Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018627.1 Corchorus olitorius cultivar O-4 contig18660, 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: 87532
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1291 original size:161 final size:161
Alignment explanation
Indices: 1026--1345 Score: 631
Period size: 161 Copynumber: 2.0 Consensus size: 161
1016 TTACCCTATG
1026 AAGACTTGTTTGTCGTTTCCTATCTTCCCTGGTATGCTGACATTGCCGATTTCTTGGTTACTCGT
1 AAGACTTGTTTGTCGTTTCCTATCTTCCCTGGTATGCTGACATTGCCGATTTCTTGGTTACTCGT
1091 CGTCTTCCTGAAGATCTAAGTAAAGGAGTTAAATTGAAGATAATAAGTGATGCTAAGTATTATGT
66 CGTCTTCCTGAAGATCTAAGTAAAGGAGTTAAATTGAAGATAATAAGTGATGCTAAGTATTATGT
1156 TTGGGATGATCCATATTTATGGAGATATGCT
131 TTGGGATGATCCATATTTATGGAGATATGCT
*
1187 AAGACTTGTTTGTCGTTTCCTATCTTCCCTGGTATGCTGACATTGTCGATTTCTTGGTTACTCGT
1 AAGACTTGTTTGTCGTTTCCTATCTTCCCTGGTATGCTGACATTGCCGATTTCTTGGTTACTCGT
1252 CGTCTTCCTGAAGATCTAAGTAAAGGAGTTAAATTGAAGATAATAAGTGATGCTAAGTATTATGT
66 CGTCTTCCTGAAGATCTAAGTAAAGGAGTTAAATTGAAGATAATAAGTGATGCTAAGTATTATGT
1317 TTGGGATGATCCATATTTATGGAGATATG
131 TTGGGATGATCCATATTTATGGAGATATG
1346 GTTCTGACCA
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 158 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (161 bp):
AAGACTTGTTTGTCGTTTCCTATCTTCCCTGGTATGCTGACATTGCCGATTTCTTGGTTACTCGT
CGTCTTCCTGAAGATCTAAGTAAAGGAGTTAAATTGAAGATAATAAGTGATGCTAAGTATTATGT
TTGGGATGATCCATATTTATGGAGATATGCT
Found at i:2599 original size:7 final size:7
Alignment explanation
Indices: 2574--2613 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
2564 GGAGGCAACC
2574 CAATTTT
1 CAATTTT
2581 -AATTTT
1 CAATTTT
2587 -AATTTT
1 CAATTTT
2593 CAATTTT
1 CAATTTT
2600 CAATTTT
1 CAATTTT
*
2607 TAATTTT
1 CAATTTT
2614 AAGTTTTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (7 bp):
CAATTTT
Found at i:2606 original size:14 final size:13
Alignment explanation
Indices: 2575--2620 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
2565 GAGGCAACCC
2575 AATTTT-AATTTT
1 AATTTTCAATTTT
2587 AATTTTCAATTTT
1 AATTTTCAATTTT
*
2600 CAATTTTTAATTTT
1 -AATTTTCAATTTT
2614 AAGTTTT
1 AA-TTTT
2621 AACTTAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.20
13 8 0.27
14 16 0.53
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (13 bp):
AATTTTCAATTTT
Found at i:2620 original size:7 final size:6
Alignment explanation
Indices: 2575--2622 Score: 60
Period size: 6 Copynumber: 7.3 Consensus size: 6
2565 GAGGCAACCC
2575 AATTTT AATTTT AATTTT CAATTTT CAATTTTT AATTTT AAGTTTT AA
1 AATTTT AATTTT AATTTT -AATTTT -AA-TTTT AATTTT AA-TTTT AA
2623 CTTAATCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.46
7 17 0.44
8 4 0.10
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (6 bp):
AATTTT
Found at i:4485 original size:18 final size:19
Alignment explanation
Indices: 4455--4490 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4445 TTTATTCCCT
*
4455 TGATTTTTGAAGTTAAATA
1 TGATTTTTGAAGTAAAATA
4474 TGATTTTT-AAGTAAAAT
1 TGATTTTTGAAGTAAAAT
4491 TTTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (19 bp):
TGATTTTTGAAGTAAAATA
Found at i:9635 original size:24 final size:24
Alignment explanation
Indices: 9624--9716 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
9614 TGAACACCAT
* *
9624 ATCGAACATGTTCATGAACACT-TT
1 ATCGAACATGTTCGTGAACA-TGTA
9648 ATCGAACATGTTCGTGAACATGTA
1 ATCGAACATGTTCGTGAACATGTA
*
9672 ATCGAACGTGTTCGTGAACATGTA
1 ATCGAACATGTTCGTGAACATGTA
*
9696 ATCGAACGTGTTCGTGAACAT
1 ATCGAACATGTTCGTGAACAT
9717 AAATGAACCG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
23 1 0.02
24 64 0.98
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (24 bp):
ATCGAACATGTTCGTGAACATGTA
Found at i:9642 original size:12 final size:12
Alignment explanation
Indices: 9627--9716 Score: 53
Period size: 12 Copynumber: 7.5 Consensus size: 12
9617 ACACCATATC
9627 GAACATGTTCAT
1 GAACATGTTCAT
9639 GAACACT-TT-AT
1 GAACA-TGTTCAT
*
9650 CGAACATGTTCGT
1 -GAACATGTTCAT
*
9663 GAACATG-TAAT
1 GAACATGTTCAT
* *
9674 CGAACGTGTTCGT
1 -GAACATGTTCAT
*
9687 GAACATG-TAAT
1 GAACATGTTCAT
* *
9698 CGAACGTGTTCGT
1 -GAACATGTTCAT
9711 GAACAT
1 GAACAT
9717 AAATGAACCG
Statistics
Matches: 57, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
11 7 0.12
12 44 0.77
13 6 0.11
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (12 bp):
GAACATGTTCAT
Found at i:12739 original size:772 final size:770
Alignment explanation
Indices: 10603--13929 Score: 3819
Period size: 772 Copynumber: 4.3 Consensus size: 770
10593 AGAAGTCCAT
* * ** * *
10603 GTATGGGTGTAAAGAATTTCTCTAAACGCCATAT-GCAAAAAGATGATTTACAAGGCTTAAACTT
1 GTATGGCTGCAAAGAA-TTCTCCGAACGCCAT-TGGCAAAAAGATGATTTCCAAGGCTCAAACTT
* * * * *
10667 CTGCTAAGAGAGCTAGGGAATCCGACCTACCATTCAAGAAATCAAAACGGGCGAACAGTTTCGTT
64 CTGCTAAGAGAGCTAGGGAATTCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTT
* * ** * * * * *
10732 GAGGAAGAAGAGATTGTTGTGAAGAGCAAGGCCAGATTTTCAGAGGCTTTTCTTTAAAGAGGATG
129 GAGGAAGAAGAGACTGCTGTGAAGAGCAAGGCCACTTTTTCGGAGGATTTTCTTGAAGGATGATG
* * *
10797 GAATAGATCTATTTGAAGGTATGTTGAAGTATGATTCAAAGGATATGAATGATTTTTATGACTTT
194 AAATAGCTCTACTTGAAGGTATGTT---G--TG-----AAGGATATGAATGATTTTTATGACTTT
*
10862 ATCAAGGACTCAATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGACGTTGAA
249 ATCAAGGACTCAATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGAGGTTGAA
* * *
10927 GAAAAAATATGAAAA-CTTGCTAAGAGATGTAAGAAGGGAAAAGGCATATTCTTTTCAAAGCTTC
314 GAAAAAATATGAAAATCTTGCTAAGAGATGTAAGAACGGAAAAGACTTATTCTTTTCAAAGCTTC
* * * *
10991 ATGATTAAAAATCATATGAACTGTCCAAGAGCATTTAGCGCAAAGAGACTTGATTACTATTTAGT
379 ATGATAAAAAATCATATGAACTGTCCAAGAGAATTTAGGGCAAAGAGACTTGATTAC-A---ACT
* * * * * * *
11056 TAGTGTGTTGGCCATACCATTCCCATATAAATTTCTCATCCCATATATTCTATTGTCACCGCCCC
440 TAGTTTGTTGGCCTTACCATTCCCATATAAATTTCTCTTCCCATACATTCTACTGTCACCACTCC
* *
11121 ACCATCAATCAACTAAAACCCATAACCTCTCCTCAACCATGG-AATAAAGCATCCCAAGCCAATC
505 ACCATCAATCAACTAAAACCCATAAACTCTCCTCATCCATGGCAA-AAAGCATCCCAAGCCAATC
* * * * *
11185 GAAAATCATCATGCTTCCTCTTGAGAAGATGAAAAGGATGAAGAGTCTTCTTCTTCTTCCAATGA
569 GAAAATCCTCCTTCTTCCTCTAGAGAAGATGAAAAGGATCAAGAGTCTTCTTCTTCTTCCAATGA
* * * *
11250 TGAGAAGTAAGAAGTTGAGTCCAAAACCAGACCCCAAAACACACCAGTCCCATAAAAGC--C--A
634 CGAGAAGCAAGAAGATGAGTCCAAAACCAGACCCCAAAACACACCAGTCCCAAAAAAGCTACAAA
* * * * * *
11311 CAAACTCCGATTGAAGAAGAATATGAGAATTTCGATGGTGGTGACTAAGACGGTAATTAC-GATT
699 CAAACT-CGGTTGAAAAAGAAGATGAGAATTCCGA-GGCGGTGACTAGGACGGTAATTACTGATT
*
11375 CCAACTCCG
762 CCGACTCCG
* ** ** *
11384 GTGTGGCTGCAAAGAATAATATGAACGCTATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
1 GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
* * *
11449 ACTAAGAGAGCTA-GGAA-TCCACCTACCACTCAAGAAATCAAAAGGGGCCAAGAGTGTCGTTGA
66 GCTAAGAGAGCTAGGGAATTCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTGA
* * * *
11512 GGAA-AAGGAGACTGCTGTGAAGAGGAAGGCCACTTTTTCGAAGAATTTTCTCCG-AGGATGATG
131 GGAAGAA-GAGACTGCTGTGAAGAGCAAGGCCACTTTTTCGGAGGATTTTCT-TGAAGGATGATG
*
11575 AAATAGCTCTACTTGAAGGTATGTTGAAGTATGATTCAAAGGATATGAATAATTTTTATGACTTT
194 AAATAGCTCTACTTGAAGGTATGTT---G--TG-----AAGGATATGAATGATTTTTATGACTTT
* * * * *
11640 ATCAA--A---GATTCATGTTAGTTTTAGTAAACCTCAGTTGGCAGACAAGGTGAGGAGGCTGAA
249 ATCAAGGACTCAATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGAGGTTGAA
* *
11700 GAAAAAATATGAAAATCTTGCTAAGAGATGTAAGAATGGAAAAGAC--ATTCTTTTGAAAGCTTC
314 GAAAAAATATGAAAATCTTGCTAAGAGATGTAAGAACGGAAAAGACTTATTCTTTTCAAAGCTTC
* * * * *
11763 ATGATGAAAAATCATATGAGCTATCCAAGAGAATTCAGGGCAAAGAGACTTGATTACTATTTAGT
379 ATGATAAAAAATCATATGAACTGTCCAAGAGAATTTAGGGCAAAGAGACTTGATTAC-A---ACT
* * ** * * * *
11828 TAGTATGTTGGCCTTATCATTCCGTTATAAAACTTCTCTTCCTATAAATTCTACTGTCACCGC-C
440 TAGTTTGTTGGCCTTACCATTCCCATAT-AAATTTCTCTTCCCATACATTCTACTGTCACCACTC
* * * * *
11892 GCACCATCAATCAACTAAAACCCATGACCTCTCTTCATCCATGGCATAAAGCATCCCAATCCAAT
504 -CACCATCAATCAACTAAAACCCATAAACTCTCCTCATCCATGGCAAAAAGCATCCCAAGCCAAT
* * *
11957 CGAAAATCCTCCTTCTTCCTCTGGAGAAGATGAAAAGGATCAAGAGTATTCTTCTTCTTCTAATG
568 CGAAAATCCTCCTTCTTCCTCTAGAGAAGATGAAAAGGATCAAGAGTCTTCTTCTTCTTCCAATG
* ***
12022 ACGAGAAGCAAGAAGATGAGTCCAAAACAAGACCATTAAACACACCAGTCCCAAAAAAGCTACAA
633 ACGAGAAGCAAGAAGATGAGTCCAAAACCAGACCCCAAAACACACCAGTCCCAAAAAAGCTACAA
* * *
12087 ACAAACTCGGTTGAAAAAGAAGATGAGAATTCCCGCA-GCGGTGACTGGGGCGATAATT-CTGAT
698 ACAAACTCGGTTGAAAAAGAAGATGAGAATT-CCG-AGGCGGTGACTAGGACGGTAATTACTGAT
*
12150 TCCGACTCCA
761 TCCGACTCCG
* * ** *
12160 GTATGGCAGCAAAGAATTCTCCGAACGCCATTGGAAAAAACCTGATTTCCAAGGCTCAAACTTAT
1 GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
* * *
12225 GCTAAGAGAGCTAGGGAATTCGACCAACCACTTAAAAAATCAAAACGGGCCAAGAGTGTCGTTGA
66 GCTAAGAGAGCTAGGGAATTCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTGA
* * * *
12290 AGAAGAAGAAACTGTTGTGAAGAGCAAGGCCACTTTTTTCGGAGGATTTTCTTGAAGGATGATGG
131 GGAAGAAGAGACTGCTGTGAAGAGCAAGGCCAC-TTTTTCGGAGGATTTTCTTGAAGGATGATGA
* * * * *
12355 AAGAGTTATACTTGAAGGTACGTTG-G-A-G-TATGAATGATTTTTATGACTTTATTAAGGACTC
195 AATAGCTCTACTTGAAGGTATGTTGTGAAGGATATGAATGATTTTTATGACTTTATCAAGGACTC
* * * * * *
12416 AATTCATGTTA-TGTTAGTAGAGCTGAGCTAGCACACAAGGTGAGGTGGTTGAAGAAAAAATTTG
260 AATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGAGGTTGAAGAAAAAATATG
*
12480 AAAATCTTGCTAAGAGATGTAAGAACGGAAAAAACTTATTCTTTTCAAAGCTTCATGATAAAAAA
325 AAAATCTTGCTAAGAGATGTAAGAACGGAAAAGACTTATTCTTTTCAAAGCTTCATGAT---AAA
* * * * *
12545 AAATCCTATGAACTGCCCAACATAATTTGGGGCAAAGAGACTTGATTACAACTTAGTTTGTCTGG
387 AAATCATATGAACTGTCCAAGAGAATTTAGGGCAAAGAGACTTGATTACAACTTAGTTTGT-TGG
* * * *
12610 CCTTCCCATTCCCATATAAATTTTTTTCTTCACATACATTCTACTGTCACCACTCAACCATCAAT
451 CCTTACCATTCCCATATAAA--TTTCTCTTCCCATACATTCTACTGTCACCACTCCACCATCAAT
* *
12675 CAACTAAAACCCAAAAACTCTCCTCATCCATGGCAAAAAACATCCCAAGCCAATCGAAAATCCTC
514 CAACTAAAACCCATAAACTCTCCTCATCCATGGCAAAAAGCATCCCAAGCCAATCGAAAATCCTC
* * * *
12740 CTCCTTCTTCTAGAGAAGATGAAAAGTATC-TGAAGTCTTCTTCTTCTTCCAATGACGAGAAGCA
579 CTTCTTCCTCTAGAGAAGATGAAAAGGATCAAG-AGTCTTCTTCTTCTTCCAATGACGAGAAGCA
* * * * *
12804 AGAAGATGAGTCCAGAATCGGACCCCAAAACACACCAGTCCCACAAAAGCTACAGACAAACTCGG
643 AGAAGATGAGTCCAAAACCAGACCCCAAAACACACCAGTCCCAAAAAAGCTACAAACAAACTCGG
* * * ** ** * *
12869 TTGAAAAAGAAGATGAGAATTCCGATGGCGGTAAATGGGACGGTAATT-CCAATTTTGATTTCG
708 TTGAAAAAGAAGATGAGAATTCCGA-GGCGGTGACTAGGACGGTAATTACTGATTCCGACTCCG
* * *
12932 GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGGAAAAAGCTGATTTCCAAGACTCAAACTTCT
1 GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
* *
12997 GCTAAGAGAGCTA-GGAATCCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTGC
66 GCTAAGAGAGCTAGGGAATTCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTGA
* * * ** * *
13061 GGAAGAATAGAGTACTGTGAAGAGCATCGCCATTTTTTCGGAGGATTTTCTTTAAGGATGATGAA
131 GGAAGAAGAGACTGCTGTGAAGAGCAAGGCCACTTTTTCGGAGGATTTTCTTGAAGGATGATGAA
*
13126 ATAGCCCTACTTGAAGGTATATTGAAGTATGATTCGAAGGATATGAATGATTTTTATGACTTTAT
196 ATAGCTCTACTTGAAGG--TA-T---GT-TG--T-GAAGGATATGAATGATTTTTATGACTTTAT
* * * * *
13191 CAAGGACTCAATTCATGTTAGTTTTAGTAGAGCTCAACTGGCAAACAAGGTGAGGAGGTCGAAGA
251 CAAGGACTCAATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGAGGTTGAAGA
* * * *
13256 AAAAATATGAAAATCTTGCTAAGAGACGTAAGGACGGAAAAGTCTTATCCTTTTCAAAGCTTCAT
316 AAAAATATGAAAATCTTGCTAAGAGATGTAAGAACGGAAAAGACTTATTCTTTTCAAAGCTTCAT
* * * * * *
13321 GA-AAAAAACTCATATGAACTGGCTAAGAGAATTTGGGGAAAAGATACTTGATTACAACTTAGTC
381 GATAAAAAA-TCATATGAACTGTCCAAGAGAATTTAGGGCAAAGAGACTTGATTACAACTTAGTT
* * * *
13385 TGTTGGCCTTCCCATTCCCATATAAATTTTTCTTCCCATGCATTCTACTGTCATCACTCCACCAT
445 TGTTGGCCTTACCATTCCCATATAAATTTCTCTTCCCATACATTCTACTGTCACCACTCCACCAT
* * * *
13450 CAATCAACTAGAACCCAGAAACACTCCTCATCCATGGCACGAAAGCATCCCAAGCCAATCGAAAA
510 CAATCAACTAAAACCCATAAACTCTCCTCATCCATGGCA-AAAAGCATCCCAAGCCAATCGAAAA
* *
13515 TCCTCCTTCTTCCTCTAGAGAAGATGAAAAAGAT-AAGGAGTCTTCTTCTTCTTCCAATGACGGG
574 TCCTCCTTCTTCCTCTAGAGAAGATGAAAAGGATCAA-GAGTCTTCTTCTTCTTCCAATGACGAG
* * * *
13579 AAGCAAGGAGATGAGTCCAAAACCAGACCCCAAATCACACCAGTCCTACAAAAA-CTACAAACTA
638 AAGCAAGAAGATGAGTCCAAAACCAGACCCCAAAACACACCAGTCCCA-AAAAAGCTACAAACAA
* * * * * * * *
13643 ACTCGGTTGAAGAAGAAGATGAGAATTCTGGTGGTGGTGATTAGGACGGTAATTCCT-AATCTGA
702 ACTCGGTTGAAAAAGAAGATGAGAATTC-CGAGGCGGTGACTAGGACGGTAATTACTGATTCCGA
13707 CTCC-
766 CTCCG
* * ** * * * * *
13711 GTATGACTGCAAAGAATTCTCCAAATTCCATTGCCAAAAAGATAATTTCCTAGGCTTAAACTTAT
1 GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
*
13776 GCTAAGAGAGCTAGGGAATTCCGACCTACCACTCAAGAAATCAAAACGGGCTAAGAGTGTCGTTG
66 GCTAAGAGAGCTAGGGAATT-CGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTG
* * *
13841 AGGAAAAAGAGATTGCTGTGAAGAGCAAGGCCACTATTTCGGAGGATTTTCTCTG-AGGATGATG
130 AGGAAGAAGAGACTGCTGTGAAGAGCAAGGCCACTTTTTCGGAGGATTTTCT-TGAAGGATGATG
13905 AAATAGCTCTACTTGAAGGTATGTT
194 AAATAGCTCTACTTGAAGGTATGTT
13930 TAATAATATT
Statistics
Matches: 2184, Mismatches: 301, Indels: 129
0.84 0.12 0.05
Matches are distributed among these distances:
765 25 0.01
766 1 0.00
767 2 0.00
769 76 0.03
770 66 0.03
771 111 0.05
772 423 0.19
773 262 0.12
774 73 0.03
775 4 0.00
776 118 0.05
777 17 0.01
778 221 0.10
779 191 0.09
780 237 0.11
781 163 0.07
782 52 0.02
783 1 0.00
784 43 0.02
785 98 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (770 bp):
GTATGGCTGCAAAGAATTCTCCGAACGCCATTGGCAAAAAGATGATTTCCAAGGCTCAAACTTCT
GCTAAGAGAGCTAGGGAATTCGACCTACCACTCAAGAAATCAAAACGGGCCAAGAGTGTCGTTGA
GGAAGAAGAGACTGCTGTGAAGAGCAAGGCCACTTTTTCGGAGGATTTTCTTGAAGGATGATGAA
ATAGCTCTACTTGAAGGTATGTTGTGAAGGATATGAATGATTTTTATGACTTTATCAAGGACTCA
ATTCATGTTAGTGTTAGTAAAGCTCAGCTGGCAGACAAGGTGAGGAGGTTGAAGAAAAAATATGA
AAATCTTGCTAAGAGATGTAAGAACGGAAAAGACTTATTCTTTTCAAAGCTTCATGATAAAAAAT
CATATGAACTGTCCAAGAGAATTTAGGGCAAAGAGACTTGATTACAACTTAGTTTGTTGGCCTTA
CCATTCCCATATAAATTTCTCTTCCCATACATTCTACTGTCACCACTCCACCATCAATCAACTAA
AACCCATAAACTCTCCTCATCCATGGCAAAAAGCATCCCAAGCCAATCGAAAATCCTCCTTCTTC
CTCTAGAGAAGATGAAAAGGATCAAGAGTCTTCTTCTTCTTCCAATGACGAGAAGCAAGAAGATG
AGTCCAAAACCAGACCCCAAAACACACCAGTCCCAAAAAAGCTACAAACAAACTCGGTTGAAAAA
GAAGATGAGAATTCCGAGGCGGTGACTAGGACGGTAATTACTGATTCCGACTCCG
Found at i:14412 original size:24 final size:25
Alignment explanation
Indices: 14385--14438 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
14375 GGATATATTG
14385 ATATTCAGTACTAACTTTCACAT-A
1 ATATTCAGTACTAACTTTCACATAA
*
14409 ATATTTAGTACTAACTTTCACATAA
1 ATATTCAGTACTAACTTTCACATAA
14434 ATATT
1 ATATT
14439 TATATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATTCAGTACTAACTTTCACATAA
Found at i:15059 original size:6 final size:6
Alignment explanation
Indices: 15050--15099 Score: 73
Period size: 6 Copynumber: 7.8 Consensus size: 6
15040 GAAAAATGAA
15050 AAAAAT AAAAAT AAAAAT AAAAAAT GAAAAAT AAAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT -AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAA
15100 CATCAAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 23 0.56
7 18 0.44
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:15059 original size:14 final size:13
Alignment explanation
Indices: 15050--15099 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
15040 GAAAAATGAA
15050 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
15062 AAAAATAAAAAAT
1 AAAAATAAAAAAT
15075 GAAAAATAAAAAAT
1 -AAAAATAAAAAAT
15089 AAAAATAAAAA
1 AAAAATAAAAA
15100 CATCAAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.17
13 17 0.47
14 13 0.36
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:15071 original size:27 final size:27
Alignment explanation
Indices: 15041--15099 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 27
15031 TTAAAGATGG
15041 AAAAATGAAAAAAATAAAAATAAAAATA
1 AAAAATGAAAAAAA-AAAAATAAAAATA
*
15069 AAAAATGAAAAATAAAAAATAAAAATA
1 AAAAATGAAAAAAAAAAAATAAAAATA
15096 AAAA
1 AAAA
15100 CATCAAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (27 bp):
AAAAATGAAAAAAAAAAAATAAAAATA
Found at i:15575 original size:22 final size:22
Alignment explanation
Indices: 15533--15581 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
15523 ATTAGTCCAG
* *
15533 CAAAAACAGAGCGACTATGTTT
1 CAAAAACAGAGCAAATATGTTT
* *
15555 TAAAAACAGAGCAAATCTGTTT
1 CAAAAACAGAGCAAATATGTTT
15577 CAAAA
1 CAAAA
15582 GCGAGTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAAAACAGAGCAAATATGTTT
Found at i:19239 original size:32 final size:32
Alignment explanation
Indices: 19200--19276 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
19190 CATCGAGCTT
19200 GAGCTCGGCTCGAATCGAGTATCGAGCTACTC
1 GAGCTCGGCTCGAATCGAGTATCGAGCTACTC
19232 GAGCTCGGCTCGAATCGAGTATCGAGCTACTC
1 GAGCTCGGCTCGAATCGAGTATCGAGCTACTC
19264 GAGCTCGGCTCGA
1 GAGCTCGGCTCGA
19277 CAAGTTCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.21
Consensus pattern (32 bp):
GAGCTCGGCTCGAATCGAGTATCGAGCTACTC
Found at i:19336 original size:6 final size:6
Alignment explanation
Indices: 19325--19350 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19315 CAGCTAAAAT
19325 TCGAGC TCGAGC TCGAGC TCGAGC TC
1 TCGAGC TCGAGC TCGAGC TCGAGC TC
19351 AACAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.19
Consensus pattern (6 bp):
TCGAGC
Found at i:20996 original size:58 final size:57
Alignment explanation
Indices: 20905--21013 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 57
20895 TCAAATATCA
*
20905 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCTTATGG
1 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACG-TTTAGGACCGAGGCTTATGG
* *
20963 AGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTAGGACCGAGGC
1 AGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTAGGACCGAGGC
21014 ATGATGCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 13 0.28
58 19 0.40
59 15 0.32
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (57 bp):
AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTAGGACCGAGGCTTATGG
Found at i:22328 original size:36 final size:36
Alignment explanation
Indices: 22281--22350 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
22271 TTCAATAACC
* *
22281 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
22317 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
22351 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:23524 original size:25 final size:24
Alignment explanation
Indices: 23490--23536 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
23480 ACGTTTGCAC
23490 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
23515 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
23537 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:23581 original size:39 final size:40
Alignment explanation
Indices: 23527--23607 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
23517 ATACCTAAGA
*
23527 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
23566 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
23606 AT
1 AT
23608 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:25949 original size:24 final size:23
Alignment explanation
Indices: 25917--25964 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
25907 TGACATGGAA
25917 TTCTACTAAAAACTAGCTAGCTTT
1 TTCTACTAAAAACTAGCTA-CTTT
**
25941 TTCTACTAAGTACTAGCTACTTT
1 TTCTACTAAAAACTAGCTACTTT
25964 T
1 T
25965 ATCTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (23 bp):
TTCTACTAAAAACTAGCTACTTT
Found at i:30857 original size:13 final size:13
Alignment explanation
Indices: 30839--30866 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30829 AGGCCAAATC
30839 ATTAAAATTCCAA
1 ATTAAAATTCCAA
30852 ATTAAAATTCCAA
1 ATTAAAATTCCAA
30865 AT
1 AT
30867 CCCCATGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAATTCCAA
Found at i:41526 original size:19 final size:20
Alignment explanation
Indices: 41471--41528 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
41461 GCTGCTCTAA
41471 TAATCTCATCTGTACAGTAC
1 TAATCTCATCTGTACAGTAC
* * *
41491 TAAATCTAATCTATACAGT-G
1 T-AATCTCATCTGTACAGTAC
*
41511 TAATCTCATTTGTACAGT
1 TAATCTCATCTGTACAGT
41529 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:42741 original size:37 final size:37
Alignment explanation
Indices: 42647--42742 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
42637 TTGAATGCTT
* * * *
42647 TGAAAAC--TATGAGAATTTTCCCAATTTGACAATTT
1 TGAAAACTGTATGAGAATTTTCCCAAATTGAAAACTA
* *
42682 TGAAAACTGGAT-AGGAACTTTCCCAAATTGAAAACTA
1 TGAAAACTGTATGA-GAATTTTCCCAAATTGAAAACTA
* *
42719 TGAAGACTTTATGAGAATTTTCCC
1 TGAAAACTGTATGAGAATTTTCCC
42743 GATCTGAAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
35 7 0.15
36 1 0.02
37 38 0.81
38 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (37 bp):
TGAAAACTGTATGAGAATTTTCCCAAATTGAAAACTA
Found at i:42805 original size:17 final size:17
Alignment explanation
Indices: 42785--42818 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42775 TTTTTTTTTT
*
42785 TTTTTTTGAGTTTTGAA
1 TTTTTTGGAGTTTTGAA
*
42802 TTTTTTGGATTTTTGAA
1 TTTTTTGGAGTTTTGAA
42819 AACCTTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (17 bp):
TTTTTTGGAGTTTTGAA
Found at i:43476 original size:25 final size:25
Alignment explanation
Indices: 43435--43497 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
43425 TTATAACTAA
*
43435 TAAAAACTAGAGCCCAAACCTAAAC
1 TAAAAACTAAAGCCCAAACCTAAAC
*
43460 TAAAAACTAAAGTCCAAACCTAAAC
1 TAAAAACTAAAGCCCAAACCTAAAC
*
43485 -AAAAACCAAAGCC
1 TAAAAACTAAAGCC
43498 ATAAATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.32
25 23 0.68
ACGTcount: A:0.56, C:0.27, G:0.06, T:0.11
Consensus pattern (25 bp):
TAAAAACTAAAGCCCAAACCTAAAC
Found at i:45604 original size:59 final size:58
Alignment explanation
Indices: 45486--45605 Score: 222
Period size: 59 Copynumber: 2.1 Consensus size: 58
45476 TTTATTTCAA
45486 TTTCAATTTTGAGCAACTTGGACCGATAAAAACTAAGAAATGAAACTGGTAAAAGGAT
1 TTTCAATTTTGAGCAACTTGGACCGATAAAAACTAAGAAATGAAACTGGTAAAAGGAT
*
45544 TTTCAATTTTGAGCAACTTGGACCGATAAAAAACTAAGAAATGAAACTGGTGAAAGGAT
1 TTTCAATTTTGAGCAACTTGGACCGAT-AAAAACTAAGAAATGAAACTGGTAAAAGGAT
45603 TTT
1 TTT
45606 GCCTATAATA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 27 0.45
59 33 0.55
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (58 bp):
TTTCAATTTTGAGCAACTTGGACCGATAAAAACTAAGAAATGAAACTGGTAAAAGGAT
Found at i:50529 original size:2 final size:2
Alignment explanation
Indices: 50524--50549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50514 ACACACACAC
50524 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50550 TTTGATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51542 original size:19 final size:19
Alignment explanation
Indices: 51518--51557 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
51508 TTGCCCCTCT
51518 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAG
* *
51537 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCCCCCACTAAG
51556 TC
1 TC
51558 AAGATAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAG
Found at i:57952 original size:17 final size:17
Alignment explanation
Indices: 57932--57970 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
57922 TCATTAGTTT
57932 CATTCAAAGTCCATTCC
1 CATTCAAAGTCCATTCC
*
57949 CATTTTAAAGTCCATTCC
1 CA-TTCAAAGTCCATTCC
57967 CATT
1 CATT
57971 TTAAAGCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (17 bp):
CATTCAAAGTCCATTCC
Found at i:57960 original size:18 final size:18
Alignment explanation
Indices: 57937--57982 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
57927 AGTTTCATTC
57937 AAAGTCCATTCCCATTTT
1 AAAGTCCATTCCCATTTT
57955 AAAGTCCATTCCCATTTT
1 AAAGTCCATTCCCATTTT
*
57973 AAAGCCCATT
1 AAAGTCCATT
57983 TCCTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (18 bp):
AAAGTCCATTCCCATTTT
Found at i:58092 original size:13 final size:13
Alignment explanation
Indices: 58074--58103 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
58064 ATGCATTTGG
58074 TCTTCTTCCTTTT
1 TCTTCTTCCTTTT
*
58087 TCTTCTTTCTTTT
1 TCTTCTTCCTTTT
58100 TCTT
1 TCTT
58104 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTCTTCCTTTT
Found at i:58111 original size:5 final size:6
Alignment explanation
Indices: 58082--58116 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
58072 GGTCTTCTTC
58082 CTTTTT CTTCTTT CTTTTT CTTTTT C-TTTT CTTTT
1 CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTTTT
58117 GGGTCCGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:58113 original size:11 final size:12
Alignment explanation
Indices: 58082--58116 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
58072 GGTCTTCTTC
58082 CTTTTTCTTCTTT
1 CTTTTTCTT-TTT
58095 CTTTTTCTTTTT
1 CTTTTTCTTTTT
58107 C-TTTTCTTTT
1 CTTTTTCTTTT
58117 GGGTCCGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:61010 original size:23 final size:23
Alignment explanation
Indices: 60983--61039 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
60973 ATTTTTGTTG
60983 GGTTTTGTTTATTCTT-ATGGGCTT
1 GGTTTT-TTTATT-TTGATGGGCTT
* *
61007 GTTTTTTTTCTTTTGATGGGCTT
1 GGTTTTTTTATTTTGATGGGCTT
61030 GGTTTTTTTA
1 GGTTTTTTTA
61040 CTTATTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.07
23 21 0.75
24 5 0.18
ACGTcount: A:0.07, C:0.07, G:0.23, T:0.63
Consensus pattern (23 bp):
GGTTTTTTTATTTTGATGGGCTT
Found at i:61049 original size:23 final size:23
Alignment explanation
Indices: 60983--61050 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
60973 ATTTTTGTTG
60983 GGTTTTGTTTA-TTCTTATGGGCTT
1 GGTTTT-TTTACTT-TTATGGGCTT
*
61007 -GTTTTTTTTCTTTTGATGGGCTT
1 GGTTTTTTTACTTTT-ATGGGCTT
61030 GGTTTTTTTACTTATT-TGGGC
1 GGTTTTTTTACTT-TTATGGGC
61051 CTTATGGGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 5 0.13
23 20 0.53
24 11 0.29
25 2 0.05
ACGTcount: A:0.07, C:0.09, G:0.24, T:0.60
Consensus pattern (23 bp):
GGTTTTTTTACTTTTATGGGCTT
Found at i:61861 original size:40 final size:38
Alignment explanation
Indices: 61764--61862 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 38
61754 GTTTTTTTTT
61764 TTGGGAAAGTTCCCACCAG---TTTTTAAGTTTTCAAA
1 TTGGGAAAGTTCCCACCAGTTTTTTTTAAGTTTTCAAA
**
61799 TTGGGAAAGTTCCCATTTAGTTTTTTTTAAAGATTTT-AAA
1 TTGGGAAAGTTCCCA-CCAGTTTTTTTT-AAG-TTTTCAAA
*
61839 TTGGGAAAATTCCCACCAAGTTTT
1 TTGGGAAAGTTCCCACC-AGTTTT
61863 AGTTTTCAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
35 15 0.29
36 2 0.04
39 5 0.10
40 26 0.50
41 4 0.08
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (38 bp):
TTGGGAAAGTTCCCACCAGTTTTTTTTAAGTTTTCAAA
Found at i:67148 original size:42 final size:42
Alignment explanation
Indices: 67084--67168 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
67074 CTCAGCTTTT
* * * *
67084 AATAGTTTAGGTATACTTATATATTTTCAAGAAAGTAAATTA
1 AATAGTTTAGATATAATGATATATTTTCAAGAAACTAAATTA
* *
67126 AATAGTTTAGATGTAATGATATATTTTCGAGAAACTAAATTA
1 AATAGTTTAGATATAATGATATATTTTCAAGAAACTAAATTA
67168 A
1 A
67169 TAATCGTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.39
Consensus pattern (42 bp):
AATAGTTTAGATATAATGATATATTTTCAAGAAACTAAATTA
Found at i:73252 original size:27 final size:27
Alignment explanation
Indices: 73214--73328 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 27
73204 TTTACTTCTT
* *
73214 ATTTTGGTCATTTACATGTCTAGGGGC
1 ATTTTGGTCATTTACACGTCCAGGGGC
* *
73241 ATTTTGGTCATTTGCACGTCCAAGGGC
1 ATTTTGGTCATTTACACGTCCAGGGGC
* * * *
73268 ATTTTGGTC---TGCACATCTAGGGGT
1 ATTTTGGTCATTTACACGTCCAGGGGC
* * *
73292 ATTTTGGTCATTTGCACATCCAGGGGT
1 ATTTTGGTCATTTACACGTCCAGGGGC
73319 ATTTTGGTCA
1 ATTTTGGTCA
73329 CTTCAAGTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
24 20 0.26
27 56 0.74
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTACACGTCCAGGGGC
Found at i:77897 original size:30 final size:31
Alignment explanation
Indices: 77826--77973 Score: 187
Period size: 32 Copynumber: 4.8 Consensus size: 31
77816 TTGCTTAAGC
77826 AAATCCAAAAGAAGATTTTGGAAAA-AGAGAGT
1 AAATCCAAAAGAAGATTTTGGAAAATA-A-AGT
* *
77858 AATTCCAAAAGAAAATTTTGGAAAATAAAG-
1 AAATCCAAAAGAAGATTTTGGAAAATAAAGT
* *
77888 AAATCCAAAAGAAGATTTTGGAAAAGGAGAGT
1 AAATCCAAAAGAAGATTTTGGAAAA-TAAAGT
*
77920 AATTCCAAAAGAAGATTTTGGAAAATAAAG-
1 AAATCCAAAAGAAGATTTTGGAAAATAAAGT
77950 AAA-CCGAAAAGAAGATTTTGGAAA
1 AAATCC-AAAAGAAGATTTTGGAAA
77974 TTAATAAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.02
30 43 0.42
31 8 0.08
32 48 0.47
33 1 0.01
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (31 bp):
AAATCCAAAAGAAGATTTTGGAAAATAAAGT
Found at i:77898 original size:62 final size:62
Alignment explanation
Indices: 77826--77973 Score: 262
Period size: 62 Copynumber: 2.4 Consensus size: 62
77816 TTGCTTAAGC
77826 AAATCCAAAAGAAGATTTTGGAAAAAGAGAGTAATTCCAAAAGAAAATTTTGGAAAATAAAG
1 AAATCCAAAAGAAGATTTTGGAAAAAGAGAGTAATTCCAAAAGAAAATTTTGGAAAATAAAG
* *
77888 AAATCCAAAAGAAGATTTTGGAAAAGGAGAGTAATTCCAAAAGAAGATTTTGGAAAATAAAG
1 AAATCCAAAAGAAGATTTTGGAAAAAGAGAGTAATTCCAAAAGAAAATTTTGGAAAATAAAG
77950 AAA-CCGAAAAGAAGATTTTGGAAA
1 AAATCC-AAAAGAAGATTTTGGAAA
77974 TTAATAAAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
61 2 0.02
62 81 0.98
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (62 bp):
AAATCCAAAAGAAGATTTTGGAAAAAGAGAGTAATTCCAAAAGAAAATTTTGGAAAATAAAG
Found at i:78790 original size:19 final size:19
Alignment explanation
Indices: 78766--78806 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
78756 AAACAGCACT
78766 AGTGAGTTCTCAACAGTGC
1 AGTGAGTTCTCAACAGTGC
78785 AGTGAGTTCTCAACAGTGC
1 AGTGAGTTCTCAACAGTGC
78804 AGT
1 AGT
78807 CCCAGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (19 bp):
AGTGAGTTCTCAACAGTGC
Found at i:80329 original size:22 final size:22
Alignment explanation
Indices: 80287--80330 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
80277 AAAACTCATG
*
80287 CCCCTTTGTTTATTCCTGAAAA
1 CCCCTTTGTTTATTCATGAAAA
*
80309 CCCCTTT-TTTATTTATCGAAAA
1 CCCCTTTGTTTATTCAT-GAAAA
80331 ATCAAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (22 bp):
CCCCTTTGTTTATTCATGAAAA
Found at i:82187 original size:22 final size:22
Alignment explanation
Indices: 82162--82205 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
82152 AGTCATGAAT
*
82162 AAAATCCCAAATTAATTTAAAG
1 AAAAGCCCAAATTAATTTAAAG
82184 AAAAGCCCAAATTAATTTAAAG
1 AAAAGCCCAAATTAATTTAAAG
82206 CACACGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.25
Consensus pattern (22 bp):
AAAAGCCCAAATTAATTTAAAG
Found at i:84120 original size:83 final size:83
Alignment explanation
Indices: 83981--84140 Score: 275
Period size: 83 Copynumber: 1.9 Consensus size: 83
83971 GCATCTGTTT
* * *
83981 TGCCCCTTGCAATTTACTACTAACTCATCTCCTTGTTTGTCCGGGTGGCCAGGGGAGACAAATAG
1 TGCCCCTTGCAATTTACTACTAACTCATCTCCTTGTTTGTCCAGGTGGCCAAGGGAGACAAAGAG
84046 CAGAATGTGTGGTGTGGA
66 CAGAATGTGTGGTGTGGA
*
84064 TGCCCCTTGCAATTTACTACTAACTCATCTCCTTGTTTGTCTAGGTGGCCAAGGGAGACAAAGAG
1 TGCCCCTTGCAATTTACTACTAACTCATCTCCTTGTTTGTCCAGGTGGCCAAGGGAGACAAAGAG
*
84129 CAGACTGTGTGG
66 CAGAATGTGTGG
84141 CATGGGGAGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (83 bp):
TGCCCCTTGCAATTTACTACTAACTCATCTCCTTGTTTGTCCAGGTGGCCAAGGGAGACAAAGAG
CAGAATGTGTGGTGTGGA
Done.