAGTAAGGACTAACCCTGAGCACACAGCAAAGGAGCCTGAA
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGAA
41304 ATACTTCCCT
Statistics
Matches: 157, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
116 4 0.03
117 153 0.97
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.18
Consensus pattern (117 bp):
ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGAAGTAATA
ACGTCCCCATCCAGCCACTCCAATAACTACAATGTGTAGGTTCCCCAGAACA
Found at i:42341 original size:30 final size:29
Alignment explanation
Indices: 42253--42351 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
42243 TTTTTAAAAT
*
42253 AATTACCAAAATAGCACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
** *
42282 AATTCTAAAAATAGGACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
*
42311 AATTCCCAGAATAGCACCCATTTT-GAATT-
1 AATTCCCAAAATAGCA-CC-TTTTCGAATTA
42340 AATTCCCAAAAT
1 AATTCCCAAAAT
42352 GTCATCTGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 48 0.81
30 7 0.12
31 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCTTTTCGAATTA
Found at i:43782 original size:22 final size:23
Alignment explanation
Indices: 43749--43793 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
43739 CTGGACCCAA
43749 AGTTTTTCTATCATGCAACTTTG
1 AGTTTTTCTATCATGCAACTTTG
43772 AGTTTTT-TATCATGCAACTTTG
1 AGTTTTTCTATCATGCAACTTTG
43794 TCCAACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (23 bp):
AGTTTTTCTATCATGCAACTTTG
Found at i:48675 original size:117 final size:117
Alignment explanation
Indices: 48495--48796 Score: 405
Period size: 117 Copynumber: 2.6 Consensus size: 117
48485 TTTTATATAT
* *
48495 TTCCCC-GAAACATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCT-GAGG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAG-TAAAGG
* * *
48557 AGCCTGTAGTAATAACGTCTCCATCCAGTCGCTTCC-ATAACTACAATGTATAGG
64 AGCCTGCAGTAATAACGTCCCCATCCAGTCAC-TCCAATAACTACAATGTATAGG
*
48611 TTCCCCAGTACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGTAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGTAAAGGAG
* * * * *
48676 CATGCAGTAATAACTTCCCCATCCAGTCACTCCAATCACTATAATGTGTAGG
66 CCTGCAGTAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTATAGG
* * * **
48728 TTTCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCTTGAGCACACAACAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGTAAAGGAG
48793 CCTG
66 CCTG
48797 AAATACTTCC
Statistics
Matches: 164, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
116 11 0.07
117 153 0.93
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (117 bp):
TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGTAAAGGAG
CCTGCAGTAATAACGTCCCCATCCAGTCACTCCAATAACTACAATGTATAGG
Found at i:49827 original size:29 final size:30
Alignment explanation
Indices: 49751--49828 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
49741 TTTTTTAAAT
* * **
49751 AATTACCAAAATAGAACCTTTTTCGAATTA
1 AATTCCCAAAATAGCACCCATTTCGAATTA
* *
49781 AATTCTCAGAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATAGCACCCATTTCGAATTA
*
49810 AATTCCCAAAATATCACCC
1 AATTCCCAAAATAGCACCC
49829 GATCAACGGT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.29
Consensus pattern (30 bp):
AATTCCCAAAATAGCACCCATTTCGAATTA
Found at i:49853 original size:17 final size:18
Alignment explanation
Indices: 49831--49869 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
49821 TATCACCCGA
*
49831 TCAAC-GGTCGGGTTGGG
1 TCAACGGGTCGGGTCGGG
49848 TCAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
49866 TCAA
1 TCAA
49870 AACCGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21
Consensus pattern (18 bp):
TCAACGGGTCGGGTCGGG
Found at i:57094 original size:18 final size:18
Alignment explanation
Indices: 57071--57131 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
57061 TTTATCAAAC
57071 CAAATTAAAACAATAAAA
1 CAAATTAAAACAATAAAA
57089 CAAATTTAAAA-AA-AAATA
1 CAAA-TTAAAACAATAAA-A
* *
57107 CAAGTTAAAACATTAAAA
1 CAAATTAAAACAATAAAA
57125 CATAATT
1 CA-AATT
57132 CATCAATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 9 0.26
18 14 0.40
19 12 0.34
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.23
Consensus pattern (18 bp):
CAAATTAAAACAATAAAA
Found at i:58397 original size:16 final size:18
Alignment explanation
Indices: 58376--58408 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
58366 TGTCACATTG
58376 ACTTTT-CAAAA-CGTTT
1 ACTTTTACAAAATCGTTT
58392 ACTTTTACAAAATCGTT
1 ACTTTTACAAAATCGTT
58409 GAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (18 bp):
ACTTTTACAAAATCGTTT
Found at i:58951 original size:19 final size:20
Alignment explanation
Indices: 58924--58976 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
58914 ATATAAAATT
*
58924 TGTCTCGAAGGACAT-TATA
1 TGTCCCGAAGGACATCTATA
*
58943 TGTCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACATC-TATA
*
58964 TATCCCGAAGGAC
1 TGTCCCGAAGGAC
58977 CTCGTAGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACATCTATA
Found at i:58969 original size:21 final size:21
Alignment explanation
Indices: 58939--58982 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
58929 CGAAGGACAT
*
58939 TATATGTCCCGAAGGACCTCG
1 TATATATCCCGAAGGACCTCG
58960 TATATATCCCGAAGGACCTCG
1 TATATATCCCGAAGGACCTCG
58981 TA
1 TA
58983 GAACCCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (21 bp):
TATATATCCCGAAGGACCTCG
Done.