Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017498.1 Corchorus olitorius cultivar O-4 contig17531, 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: 95351
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6181 original size:24 final size:23
Alignment explanation
Indices: 6154--6205 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6144 AGGTTGCGCA
*
6154 AACTTCAGGGTTCAACCTGGCCCC
1 AACTTCAGGGGT-AACCTGGCCCC
* **
6178 AACTTGAGGGGTAAGTTGGCCCC
1 AACTTCAGGGGTAACCTGGCCCC
6201 AACTT
1 AACTT
6206 GGTGTTCGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (23 bp):
AACTTCAGGGGTAACCTGGCCCC
Found at i:8153 original size:50 final size:50
Alignment explanation
Indices: 7992--8685 Score: 627
Period size: 50 Copynumber: 13.8 Consensus size: 50
7982 AAAAATTGAA
* * ** * * * * *
7992 TTTAATTGAAAGATTAAACTTTTAAGTGATTTATGAATAAAGATAGAATT
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * *** * * * *
8042 TTTAAGTGAAAA-ATTGAAGCTTTCAATTGATTGGTGAATAAAAATTGGATT
1 TTTAA-TTAAAAGATTGAA-CTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * * *
8093 TTTGATTAAAAGA-TGAATCTTTTAAGAAATTTATGAATAAAGATCGGACT
1 TTTAATTAAAAGATTGAA-CTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * *
8143 TTTAATTAAAAGATTGAAACTTTTGAA-CAATTGGTAAATAAAGGTTGGACT
1 TTTAATTAAAAGATTG-AACTTTT-AAGAAATTTGTAAATAAAGATTGGACT
*
8194 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAA-AGTTGAACT
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGA-TTGGACT
* *
8244 TTTAATTAAAAGATTGAACTTTTAGGAAATTTGTAAATAAAGGTTGGA-T
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * * * *
8293 TTGGAAGTAAAAGATCGAACTTTTAAGAAATTTGTAAACAAA-AGTTGAACT
1 TT-TAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGA-TTGGACT
*
8344 TTTAATTAAAAGATTGAACTTTTAGGAAATTTGTAAATAAAGATTGGA-T
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * * * * *
8393 TTGTAAGTAAAAGATCGAAGTTTTAAGTAATTTGTAAACAAA-AGTTGAACT
1 TT-TAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGA-TTGGACT
* * * *
8444 TTTAATTAAAAGATTGAACTTTTAGGAAATTTGTGAATAAAGGTTTGA-T
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
** * *
8493 TTGTAATTAAAAGATCAAACTTTCAAGAAATTTGTAAATAAAGGTTGGACT
1 TT-TAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * * *
8544 TTTAATTAAAAGA-TGAATCTTCTAGGAAATTCGTAAATAAAGGTTGGACT
1 TTTAATTAAAAGATTGAA-CTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * * * * *
8594 TTTAATTAAAAGATTGAAACTTTTGAGTAATTTGTAATTAAAGGTTGAATT
1 TTTAATTAAAAGATTG-AACTTTTAAGAAATTTGTAAATAAAGATTGGACT
* * **
8645 TTTGATTAAAAGATTGAATTTTTTAAGCGATTTG-AAATAAA
1 TTTAATTAAAAGATTGAA-CTTTTAAGAAATTTGTAAATAAA
8686 AACAAAGCCT
Statistics
Matches: 529, Mismatches: 92, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
49 14 0.03
50 372 0.70
51 137 0.26
52 6 0.01
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (50 bp):
TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGATTGGACT
Found at i:8318 original size:100 final size:100
Alignment explanation
Indices: 8086--8667 Score: 753
Period size: 100 Copynumber: 5.8 Consensus size: 100
8076 TGAATAAAAA
* * * * * *
8086 TTGGATTTTTGATTAAAAGAT-GAATCTTTTAAGAAATTTATGAAT-AAAGATCGGACTTTTAAT
1 TTGGATTTGTAATTAAAAGATCGAA-CTTTTAAGAAATTTGTAAATAAAAG-TTGAACTTTTAAT
* *
8149 TAAAAGATTGAAACTTTT-GAACAATTGGTAAATAAAGG
64 TAAAAGATTG-AACTTTTAGGA-AATTTGTAAATAAAGG
*
8187 TTGGACTTT-TAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATT
1 TTGGA-TTTGTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATT
8251 AAAAGATTGAACTTTTAGGAAATTTGTAAATAAAGG
65 AAAAGATTGAACTTTTAGGAAATTTGTAAATAAAGG
* * *
8287 TTGGATTTGGAAGTAAAAGATCGAACTTTTAAGAAATTTGTAAACAAAAGTTGAACTTTTAATTA
1 TTGGATTTGTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATTA
*
8352 AAAGATTGAACTTTTAGGAAATTTGTAAATAAAGA
66 AAAGATTGAACTTTTAGGAAATTTGTAAATAAAGG
* * * *
8387 TTGGATTTGTAAGTAAAAGATCGAAGTTTTAAGTAATTTGTAAACAAAAGTTGAACTTTTAATTA
1 TTGGATTTGTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATTA
*
8452 AAAGATTGAACTTTTAGGAAATTTGTGAATAAAGG
66 AAAGATTGAACTTTTAGGAAATTTGTAAATAAAGG
* * * * *
8487 TTTGATTTGTAATTAAAAGATCAAACTTTCAAGAAATTTGTAAATAAAGGTTGGACTTTTAATTA
1 TTGGATTTGTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATTA
* *
8552 AAAGA-TGAATCTTCTAGGAAATTCGTAAATAAAGG
66 AAAGATTGAA-CTTTTAGGAAATTTGTAAATAAAGG
* * * * * * *
8587 TTGGACTTT-TAATTAAAAGATTGAAACTTTTGAGTAATTTGTAATTAAAGGTTGAATTTTTGAT
1 TTGGA-TTTGTAATTAAAAGATCG-AACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAAT
*
8651 TAAAAGATTGAATTTTT
64 TAAAAGATTGAACTTTT
8668 TAAGCGATTT
Statistics
Matches: 431, Mismatches: 41, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
99 7 0.02
100 307 0.71
101 103 0.24
102 14 0.03
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (100 bp):
TTGGATTTGTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATTA
AAAGATTGAACTTTTAGGAAATTTGTAAATAAAGG
Found at i:8374 original size:150 final size:151
Alignment explanation
Indices: 7992--8686 Score: 696
Period size: 150 Copynumber: 4.6 Consensus size: 151
7982 AAAAATTGAA
* ** * * * * * *
7992 TTTAATTGAAAGATT-AAACTTTTAAGTGATTTATGAATAAAGATAGAATTTTTAAGTGAAAA-A
1 TTTAATTAAAAGATTGAAACTTTTAAGAAATTTGTAAATAAAGGTTGAACTTTTAA-TTAAAAGA
* *** * * * * *
8055 TTGAAGCTTTCAATTGATTGGTGAATAAAAATTGGATTTTTGATTAAAAGATGAATCTTTTAAGA
65 TTGAA-CTTTTAAGAAATTTGTAAATAAAAGTTGGACTTTTAATTAAAAGATGAATCTTTTAAGA
* * * *
8120 AATTTATGAATAAAGATCGGACT
129 AATTTGTAAATAAAGGTTGGACT
* * *
8143 TTTAATTAAAAGATTGAAACTTTTGAA-CAATTGGTAAATAAAGGTTGGACTTTTAATTAAAAGA
1 TTTAATTAAAAGATTGAAACTTTT-AAGAAATTTGTAAATAAAGGTTGAACTTTTAATTAAAAGA
* *
8207 TTGAACTTTTAAGAAATTTGTAAATAAAAGTTGAACTTTTAATTAAAAGATTGAA-CTTTTAGGA
65 TTGAACTTTTAAGAAATTTGTAAATAAAAGTTGGACTTTTAATTAAAAGA-TGAATCTTTTAAGA
8271 AATTTGTAAATAAAGGTTGGA-T
129 AATTTGTAAATAAAGGTTGGACT
* * * * *
8293 TTGGAAGTAAAAGATCG-AACTTTTAAGAAATTTGTAAACAAAAGTTGAACTTTTAATTAAAAGA
1 TT-TAATTAAAAGATTGAAACTTTTAAGAAATTTGTAAATAAAGGTTGAACTTTTAATTAAAAGA
* * *
8357 TTGAACTTTTAGGAAATTTGTAAAT-AAAGATTGGA-TTTGTAAGTAAAAGATCGAA-GTTTTAA
65 TTGAACTTTTAAGAAATTTGTAAATAAAAG-TTGGACTTT-TAATTAAAAGAT-GAATCTTTTAA
* * * *
8419 GTAATTTGTAAACAAAAGTTGAACT
127 GAAATTTGTAAATAAAGGTTGGACT
* *
8444 TTTAATTAAAAGATTG-AACTTTTAGGAAATTTGTGAATAAAGGTTTG-A-TTTGTAATTAAAAG
1 TTTAATTAAAAGATTGAAACTTTTAAGAAATTTGTAAATAAAGG-TTGAACTTT-TAATTAAAAG
** * * * *
8506 ATCAAACTTTCAAGAAATTTGTAAATAAAGGTTGGACTTTTAATTAAAAGATGAATCTTCTAGGA
64 ATTGAACTTTTAAGAAATTTGTAAATAAAAGTTGGACTTTTAATTAAAAGATGAATCTTTTAAGA
*
8571 AATTCGTAAATAAAGGTTGGACT
129 AATTTGTAAATAAAGGTTGGACT
* * * * *
8594 TTTAATTAAAAGATTGAAACTTTTGAGTAATTTGTAATTAAAGGTTGAATTTTTGATTAAAAGAT
1 TTTAATTAAAAGATTGAAACTTTTAAGAAATTTGTAAATAAAGGTTGAACTTTTAATTAAAAGAT
* **
8659 TGAATTTTTTAAGCGATTTG-AAATAAAA
66 TGAA-CTTTTAAGAAATTTGTAAATAAAA
8687 ACAAAGCCTT
Statistics
Matches: 448, Mismatches: 77, Indels: 38
0.80 0.14 0.07
Matches are distributed among these distances:
149 16 0.04
150 233 0.52
151 145 0.32
152 52 0.12
153 2 0.00
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (151 bp):
TTTAATTAAAAGATTGAAACTTTTAAGAAATTTGTAAATAAAGGTTGAACTTTTAATTAAAAGAT
TGAACTTTTAAGAAATTTGTAAATAAAAGTTGGACTTTTAATTAAAAGATGAATCTTTTAAGAAA
TTTGTAAATAAAGGTTGGACT
Found at i:8859 original size:21 final size:18
Alignment explanation
Indices: 8802--8859 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
8792 GATCCTCGAA
* *
8802 ATAAAGGATTAATTTATG
1 ATAAAAGATTAATTTTTG
*
8820 ATAAAAGCTTAATTTTTG
1 ATAAAAGATTAATTTTTG
8838 ATAAAAAGATTGAATCTTTTG
1 AT-AAAAGATT-AAT-TTTTG
8859 A
1 A
8860 GCGATTTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 17 0.52
19 7 0.21
20 3 0.09
21 6 0.18
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
ATAAAAGATTAATTTTTG
Found at i:9474 original size:48 final size:48
Alignment explanation
Indices: 9403--9618 Score: 351
Period size: 48 Copynumber: 4.5 Consensus size: 48
9393 ACAATGTTTT
* * *
9403 TCTTCAATATCTTATGCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
1 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
* * *
9451 TTTTCAATATTTTATTCCTGTTTTGCCATTCCCGGTCGGAGGGTGTTG
1 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
9499 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
1 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
9547 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
1 TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
* * *
9595 TTTTCAATGTCTTATTCCTGTTTT
1 TCTTCAATATTTTATTCCTGTTTT
9619 CAATGTTTTA
Statistics
Matches: 156, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 156 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (48 bp):
TCTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
Found at i:9618 original size:20 final size:20
Alignment explanation
Indices: 9593--9632 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9583 CGGAAGGTGT
9593 TGTTTTCAATGTCTTATTCC
1 TGTTTTCAATGTCTTATTCC
*
9613 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTCTTATTCC
9633 CGTGTTGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (20 bp):
TGTTTTCAATGTCTTATTCC
Found at i:9658 original size:68 final size:68
Alignment explanation
Indices: 9549--10220 Score: 823
Period size: 68 Copynumber: 10.0 Consensus size: 68
9539 AGGTGTTGTC
* * *
9549 TTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9614 GTT
66 GTT
9617 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATT-C-
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9680 ---
66 GTT
* * *
9680 --C--TG-TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9740 GTT
66 GTT
* * * *
9743 TTCAAT-TTTTATTCCTGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9807 GTT
66 GTT
* *
9810 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCCGTCGGAGGGTGTTGTTTTCAATGTCTTATTCCT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9875 GTT
66 GTT
9878 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
9943 GTT
66 GTT
* * * *
9946 TTCAATGTTTTATCCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTT
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
*
10011 GCT
66 GTT
** * * ** * * * * *
10014 TTCAATGTTTTATTCCTATTTTGCCCTTCCTGGTCGGAAGACGTT-ATTTCAATATTTTTTTTCA
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-GTCTTATTCC
10078 TGTT
65 TGTT
* ** * * * *
10082 TTCAACGTTTCGTTCCCGT-TTCGCCCTTTCCGGTCGGAAGGTGTTGTTTTCATTGTTTTATTCT
1 TTCAATGTTTTATTCCCGTGTT-GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCC
10146 TGCTT
65 TG-TT
* * ** * * *
10151 TT-AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCATAAGATGTTGTTTTTTAATGTTTTATTCC
1 TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTG-TTTTCAATGTCTTATTCC
*
10215 CGTT
65 TGTT
10219 TT
1 TT
10221 GCCCTTCCCC
Statistics
Matches: 532, Mismatches: 55, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
58 51 0.10
59 3 0.01
61 1 0.00
65 1 0.00
67 76 0.14
68 372 0.70
69 28 0.05
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (68 bp):
TTCAATGTTTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCT
GTT
Found at i:9718 original size:58 final size:58
Alignment explanation
Indices: 9625--9810 Score: 255
Period size: 58 Copynumber: 3.1 Consensus size: 58
9615 TTTTCAATGT
* * *
9625 TTTATTCCCGTGTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTCTTATTCCTG
1 TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCTG
9683 TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCTG
1 TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCTG
*
9741 TTTTCAATTTTTATTCCTGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCC
1 ---------TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCC
9806 TG
57 TG
9808 TTT
1 TTT
9811 TCAATGTTTT
Statistics
Matches: 115, Mismatches: 4, Indels: 18
0.84 0.03 0.13
Matches are distributed among these distances:
58 58 0.50
67 57 0.50
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (58 bp):
TTTATTCCCGTGTTGCCCTTCCCGGTCGGAGGGTGTTATTTTCAATGACTTATTCCTG
Found at i:9879 original size:20 final size:20
Alignment explanation
Indices: 9854--9893 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9844 CGGAGGGTGT
9854 TGTTTTCAATGTCTTATTCC
1 TGTTTTCAATGTCTTATTCC
*
9874 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTCTTATTCC
9894 CGTGTTGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (20 bp):
TGTTTTCAATGTCTTATTCC
Found at i:9966 original size:20 final size:20
Alignment explanation
Indices: 9923--9967 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9913 GGAAGGTGTT
* *
9923 GTTTTCAATGTCTTATTCCT
1 GTTTTCAATGTCTTATCCCC
*
9943 GTTTTCAATGTTTTATCCCC
1 GTTTTCAATGTCTTATCCCC
9963 GTTTT
1 GTTTT
9968 GCCCTTCCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (20 bp):
GTTTTCAATGTCTTATCCCC
Found at i:28132 original size:3 final size:3
Alignment explanation
Indices: 28124--28151 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28114 TGGGGAGTAG
28124 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
28152 AACCCACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:32738 original size:21 final size:22
Alignment explanation
Indices: 32714--32762 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
32704 GCTCCCCTTT
32714 TTTTGGTTTGAGCTTGGTT-TG
1 TTTTGGTTTGAGCTTGGTTCTG
*
32735 TTTTTGTTTGAGCTTGGTTCTG
1 TTTTGGTTTGAGCTTGGTTCTG
*
32757 GTTTGG
1 TTTTGG
32763 ACAGTGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.04, C:0.06, G:0.33, T:0.57
Consensus pattern (22 bp):
TTTTGGTTTGAGCTTGGTTCTG
Found at i:36180 original size:925 final size:913
Alignment explanation
Indices: 34306--36346 Score: 3504
Period size: 925 Copynumber: 2.2 Consensus size: 913
34296 GGTGTCTACA
* * * *
34306 AGTTTTTTGTGTGTTACATTGGTATATAATTATTAATATTATGTATTATATATATAGTGTATGTA
1 AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
* *
34371 GGTGTATATATACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
66 TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
* * * * *
34436 TTTACTGTGGATATTATATATATACTTGTTTCTTTGTTTTTTAGGTACAATGTTAATTACTCCAT
131 TTTATTGTGGATATTATATATATAGTTGTTTCTTTGTTTTTTAGGTGCAAGGTTAA-TACTCCAC
*
34501 CCTTTTGCAGTGCATGCAGAAGCAAGATTTGATGCTGAAGGGTCGCATGAGATCTGTGGAATTGT
195 CCTTTTGCAGTGCATGCAGAAGCAAGATTTGATGCTGAAGAGTCGCATGAGATCTGTGGAATTGT
* * * * *
34566 TGGTTTTTTCACCTAGATTGTTGCTTAATTAATTCCAGGGTGATTTTCTTTCTGACAAAAAGATA
260 TGGCTTTTTCACCTAGATTGTTGCTTAACTAAGTCCAGGGTGACTATCTTTCTGACAAAAAGATA
* *
34631 AAAACTCAGGGTGAGAGGTCATTATCACGATGATTCTAACAAAAAACAGTGCATTGATTGGTAAA
325 AAAACTCAAGGTGAGAGGTCATTATCACGATGATTCTAACAAAAAACAATGCATTGATTGGTAAA
34696 TTCAAGATGAAATTAACCAGGTTTACAAAAGATCCTCTATGAAACCTAAAAGTGCGAACATGCCC
390 TTCAAGATGAAATTAACCAGGTTTACAAAAGATCCTCTATGAAACCTAAAAGTGCGAACATGCCC
34761 TTTGGAAACCTTAACAGGGCTCCAAAAGAAGGTGAAGCTGTTTCTCATGGACATAGATAAGTCTA
455 TTTGGAAACCTTAACAGGGCTCCAAAAGAAGGTGAAGCTGTTTCTCATGGACATAGATAAGTCTA
34826 AAGATGCAACTTATTGTTGTGACAAAAACACGCCAAATGATATTTGTTGCAACAGTAAAGCACAA
520 AAGATGCAACTTATTGTTGTGACAAAAACACGCCAAATGATATTTGTTGCAACAGTAAAGCACAA
34891 AAGGATTATGTTGGTTATCATATGTCTGTTAGCAAGGTGTTTTTTTCCAACAAGACTGATGGGAT
585 AAGGATTATGTTGGTTATCATATGTCTGTTAGCAAGGTGTTTTTTTCCAACAAGACTGATGGGAT
34956 TTCAAGCATGCTATGGTGCAATAACATAAGATTATTTTTCAGAGTGCCAGCCAAGTTATATATAG
650 TTCAAGCATGCTATGGTGCAATAACATAAGATTATTTTTCAGAGTGCCAGCCAAGTTATATATAG
35021 ATACACACACACACACATCATTAGACTATTTATAGCTATAACATAGCTAAATGAACAGAGAAAAC
715 ATA-ACACACACACACATCATTAGACTATTTATAGCTATAACATAGCTAAATGAACAGAGAAAAC
*
35086 CCTAAACCCATACCCTGATACTAATTAAGTATAAACTGACTCTGATACCGCCTATTTGGATAGCA
779 CCTAAACCCATACCCTGATACTAATTAAGTATAAACTGACTCTGATACCACCTATTTGGATAGCA
35151 AATACAGTAAATACTCGATAAACGACCCATATACATTTTATAGAACTTAAATCCAAAAAAATAAA
844 AATACAGTAAATACTCGATAAACGACCCATATACATTTTATAGAACTTAAATCCAAAAAAATAAA
35216 CTATT
909 CTATT
35221 AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
1 AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
35286 TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
66 TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
*
35351 TTTATTGTGGATATTATATATATAGTTGTTTCTTTGTTTTTTAGGTGCAAGGTCAATACTCCACC
131 TTTATTGTGGATATTATATATATAGTTGTTTCTTTGTTTTTTAGGTGCAAGGTTAATACTCCACC
*
35416 CTTTTGCAGTGCATGGAGAAGCAAGATTTGATGCTGAAGAGTCGCATGAGATCTGTGGAATTGTT
196 CTTTTGCAGTGCATGCAGAAGCAAGATTTGATGCTGAAGAGTCGCATGAGATCTGTGGAATTGTT
* ** * *
35481 GGCTTTTTCATCTAGATTGTTGCTTAACTAAGTGTATGGTGACTATCTTTCT-A-ATAATA-A-A
261 GGCTTTTTCACCTAGATTGTTGCTTAACTAAGTCCAGGGTGACTATCTTTCTGACA-AAAAGATA
* *
35542 AAAACTCAAGGT-AGAGGTCATTATCACGATGATTTTAACAAAAAACAATGCATTGATTGGTGAA
325 AAAACTCAAGGTGAGAGGTCATTATCACGATGATTCTAACAAAAAACAATGCATTGATTGGTAAA
* **
35606 TTCAAGATGAAATTAA-CAGGGTTTACAAAAGATCCTCT-TTAGGGCCTAAAAGTGCGAACATGC
390 TTCAAGATGAAATTAACCA-GGTTTACAAAAGATCCTCTATGA-AACCTAAAAGTGCGAACATGC
35669 CCTTTGGAAACCTTAACAGGGCTCCAAAAGAAGGTGAAGCGGTATCACCTCTACCATTGTTTCTC
453 CCTTTGGAAACCTTAACAGGGCTCCAAAAGAAGGTGAA---G------------C--TGTTTCTC
35734 ATGGACATAGATAAGTCTAAAGATGCAACTTATTGTTGTGACAAAAACACGCCAAATGATATTTG
501 ATGGACATAGATAAGTCTAAAGATGCAACTTATTGTTGTGACAAAAACACGCCAAATGATATTTG
35799 TTGCAACAGTAAAGCACAAAAGGATTATGTTGGTTATCATATGTCTGTTAGCAAGGTGTTTTTTT
566 TTGCAACAGTAAAGCACAAAAGGATTATGTTGGTTATCATATGTCTGTTAGCAAGGTGTTTTTTT
35864 CCAACAAGACTGATGGGATTTCAAGCATGCTATGGTGCAATAACATAAGATTATTTTTCAGAGTG
631 CCAACAAGACTGATGGGATTTCAAGCATGCTATGGTGCAATAACATAAGATTATTTTTCAGAGTG
35929 CCAGCCAAGTTATATATAGAT-ACACACACACACATCATTAGACTATTTATAGCTATAACATAGC
696 CCAGCCAAGTTATATATAGATAACACACACACACATCATTAGACTATTTATAGCTATAACATAGC
35993 TAAATGAACAGAGAAAACCCTAAACCCATACCCTGATACTAATTAAGTATAAACTGACTCTGATA
761 TAAATGAACAGAGAAAACCCTAAACCCATACCCTGATACTAATTAAGTATAAACTGACTCTGATA
* *
36058 CCACCTATTTGGATAGCAAATACAGTAAATACTCGATAAATGACCCATATACGTTTTATAGAACT
826 CCACCTATTTGGATAGCAAATACAGTAAATACTCGATAAACGACCCATATACATTTTATAGAACT
36123 TAAATCCAAAAAAATAAACTATT
891 TAAATCCAAAAAAATAAACTATT
36146 AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
1 AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
36211 TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
66 TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
*
36276 TTTATTGTGGATATTATATATATGGTTGTTTCTTTGTTTTTTAGGTGCAAGGTTAATCACTCCAC
131 TTTATTGTGGATATTATATATATAGTTGTTTCTTTGTTTTTTAGGTGCAAGGTTAAT-ACTCCAC
36341 CCTTTT
195 CCTTTT
36347 TTACAAGTGA
Statistics
Matches: 1069, Mismatches: 36, Indels: 31
0.94 0.03 0.03
Matches are distributed among these distances:
909 4 0.00
910 141 0.13
911 12 0.01
912 2 0.00
913 5 0.00
914 114 0.11
915 175 0.16
925 379 0.35
926 13 0.01
927 224 0.21
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (913 bp):
AGTTTTTTGTGTCTTACGTAGGTATATACTTATTAATATTATGTATTATATATATAGTGTATGTA
TGTGTATATACACACATATATACAACTCCTTATATATGTAAATTTCAAACAAATAATGTAATAAA
TTTATTGTGGATATTATATATATAGTTGTTTCTTTGTTTTTTAGGTGCAAGGTTAATACTCCACC
CTTTTGCAGTGCATGCAGAAGCAAGATTTGATGCTGAAGAGTCGCATGAGATCTGTGGAATTGTT
GGCTTTTTCACCTAGATTGTTGCTTAACTAAGTCCAGGGTGACTATCTTTCTGACAAAAAGATAA
AAACTCAAGGTGAGAGGTCATTATCACGATGATTCTAACAAAAAACAATGCATTGATTGGTAAAT
TCAAGATGAAATTAACCAGGTTTACAAAAGATCCTCTATGAAACCTAAAAGTGCGAACATGCCCT
TTGGAAACCTTAACAGGGCTCCAAAAGAAGGTGAAGCTGTTTCTCATGGACATAGATAAGTCTAA
AGATGCAACTTATTGTTGTGACAAAAACACGCCAAATGATATTTGTTGCAACAGTAAAGCACAAA
AGGATTATGTTGGTTATCATATGTCTGTTAGCAAGGTGTTTTTTTCCAACAAGACTGATGGGATT
TCAAGCATGCTATGGTGCAATAACATAAGATTATTTTTCAGAGTGCCAGCCAAGTTATATATAGA
TAACACACACACACATCATTAGACTATTTATAGCTATAACATAGCTAAATGAACAGAGAAAACCC
TAAACCCATACCCTGATACTAATTAAGTATAAACTGACTCTGATACCACCTATTTGGATAGCAAA
TACAGTAAATACTCGATAAACGACCCATATACATTTTATAGAACTTAAATCCAAAAAAATAAACT
ATT
Found at i:38421 original size:2 final size:2
Alignment explanation
Indices: 38414--38443 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38404 CCTGCCAGGT
*
38414 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38444 AAAATAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48063 original size:15 final size:15
Alignment explanation
Indices: 48040--48077 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
48030 GAAAGTAATA
*
48040 AAACAAAATTAAACT
1 AAACTAAATTAAACT
48055 AAACTAAATTAAACT
1 AAACTAAATTAAACT
48070 AAAGCTAA
1 AAA-CTAA
48078 GGAAAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.21
Consensus pattern (15 bp):
AAACTAAATTAAACT
Found at i:49429 original size:28 final size:28
Alignment explanation
Indices: 49393--49488 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
49383 GTCACCTAAG
*
49393 GGGGCATTTTGATCATTTTGCATGACCA
1 GGGGCATTTTGATCATTTTGCATGTCCA
* *
49421 GGGGCATTTTGGTCATTTTGCATGTTCA
1 GGGGCATTTTGATCATTTTGCATGTCCA
* * *
49449 GGGGCATCTTGACCATTTTGCACGTCCA
1 GGGGCATTTTGATCATTTTGCATGTCCA
49477 GGAGGCATTTTG
1 GG-GGCATTTTG
49489 GGTCACTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 50 0.86
29 8 0.14
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (28 bp):
GGGGCATTTTGATCATTTTGCATGTCCA
Found at i:50053 original size:25 final size:24
Alignment explanation
Indices: 50024--50074 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
50014 TGGTAGTTTT
50024 ACTCTACATTTACATTTCTTTTTGC
1 ACTCTACATTTACATTTC-TTTTGC
50049 ACTCTACATTTACATTTCTTTTGC
1 ACTCTACATTTACATTTCTTTTGC
50073 AC
1 AC
50075 CAAATGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.22, C:0.25, G:0.04, T:0.49
Consensus pattern (24 bp):
ACTCTACATTTACATTTCTTTTGC
Found at i:50705 original size:17 final size:17
Alignment explanation
Indices: 50683--50717 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
50673 CTCAAGCATA
*
50683 AGCATTTCATCCTAAAG
1 AGCATTTCATCATAAAG
50700 AGCATTTCATCATAAAG
1 AGCATTTCATCATAAAG
50717 A
1 A
50718 AACAGTGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (17 bp):
AGCATTTCATCATAAAG
Found at i:53760 original size:17 final size:18
Alignment explanation
Indices: 53738--53774 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53728 ATAGAGATAG
*
53738 AAAAAGA-AGAAAATCAA
1 AAAAAGAGAAAAAATCAA
53755 AAAAAGAGAAAAAATCAA
1 AAAAAGAGAAAAAATCAA
53773 AA
1 AA
53775 GAGGTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAAAAAATCAA
Found at i:53804 original size:16 final size:16
Alignment explanation
Indices: 53783--53815 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53773 AAGAGGTAAT
*
53783 AAAAGGTTTTTTTCAA
1 AAAAGGTTTTTCTCAA
53799 AAAAGGTTTTTCTCAA
1 AAAAGGTTTTTCTCAA
53815 A
1 A
53816 TCATGTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
AAAAGGTTTTTCTCAA
Found at i:55665 original size:39 final size:39
Alignment explanation
Indices: 55605--55681 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
55595 TTGCGTTGAG
* *
55605 TCACTTTGGTTATTCCTTTAATTTGCATTAGAATCACTT
1 TCACTTTGGTTATTCCCTTAATTTGCATTACAATCACTT
55644 TCACTTTGGCTT-TTCCCTTAATTTGCATTACAATCACT
1 TCACTTTGG-TTATTCCCTTAATTTGCATTACAATCACT
55682 AGTTGTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (39 bp):
TCACTTTGGTTATTCCCTTAATTTGCATTACAATCACTT
Found at i:57971 original size:14 final size:14
Alignment explanation
Indices: 57951--57989 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
57941 GAGAGAGGGA
*
57951 AGAAGAAAGAACAAG
1 AGAAGAAA-AAAAAG
57966 -GAAGAAAAAAAAG
1 AGAAGAAAAAAAAG
57979 AGAAGAAAAAA
1 AGAAGAAAAAA
57990 TAAAAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAAAG
Found at i:58344 original size:19 final size:19
Alignment explanation
Indices: 58309--58346 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58299 TAGAGTTAGC
* *
58309 AATTAATTAGTATTTTCAT
1 AATTAATTAGAAATTTCAT
58328 AATTAATTAGAAATTTCAT
1 AATTAATTAGAAATTTCAT
58347 TTTGCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
AATTAATTAGAAATTTCAT
Found at i:59979 original size:46 final size:46
Alignment explanation
Indices: 59929--60146 Score: 282
Period size: 46 Copynumber: 4.8 Consensus size: 46
59919 AAAGAGGAAT
*
59929 GTTTTTTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAA
1 GTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAA
* * *
59975 GTTTTCTAGTCAAGTAATTCCAAAAGAAAATTTT-GGAAAATAAAA
1 GTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAA
* * *
60020 ATTTTCTCTTTAAGTAATTCCAAAAAAAGATTTTGGGAAAATAAAA
1 GTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAA
* * *
60066 GTTTTCTAGTCAAGTAATTCCAAAAGAAGATTTT-GGAAAATGAAAG
1 GTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAAT-AAAA
* *
60112 GTTTT-TATTTTAAG-AAATCCAAAAGAAAATTTTGG
1 GTTTTCTA-TTTAAGTAATTCCAAAAGAAGATTTTGG
60147 AAATTAATAA
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
45 65 0.44
46 83 0.56
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (46 bp):
GTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAA
Found at i:60035 original size:91 final size:92
Alignment explanation
Indices: 59931--60146 Score: 332
Period size: 91 Copynumber: 2.4 Consensus size: 92
59921 AGAGGAATGT
59931 TTTTTA-TTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAAGTTTTCTAGTCAAGTAATTC
1 TTTTTACTTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAAGTTTTCTAGTCAAGTAATTC
59995 CAAAAGAAAATTTTGGAAAAT-AAAAA
66 CAAAAGAAAATTTTGGAAAATGAAAAA
*
60021 TTTTCT-CTTTAAGTAATTCCAAAAAAAGATTTTGGGAAAATAAAAGTTTTCTAGTCAAGTAATT
1 TTTT-TACTTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAAGTTTTCTAGTCAAGTAATT
* **
60085 CCAAAAGAAGATTTTGGAAAATGAAAGG
65 CCAAAAGAAAATTTTGGAAAATGAAAAA
* * *
60113 TTTTTATTTTAAG-AAATCCAAAAGAAAATTTTGG
1 TTTTTACTTTAAGTAATTCCAAAAGAAGATTTTGG
60147 AAATTAATAA
Statistics
Matches: 114, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
90 4 0.04
91 97 0.85
92 13 0.11
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.34
Consensus pattern (92 bp):
TTTTTACTTTAAGTAATTCCAAAAGAAGATTTTGGGAAAATAAAAGTTTTCTAGTCAAGTAATTC
CAAAAGAAAATTTTGGAAAATGAAAAA
Found at i:61155 original size:9 final size:9
Alignment explanation
Indices: 61143--61172 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
61133 TTCTGCCGAA
61143 TCTCTGCTT
1 TCTCTGCTT
61152 TCTCTGCTT
1 TCTCTGCTT
61161 TCTCTGCTT
1 TCTCTGCTT
61170 TCT
1 TCT
61173 TTTACTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.10, T:0.57
Consensus pattern (9 bp):
TCTCTGCTT
Found at i:74090 original size:83 final size:83
Alignment explanation
Indices: 73979--74144 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 83
73969 GTGGAAGACC
* *
73979 ATCATATATCATGTTTCGAAATTAATTATGATTCGAAGCAACTAATTATTGTAATCTAATATAAT
1 ATCATATATCATATTTCAAAATTAATTATGATTCGAAGCAACTAATTATTGTAATCTAATATAAT
*
74044 TAAATTACTATAAAAAAA
66 TAAATTACTAGAAAAAAA
* *
74062 ATCATATATCATATTTCAAAATTAATTATGATTCGAAGTAACTAATTGTTGTAATCTAATATAAT
1 ATCATATATCATATTTCAAAATTAATTATGATTCGAAGCAACTAATTATTGTAATCTAATATAAT
*
74127 TAAATTATTAGAAAAAAA
66 TAAATTACTAGAAAAAAA
74145 TATAATTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (83 bp):
ATCATATATCATATTTCAAAATTAATTATGATTCGAAGCAACTAATTATTGTAATCTAATATAAT
TAAATTACTAGAAAAAAA
Found at i:77128 original size:24 final size:24
Alignment explanation
Indices: 77076--77133 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
77066 CCACTTGCAC
*
77076 TTCCTCCACCTCAGAATCGGAACG
1 TTCCTCCACCTCAGAATCGGAACA
* *
77100 CTCCTCCACCTCAGAATCGGAATA
1 TTCCTCCACCTCAGAATCGGAACA
77124 TTCCTCCACC
1 TTCCTCCACC
77134 GATTCCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.22
Consensus pattern (24 bp):
TTCCTCCACCTCAGAATCGGAACA
Found at i:84435 original size:28 final size:27
Alignment explanation
Indices: 84366--84439 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
84356 TAGCATTTAG
*
84366 GGGCAAAACTGTAA-TTTAGTCAACCAA
1 GGGCAAAAC-GTAATTTTAGCCAACCAA
* * *
84393 GGGTAAAATGATAATTTTAGCCGACCAA
1 GGGCAAAACG-TAATTTTAGCCAACCAA
84421 GGGCAAATACGTAATTTTA
1 GGGCAAA-ACGTAATTTTA
84440 ACGTCATAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 10 0.26
28 25 0.66
29 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (27 bp):
GGGCAAAACGTAATTTTAGCCAACCAA
Found at i:85403 original size:34 final size:35
Alignment explanation
Indices: 85337--85414 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 35
85327 AGCTTGAGCA
*
85337 CTGGGCCATGGCTGGCCCGCGCACCAGGCCTGGGCG
1 CTGGGCCATAGCTGGCCCGCG-ACCAGGCCTGGGCG
85373 CTGGGCCATAGCTGGCCCGCG-CCAGGCCTGGGCG
1 CTGGGCCATAGCTGGCCCGCGACCAGGCCTGGGCG
85407 CTTGGGCC
1 C-TGGGCC
85415 GCGCCAGGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
34 14 0.35
35 6 0.15
36 20 0.50
ACGTcount: A:0.08, C:0.38, G:0.41, T:0.13
Consensus pattern (35 bp):
CTGGGCCATAGCTGGCCCGCGACCAGGCCTGGGCG
Found at i:85438 original size:24 final size:24
Alignment explanation
Indices: 85389--85438 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
85379 CATAGCTGGC
* **
85389 CCGCGCCAGGCCTGGGCGCTTGGG
1 CCGCGCCAGGCCTGGGCCCAAGGG
85413 CCGCGCCAGGCCT-GGCCCAAGCGG
1 CCGCGCCAGGCCTGGGCCCAAG-GG
85437 CC
1 CC
85439 CTAGCTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.08, C:0.44, G:0.40, T:0.08
Consensus pattern (24 bp):
CCGCGCCAGGCCTGGGCCCAAGGG
Found at i:85472 original size:16 final size:16
Alignment explanation
Indices: 85453--85484 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
85443 CTCTCATCAA
85453 TTTTTTTTC-TCTTCT
1 TTTTTTTTCTTCTTCT
85468 TTTTTTTTCTTCTTCT
1 TTTTTTTTCTTCTTCT
85484 T
1 T
85485 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTTCTTCT
Found at i:87357 original size:44 final size:44
Alignment explanation
Indices: 87289--87518 Score: 204
Period size: 44 Copynumber: 5.2 Consensus size: 44
87279 TAGAAGAGTG
* * * *
87289 GTTATCAAGATTTCATA-AGATGGTTATTATAATTTCATGAGGAA
1 GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCAT-AGGAA
* *
87333 GTTATCAAAATTCCATAGTG-TGGTTACCAAAATTTCATATGGAA
1 GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATA-GGAA
* **
87377 G-TATCAAAATTTCAT-GTGAAGGTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GAA
* * *
87420 GTTACCAAAATTTCATAG-GATCAGGTTATTAAAATTTCTTAGGAA
1 GTTATCAAAATTTCATAGTGAT--GGTTATCAAAATTTCATAGGAA
** *
87465 GGTTATTGAAATTTCATAGTG-TGGTTATCACAAATTT-ATAGAAA
1 -GTTATCAAAATTTCATAGTGATGGTTATCA-AAATTTCATAGGAA
87509 GGTTATCAAA
1 -GTTATCAAA
87519 GAGATTATAA
Statistics
Matches: 150, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.03
43 33 0.22
44 70 0.47
45 9 0.06
46 33 0.22
47 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
Found at i:87386 original size:21 final size:22
Alignment explanation
Indices: 87288--87518 Score: 154
Period size: 22 Copynumber: 10.5 Consensus size: 22
87278 TTAGAAGAGT
* * *
87288 GGTTATCAAGATTTCATAAGAT
1 GGTTATCAAAATTTCATATGAA
* * *
87310 GGTTATTATAATTTCATGAGGAA
1 GGTTATCAAAATTTCAT-ATGAA
* *
87333 -GTTATCAAAATTCCATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
*
87354 GGTTACCAAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAT-GAA
*
87377 -G-TATCAAAATTTCATGTGAA
1 GGTTATCAAAATTTCATATGAA
*
87397 GGTTATCAAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
* *
87419 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATATGA--A
* * *
87443 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATATGAA
** *
87465 GGTTATTGAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
87487 GGTTATCACAAATTT-ATA-GAAA
1 GGTTATCA-AAATTTCATATG-AA
87509 GGTTATCAAA
1 GGTTATCAAA
87519 GAGATTATAA
Statistics
Matches: 164, Mismatches: 30, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.02
21 20 0.12
22 110 0.67
23 12 0.07
24 18 0.11
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGAA
Found at i:87481 original size:68 final size:67
Alignment explanation
Indices: 87286--87514 Score: 249
Period size: 65 Copynumber: 3.5 Consensus size: 67
87276 AATTAGAAGA
* * * * * *
87286 GTGGTTATCAAGATTTCATAAGAT-GGTTATTATAATTTCATGAGGAA-GTTATCAAAATTCCAT
1 GTGGTTACCAAAATTTCATAGGATAGGTTATTAAAATTTC-TTAGGAAGGTTATCAAAATTTCAT
87349 AGT
65 AGT
* *
87352 GTGGTTACCAAAATTTCATATGGA-A-G-TATCAAAATTTCAT-GTGAAGGTTATCAAAATTTCA
1 GTGGTTACCAAAATTTCATA-GGATAGGTTATTAAAATTTCTTAG-GAAGGTTATCAAAATTTCA
87413 TAGT
64 TAGT
**
87417 GTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTCAT
1 GTGGTTACCAAAATTTCATAGGAT-AGGTTATTAAAATTTCTTAGGAAGGTTATCAAAATTTCAT
87482 AGT
65 AGT
* *
87485 GTGGTTATCACAAATTT-ATA-GAAAGGTTAT
1 GTGGTTACCA-AAATTTCATAGGATAGGTTAT
87515 CAAAGAGATT
Statistics
Matches: 139, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 6 0.04
65 48 0.35
66 27 0.19
67 5 0.04
68 45 0.32
69 7 0.05
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (67 bp):
GTGGTTACCAAAATTTCATAGGATAGGTTATTAAAATTTCTTAGGAAGGTTATCAAAATTTCATA
GT
Found at i:87545 original size:22 final size:22
Alignment explanation
Indices: 87519--87561 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
87509 GGTTATCAAA
87519 GAGATTATAAAAATTCCATAGC
1 GAGATTATAAAAATTCCATAGC
* *
87541 GAGATTATAAGAATTTCATAG
1 GAGATTATAAAAATTCCATAG
87562 TGTGGTTAAC
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:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (22 bp):
GAGATTATAAAAATTCCATAGC
Found at i:87577 original size:22 final size:22
Alignment explanation
Indices: 87552--87669 Score: 100
Period size: 22 Copynumber: 5.4 Consensus size: 22
87542 AGATTATAAG
*
87552 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGTGGTTATCAA
*
87574 AATTTCATAAG-GAGG-TA-CTAA
1 AATTTCAT-AGTGTGGTTATC-AA
* * * * *
87595 TATATCATGGGGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
87617 AATTTCATAGTGTGGTTATCAAA
1 AATTTCATAGTGTGGTTATC-AA
* *
87640 AATTT-TTTGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
87661 AATTTCATA
1 AATTTCATA
87670 TGAAGGTTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
20 2 0.03
21 21 0.28
22 43 0.57
23 10 0.13
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:87677 original size:22 final size:21
Alignment explanation
Indices: 87606--87683 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
87596 ATATCATGGG
87606 GAGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATA-T
* ** *
87628 GTGGTTATCAAAAATTTTTTGT
1 GAGGTTATC-AAAATTTCATAT
*
87650 GTGGTTATCAAAATTTCATAT
1 GAGGTTATCAAAATTTCATAT
87671 GAAGGTTAT-AAAA
1 G-AGGTTATCAAAA
87684 GTCTCAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.30
22 24 0.52
23 8 0.17
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAT
Found at i:87747 original size:21 final size:22
Alignment explanation
Indices: 87723--87763 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
87713 TGATAGAAGG
87723 TTATC-AAATCTCATAGAGTGA
1 TTATCGAAATCTCATAGAGTGA
*
87744 TTATCGAAATTTCATAGAGT
1 TTATCGAAATCTCATAGAGT
87764 TCGGATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCGAAATCTCATAGAGTGA
Found at i:88265 original size:25 final size:21
Alignment explanation
Indices: 88215--88262 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
88205 AATTTGAGGG
88215 GTGAGTACACGAATGTACTCA
1 GTGAGTACACGAATGTACTCA
88236 GTGAGTACACGAATGTACTCA
1 GTGAGTACACGAATGTACTCA
88257 GTGAGT
1 GTGAGT
88263 GAGCCACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGAGTACACGAATGTACTCA
Found at i:90224 original size:35 final size:36
Alignment explanation
Indices: 90150--90234 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
90140 GGCCCAAACT
* *
90150 TGGGCGCTGGGCCAGGGCTAGACCGCGCGCCAGGCC
1 TGGGCGCTGGGCCAGCGCTAGACCGCGCGCCAGGAC
* *
90186 TGGGCGCTGGGCCATGCGCT-GGCC-CGCGCCTGGAC
1 TGGGCGCTGGGCCA-GCGCTAGACCGCGCGCCAGGAC
90221 TGGGCGCTTGGGCC
1 TGGGCGC-TGGGCC
90235 GTGCCAGGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 16 0.37
36 23 0.53
37 4 0.09
ACGTcount: A:0.07, C:0.35, G:0.45, T:0.13
Consensus pattern (36 bp):
TGGGCGCTGGGCCAGCGCTAGACCGCGCGCCAGGAC
Done.