Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013430.1 Kokia drynarioides strain JFW-HI SEQ_128456, 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: 105439
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:2874 original size:13 final size:14
Alignment explanation
Indices: 2845--2874 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2835 TTCAATACAT
2845 TGACATTTAACCTC
1 TGACATTTAACCTC
2859 TGACATTTAA-CTC
1 TGACATTTAACCTC
2872 TGA
1 TGA
2875 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:8622 original size:14 final size:14
Alignment explanation
Indices: 8593--8641 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
8583 CACGAACAAT
8593 TATACGAATGAATAAA
1 TATACGAA--AATAAA
8609 TATACGAAAATAAA
1 TATACGAAAATAAA
*
8623 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
8638 -ATAC
1 TATAC
8642 AAATCATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 14 0.47
15 8 0.27
16 8 0.27
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.22
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:8675 original size:19 final size:18
Alignment explanation
Indices: 8653--8699 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
8643 AATCATGAAT
8653 CAAAATAAATGATAAAATA
1 CAAAATAAATGA-AAAATA
* *
8672 CAAAATTAATTAAAAATA
1 CAAAATAAATGAAAAATA
*
8690 CAAAAAAAAT
1 CAAAATAAAT
8700 AGTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.21
Consensus pattern (18 bp):
CAAAATAAATGAAAAATA
Found at i:8814 original size:29 final size:28
Alignment explanation
Indices: 8781--9180 Score: 250
Period size: 30 Copynumber: 13.6 Consensus size: 28
8771 GGGTTTAAAC
*
8781 GTAATTTTAGAAAGTTTAGGAGTAAAAAT
1 GTAATTTTTGAAAGTTTAGG-GTAAAAAT
* * * *
8810 TTAATTTTGGGAAAGTTCAAGGT-AAAAT
1 GTAATTTT-TGAAAGTTTAGGGTAAAAAT
* *
8838 GTGATTTTTGAGAAGATTAGGGTAAAAAT
1 GTAATTTTTGA-AAGTTTAGGGTAAAAAT
* * ** **
8867 ATGATTTCTAAAAAGTTCGGGGTAAAAAT
1 GTAATTT-TTGAAAGTTTAGGGTAAAAAT
* * *
8896 GTGATTTTTGGAAGTTCTAAGGTAAAAAT
1 GTAATTTTTGAAAGTT-TAGGGTAAAAAT
* * *
8925 GTAATTTTTAAGAAGTTTGAGAGTAAAAAG
1 GTAATTTTTGA-AAGTTT-AGGGTAAAAAT
**
8955 GTAATTTTT-AGAAGTTCGGGGTAAAAAT
1 GTAATTTTTGA-AAGTTTAGGGTAAAAAT
** *
8983 GTAATTTTTGAGAAGTTCGGGAGTAAAAAA
1 GTAATTTTTGA-AAGTTTAGG-GTAAAAAT
* * * *
9013 ATTATTTTTGGAAGTTCAGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTA--GGGTAAAAAT
9043 GTAATTTTTGAGAAGTTTAGGGGTAAAAAT
1 GTAATTTTTGA-AAGTTTA-GGGTAAAAAT
* *
9073 GTGATTTTTGGAAGTTTAAGGG-AAAAATT
1 GTAATTTTTGAAAGTTT-AGGGTAAAAA-T
* *
9102 GTAATTTTTGAGAAG-TTCGGTGTTAAACAT
1 GTAATTTTTGA-AAGTTTAGG-G-TAAAAAT
* * *
9132 GTGAGTTTTAAAAGTTTTGAGGGTAAAAAT
1 GTAATTTTTGAAAG-TTT-AGGGTAAAAAT
*
9162 ATAATTTTTGAGAAGTTTA
1 GTAATTTTTGA-AAGTTTA
9181 AGGGCCTCTT
Statistics
Matches: 291, Mismatches: 58, Indels: 44
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.01
28 49 0.17
29 108 0.37
30 112 0.38
31 18 0.06
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (28 bp):
GTAATTTTTGAAAGTTTAGGGTAAAAAT
Found at i:8951 original size:30 final size:30
Alignment explanation
Indices: 8781--9184 Score: 286
Period size: 29 Copynumber: 13.8 Consensus size: 30
8771 GGGTTTAAAC
*
8781 GTAATTTTAGA-AAGTTT-AGGAGTAAAAAT
1 GTAATTTTTGAGAAGTTTGAGG-GTAAAAAT
* * * *
8810 TTAA-TTTTGGGAAAG-TTCAAGGT-AAAAT
1 GTAATTTTTGAG-AAGTTTGAGGGTAAAAAT
* *
8838 GTGATTTTTGAGAAGATT-AGGGTAAAAAT
1 GTAATTTTTGAGAAGTTTGAGGGTAAAAAT
* * * * * *
8867 ATGATTTCTAAAAAGTTCG-GGGTAAAAAT
1 GTAATTTTTGAGAAGTTTGAGGGTAAAAAT
* *
8896 GTGATTTTTG-GAAGTTCT-AAGGTAAAAAT
1 GTAATTTTTGAGAAGTT-TGAGGGTAAAAAT
* * *
8925 GTAATTTTTAAGAAGTTTGAGAGTAAAAAG
1 GTAATTTTTGAGAAGTTTGAGGGTAAAAAT
*
8955 GTAATTTTT-AGAAGTTCG-GGGTAAAAAT
1 GTAATTTTTGAGAAGTTTGAGGGTAAAAAT
* *
8983 GTAATTTTTGAGAAGTTCG-GGAGTAAAAAA
1 GTAATTTTTGAGAAGTTTGAGG-GTAAAAAT
* * * *
9013 ATTATTTTTG-GAAGTTCAGGGGGTAAAAAT
1 GTAATTTTTGAGAAGTT-TGAGGGTAAAAAT
9043 GTAATTTTTGAGAAGTTT-AGGGGTAAAAAT
1 GTAATTTTTGAGAAGTTTGA-GGGTAAAAAT
* *
9073 GTGATTTTTG-GAAGTTTAAGGG-AAAAATT
1 GTAATTTTTGAGAAGTTTGAGGGTAAAAA-T
* * *
9102 GTAATTTTTGAGAAGTTCG-GTGTTAAACAT
1 GTAATTTTTGAGAAGTTTGAG-GGTAAAAAT
* * *
9132 GTGAGTTTT-AAAAGTTTTGAGGGTAAAAAT
1 GTAATTTTTGAGAAG-TTTGAGGGTAAAAAT
* *
9162 ATAATTTTTGAGAAGTTTAAGGG
1 GTAATTTTTGAGAAGTTTGAGGG
9185 CCTCTTGAGC
Statistics
Matches: 296, Mismatches: 54, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
28 45 0.15
29 117 0.40
30 117 0.40
31 17 0.06
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
GTAATTTTTGAGAAGTTTGAGGGTAAAAAT
Found at i:11382 original size:51 final size:50
Alignment explanation
Indices: 11151--11819 Score: 403
Period size: 49 Copynumber: 13.5 Consensus size: 50
11141 TAAAGTGCTA
* * * ** *
11151 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCGTATCTTC-ATGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * *
11200 GGTTCGCCGTT-CAGCCTCAACCTTTCCTATCATATCTTTTAAGGTACCA
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * * * * *
11249 GATTCACCATCGTGGCCTCGATCATTCCCTTCATC-TCTTC-ATGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCA-CATCTTCTAAGGTACCG
* * * *
11298 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGTTATCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
*
11348 GGTTCACCGTTGCGGCCTTAACCTCTTCCCATCACATCTTCTAAGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCT-TTCCCATCACATCTTCTAAGGTACCG
* * * * * * * *
11399 GATTCACCGTCGTGGTCTCAATCC-TTCCCTTCAAATCTTC-ATGGTACTG
1 GGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * * * *
11448 GATTCGCCATTGCAGCCTTAACTTTTCCCATCACATCTTCTAAGGTATCA
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * *
11498 GATTCGCCGTCGCGGCCTCAATCC-TTCCCTTCAAATCTTC-ATGGTACCG
1 GGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCG
*** ** * * *
11547 GGTTTGTCGTTGC-AACTTAACCTTTCCCGTCACATATTCTAAGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* ** * * * * **
11596 GATTC-CTCGTCACGGTCTCAATCC-TTCCCTTCAAATCTTC-ATGGTACTA
1 GGTTCAC-CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * **
11645 AGTTCGCCGTTGCAGCCTAAACTTTTCCCATCACATCTTCTAAGGTATTG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* * * * * *
11695 GATTCGCCGTCGCGGCCTCAATCC-TTCCCTTCAAATCTTC-ATGGTACCG
1 GGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCG
* * * * *
11744 GGTTCGCCGTTGCAGCCTCGACCTTTCCTATCACATCTTCTAAGGTACTG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
* * *
11794 AGTTCGCCGTTGTGGCCTCAACCTTT
1 GGTTCACCGTTGCGGCCTCAACCTTT
11820 GCCTTCATAT
Statistics
Matches: 463, Mismatches: 136, Indels: 41
0.72 0.21 0.06
Matches are distributed among these distances:
47 2 0.00
48 44 0.10
49 193 0.42
50 179 0.39
51 43 0.09
52 2 0.00
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (50 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
Found at i:11638 original size:197 final size:198
Alignment explanation
Indices: 11300--11791 Score: 686
Period size: 197 Copynumber: 2.5 Consensus size: 198
11290 TGGTACCGGG
* * * * * * * * * *
11300 TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTTTAAGTTATCGGGTTCACCGTTGCGGC
1 TTCGCCGTCGCGGCCTCAATCC-TTCCCTTCAAATC-TTCATGGTACCGGGTTCGCCGTTGCAGA
**
11364 CTTAACCTCTTCCCATCACATCTTCTAAGGTACCGGATTCACCGTCGTGGTCTCAATCCTTCCCT
64 CTTAACCT-TTCCCATCACATCTTCTAAGGTACCGGATTCACCGTCACGGTCTCAATCCTTCCCT
* *
11429 TCAAATCTTCATGGTACT-GGATTCGCCATTGCAGCCTTAACTTTTCCCATCACATCTTCTAAGG
128 TCAAATCTTCATGGTACTAAG-TTCGCCATTGCAGCCTAAACTTTTCCCATCACATCTTCTAAGG
11493 TATCAGA
192 TATCAGA
* *
11500 TTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTTGTCGTTGCA-ACT
1 TTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCAGACT
* *
11564 TAACCTTTCCCGTCACATATTCTAAGGTACCGGATTC-CTCGTCACGGTCTCAATCCTTCCCTTC
66 TAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCAC-CGTCACGGTCTCAATCCTTCCCTTC
*
11628 AAATCTTCATGGTACTAAGTTCGCCGTTGCAGCCTAAACTTTTCCCATCACATCTTCTAAGGTAT
130 AAATCTTCATGGTACTAAGTTCGCCATTGCAGCCTAAACTTTTCCCATCACATCTTCTAAGGTAT
**
11693 TGGA
195 CAGA
*
11697 TTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCAGCCT
1 TTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCAGACT
** *
11762 CGACCTTTCCTATCACATCTTCTAAGGTAC
66 TAACCTTTCCCATCACATCTTCTAAGGTAC
11792 TGAGTTCGCC
Statistics
Matches: 259, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
196 1 0.00
197 173 0.67
198 36 0.14
199 18 0.07
200 29 0.11
201 2 0.01
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (198 bp):
TTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCAGACT
TAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCACCGTCACGGTCTCAATCCTTCCCTTCA
AATCTTCATGGTACTAAGTTCGCCATTGCAGCCTAAACTTTTCCCATCACATCTTCTAAGGTATC
AGA
Found at i:11826 original size:99 final size:99
Alignment explanation
Indices: 11291--11818 Score: 609
Period size: 99 Copynumber: 5.3 Consensus size: 99
11281 ATCTCTTCAT
* * * * * * * * * *
11291 GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTTTAAGTTATCGGGTTCAC
1 GGTACTGGATTCGCCGTCGCGGCCTCAATCC-TTCCCTTCAAATC-TTCATGGTACCGGGTTCGC
*
11355 CGTTGCGGCCTTAACCTCTTCCCATCACATCTTCTAA
64 CGTTGCAGCCTTAACCT-TTCCCATCACATCTTCTAA
* * * * * * *
11392 GGTACCGGATTCACCGTCGTGGTCTCAATCCTTCCCTTCAAATCTTCATGGTACTGGATTCGCCA
1 GGTACTGGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCG
*
11457 TTGCAGCCTTAACTTTTCCCATCACATCTTCTAA
66 TTGCAGCCTTAACCTTTCCCATCACATCTTCTAA
* * *
11491 GGTA-TCAGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTTGTC
1 GGTACT-GGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCC
* * *
11555 GTTGCA-ACTTAACCTTTCCCGTCACATATTCTAA
65 GTTGCAGCCTTAACCTTTCCCATCACATCTTCTAA
* * * ***
11589 GGTACCGGATTC-CTCGTCACGGTCTCAATCCTTCCCTTCAAATCTTCATGGTACTAAGTTCGCC
1 GGTACTGGATTCGC-CGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCC
* *
11653 GTTGCAGCCTAAACTTTTCCCATCACATCTTCTAA
65 GTTGCAGCCTTAACCTTTCCCATCACATCTTCTAA
*
11688 GGTATTGGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCG
1 GGTACTGGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCG
** *
11753 TTGCAGCCTCGACCTTTCCTATCACATCTTCTAA
66 TTGCAGCCTTAACCTTTCCCATCACATCTTCTAA
* *
11787 GGTACT-GAGTTCGCCGTTGTGGCCTCAA-CCTT
1 GGTACTGGA-TTCGCCGTCGCGGCCTCAATCCTT
11819 TGCCTTCATA
Statistics
Matches: 361, Mismatches: 59, Indels: 17
0.83 0.14 0.04
Matches are distributed among these distances:
97 1 0.00
98 88 0.24
99 209 0.58
100 27 0.07
101 34 0.09
102 2 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (99 bp):
GGTACTGGATTCGCCGTCGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCG
TTGCAGCCTTAACCTTTCCCATCACATCTTCTAA
Found at i:20642 original size:40 final size:40
Alignment explanation
Indices: 20595--20675 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
20585 CCTGTAATTC
* * *
20595 CAAAACAGTATACTCACACGGTCTAACACATGCCTGTGTG
1 CAAAACAGTATACACACACGATCTAACACACGCCTGTGTG
* *
20635 CAAAACAGTATACACAGACGATCTAGCACACGCCTGTGTG
1 CAAAACAGTATACACACACGATCTAACACACGCCTGTGTG
20675 C
1 C
20676 CCCACCTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (40 bp):
CAAAACAGTATACACACACGATCTAACACACGCCTGTGTG
Found at i:20685 original size:13 final size:13
Alignment explanation
Indices: 20667--20691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20657 CTAGCACACG
20667 CCTGTGTGCCCCA
1 CCTGTGTGCCCCA
20680 CCTGTGTGCCCC
1 CCTGTGTGCCCC
20692 TATACCTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (13 bp):
CCTGTGTGCCCCA
Found at i:24809 original size:43 final size:43
Alignment explanation
Indices: 24748--24837 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
24738 GTTCTTAGGG
24748 TAACTCTTTTTTATGCATAGTCCGAACTCACCCTGTGCTCAAC
1 TAACTCTTTTTTATGCATAGTCCGAACTCACCCTGTGCTCAAC
24791 TAACTCTTTTTTATGCATAGTCCGAACTCACCCTGTGCTCAAC
1 TAACTCTTTTTTATGCATAGTCCGAACTCACCCTGTGCTCAAC
24834 TAAC
1 TAAC
24838 CAGTCCATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.34
Consensus pattern (43 bp):
TAACTCTTTTTTATGCATAGTCCGAACTCACCCTGTGCTCAAC
Found at i:27695 original size:53 final size:53
Alignment explanation
Indices: 27603--27707 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
27593 CCTTAATTCC
* * * * * *
27603 CAAAACAGTATGCACACATAGTCTGACACATGCCTGTGTGTCTAGTCCATGTT
1 CAAAACAGTATACACACAGAGTCTGACACACGCCCGTGTGTCCAGCCCATGTT
27656 CAAAACAGTATACACACACGA-TCT-AGCACACGCCCGTGTGTCCAGCCCATGT
1 CAAAACAGTATACACACA-GAGTCTGA-CACACGCCCGTGTGTCCAGCCCATGT
27708 GTCCCCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
52 1 0.02
53 42 0.95
54 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (53 bp):
CAAAACAGTATACACACAGAGTCTGACACACGCCCGTGTGTCCAGCCCATGTT
Found at i:29603 original size:53 final size:51
Alignment explanation
Indices: 29522--29669 Score: 149
Period size: 51 Copynumber: 2.9 Consensus size: 51
29512 GAACTCATTT
* **
29522 AATTTA-ATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCAT-ATAGG
1 AATTTATATACTCACGATGAC-TCTAGTCATCGGACCT-TTAATCCATCAT-GG
*
29574 AATTTATATACTCACGATGACTCTGAGTCATTGGACCTTTAATCCATCATGG
1 AATTTATATACTCACGATGACTCT-AGTCATCGGACCTTTAATCCATCATGG
* * * * *
29626 -ATTCATTTACTCACAATAACACTTAGTCATCGGACCTTTAATCC
1 AATTTATATACTCACGATGACTC-TAGTCATCGGACCTTTAATCC
29670 GTAAAGGGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
51 36 0.44
52 18 0.22
53 28 0.34
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
AATTTATATACTCACGATGACTCTAGTCATCGGACCTTTAATCCATCATGG
Found at i:29654 original size:51 final size:51
Alignment explanation
Indices: 29545--29741 Score: 214
Period size: 51 Copynumber: 3.8 Consensus size: 51
29535 CGATGACATA
** * * * * * *
29545 TAGTCATCGGACCTCTTGTTCCATATAGGAATTTATATACTCACGATGACTCT
1 TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATTTACTCACAATAACACT
* * * *
29598 GAGTCATTGGACCTTTAATCCATCATGGATTCATTTACTCACAATAACACT
1 TAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACAATAACACT
* * * * *
29649 TAGTCATCGGACCTTTAATCCGTAAAGGGTTCATTTACTCATAGTGACACT
1 TAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACAATAACACT
*
29700 TAGTCATCAGACCTTTAATCCATAAAGGATTCATTTACTCAC
1 TAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCAC
29742 GATGATTTAC
Statistics
Matches: 119, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
51 98 0.82
52 9 0.08
53 12 0.10
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (51 bp):
TAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACAATAACACT
Found at i:34864 original size:25 final size:23
Alignment explanation
Indices: 34836--34881 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
34826 GTTGGATCCA
34836 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
34861 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
34882 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:36101 original size:23 final size:24
Alignment explanation
Indices: 36075--36124 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
36065 TCCAGCATTC
*
36075 TCTAACATTCTTCATT-TTTTTTT
1 TCTAACATTCTTCATTATTTTTCT
36098 TCTAACATTCTTCATTATTTTTCT
1 TCTAACATTCTTCATTATTTTTCT
36122 TCT
1 TCT
36125 TTCTCAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (24 bp):
TCTAACATTCTTCATTATTTTTCT
Found at i:42077 original size:143 final size:142
Alignment explanation
Indices: 41885--42166 Score: 383
Period size: 143 Copynumber: 2.0 Consensus size: 142
41875 TTTTGATTTT
*
41885 TTTTTTTAAAAAAAGAAAGTTTAAATTTTTAAAAATAAAAATCAA-TTTTTA-GTCATTTTAAAG
1 TTTTTTTAAAAAAAGAAACTTTAAATTTTTAAAAATAAAAATCAATTTTTTAGGT-ATTTTAAA-
* *
41948 GAAAAAGTTTAAATTTTTTAAATAATGTTTTGATTTTTTTAAACTATTTCAAAATAAAAGCTTTG
64 GAAAAAGTTTAAA-TTTTTAAATAAAG-TTTGATTTTTTTAAAC-ATTTCAAAATAAAAGCTTTA
42013 ATGATTAAGAAAAGTAA
126 ATGATTAAGAAAAGTAA
* **
42030 TTTTTTT-AAAAAA-AAACTTTAAGTTTTTAAAAATAAAAATCTGTTTTTTTAGGTATTTTAAAG
1 TTTTTTTAAAAAAAGAAACTTTAAATTTTTAAAAATAAAAATC-AATTTTTTAGGTATTTTAAAG
* * * **
42093 AAAAAGTTTTAATTTTTAAATAAAGTTTGATTTTTTTAATCATTTCAAAATAAAAGTTTTAATTT
65 AAAAAGTTTAAATTTTTAAATAAAGTTTGATTTTTTTAAACATTTCAAAATAAAAGCTTTAATGA
42158 TTAAGAAAA
130 TTAAGAAAA
42167 ATAGTGTTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
141 29 0.24
142 15 0.12
143 38 0.31
144 18 0.15
145 21 0.17
146 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (142 bp):
TTTTTTTAAAAAAAGAAACTTTAAATTTTTAAAAATAAAAATCAATTTTTTAGGTATTTTAAAGA
AAAAGTTTAAATTTTTAAATAAAGTTTGATTTTTTTAAACATTTCAAAATAAAAGCTTTAATGAT
TAAGAAAAGTAA
Found at i:58969 original size:22 final size:22
Alignment explanation
Indices: 58944--58991 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
58934 ATTTTATAAA
*
58944 TAAATAAAACCTAAAAAAACCT
1 TAAATAAAACCTAAAAAAACCC
** *
58966 TAAATAACCCCTAAGAAAACCC
1 TAAATAAAACCTAAAAAAACCC
58988 TAAA
1 TAAA
58992 ACCTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAATAAAACCTAAAAAAACCC
Found at i:67872 original size:11 final size:11
Alignment explanation
Indices: 67833--67897 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
67823 GCCTCTCACT
67833 TTTCTTTCTCA
1 TTTCTTTCTCA
67844 TTT-TTCTCTCA
1 TTTCTT-TCTCA
* *
67855 TTCCTTTCTTA
1 TTTCTTTCTCA
67866 TTTCTTTCT-A
1 TTTCTTTCTCA
67876 TTTTCTTT-TCCA
1 -TTTCTTTCT-CA
67888 TTTCTTTCTC
1 TTTCTTTCTC
67898 TTTTAATCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.09
11 37 0.82
12 4 0.09
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTCTTTCTCA
Found at i:68412 original size:7 final size:7
Alignment explanation
Indices: 68400--68460 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
68390 CAAGTCAAAT
68400 CGTTGAC
1 CGTTGAC
68407 CGTTGA-
1 CGTTGAC
**
68413 ATTTGAC
1 CGTTGAC
68420 CGTTGAC
1 CGTTGAC
68427 CGTTGAC
1 CGTTGAC
* *
68434 AGTGGA-
1 CGTTGAC
*
68440 CTTTGAC
1 CGTTGAC
68447 CGTTGAC
1 CGTTGAC
68454 CGTTGAC
1 CGTTGAC
68461 TTTTTTGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 7 0.17
7 35 0.83
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (7 bp):
CGTTGAC
Found at i:68431 original size:27 final size:27
Alignment explanation
Indices: 68400--68460 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
68390 CAAGTCAAAT
* *
68400 CGTTGACCGTTGAATTTGACCGTTGAC
1 CGTTGACAGTGGAATTTGACCGTTGAC
*
68427 CGTTGACAGTGGACTTTGACCGTTGAC
1 CGTTGACAGTGGAATTTGACCGTTGAC
68454 CGTTGAC
1 CGTTGAC
68461 TTTTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (27 bp):
CGTTGACAGTGGAATTTGACCGTTGAC
Found at i:68445 original size:20 final size:20
Alignment explanation
Indices: 68422--68463 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
68412 AATTTGACCG
68422 TTGACCGTTGACAGTGGACT
1 TTGACCGTTGACAGTGGACT
* *
68442 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACAGTGGACT
68462 TT
1 TT
68464 TTTGAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGACCGTTGACAGTGGACT
Found at i:68855 original size:3 final size:3
Alignment explanation
Indices: 68834--68872 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
68824 AAATTTATAA
68834 TAT T-T TAT T-T TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
68873 TTGGAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:71047 original size:26 final size:26
Alignment explanation
Indices: 71018--71071 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
71008 CTCTGAGGAC
71018 TTCTGATGACCAACAGATAACCCTAG
1 TTCTGATGACCAACAGATAACCCTAG
* *
71044 TTCTGATGACCGACAGATAACCTTAG
1 TTCTGATGACCAACAGATAACCCTAG
71070 TT
1 TT
71072 GGTGAGCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (26 bp):
TTCTGATGACCAACAGATAACCCTAG
Found at i:74318 original size:13 final size:13
Alignment explanation
Indices: 74300--74324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74290 TCCTAAAGCC
74300 TCTCATTTTTCTT
1 TCTCATTTTTCTT
74313 TCTCATTTTTCT
1 TCTCATTTTTCT
74325 CTCATTCCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTCATTTTTCTT
Found at i:74357 original size:22 final size:21
Alignment explanation
Indices: 74306--74375 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
74296 AGCCTCTCAT
74306 TTTTCTTTCTCATTT-TTCTC
1 TTTTCTTTCTCATTTCTTCTC
* *
74326 TCATTCCTTTCTTATTTCTTACTC
1 T--TTTCTTTCTCATTTCTT-CTC
74350 TTTTCTTT-TCCATTTCTTTCTC
1 TTTTCTTTCT-CATTTC-TTCTC
74372 TTTT
1 TTTT
74376 AATCACTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 30 0.75
23 4 0.10
24 4 0.10
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCTTTCTCATTTCTTCTC
Found at i:74920 original size:13 final size:13
Alignment explanation
Indices: 74902--74953 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
74892 AGTCAAATAG
74902 TTGACCGTTGACT
1 TTGACCGTTGACT
*
74915 TTGACCGTTGCCT
1 TTGACCGTTGACT
*
74928 ATTGATCGTTGACT
1 -TTGACCGTTGACT
*
74942 TTGACAGTTGAC
1 TTGACCGTTGAC
74954 CGTTGACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:74959 original size:27 final size:27
Alignment explanation
Indices: 74901--74960 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
74891 AAGTCAAATA
*
74901 GTTGACCGTTGACTTTGACCGTTGCCT
1 GTTGACCGTTGACTTTGACAGTTGCCT
* *
74928 ATTGATCGTTGACTTTGACAGTTGACC-
1 GTTGACCGTTGACTTTGACAGTTG-CCT
74955 GTTGAC
1 GTTGAC
74961 TTTTTCCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (27 bp):
GTTGACCGTTGACTTTGACAGTTGCCT
Found at i:76029 original size:3 final size:3
Alignment explanation
Indices: 76014--76043 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
76004 TGCAAAATTT
*
76014 ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
76044 TTATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:79691 original size:6 final size:6
Alignment explanation
Indices: 79677--79721 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
79667 TGATCAAAAT
* * * *
79677 TGAATG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
79722 TATGAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.24
Consensus pattern (6 bp):
TGAAAG
Found at i:86238 original size:34 final size:34
Alignment explanation
Indices: 86195--86263 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
86185 AAAACCCTAA
86195 AATATCATTTTCTCCTTTATCCTTTTTTGTCGTT
1 AATATCATTTTCTCCTTTATCCTTTTTTGTCGTT
86229 AATATCATTTTCTCCTTTATCCTTTTTTGTCGTT
1 AATATCATTTTCTCCTTTATCCTTTTTTGTCGTT
86263 A
1 A
86264 CCCTCACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (34 bp):
AATATCATTTTCTCCTTTATCCTTTTTTGTCGTT
Found at i:86256 original size:17 final size:17
Alignment explanation
Indices: 86202--86256 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
86192 TAAAATATCA
86202 TTTTCTCCTTTATCCTT
1 TTTTCTCCTTTATCCTT
* * *
86219 TTTTGTCGTTAATAT-C-A
1 TTTTCTCCTT--TATCCTT
86236 TTTTCTCCTTTATCCTT
1 TTTTCTCCTTTATCCTT
86253 TTTT
1 TTTT
86257 GTCGTTACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 3 0.11
16 1 0.04
17 20 0.71
18 1 0.04
19 3 0.11
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTCTCCTTTATCCTT
Found at i:89819 original size:43 final size:43
Alignment explanation
Indices: 89771--90149 Score: 312
Period size: 43 Copynumber: 8.8 Consensus size: 43
89761 ATGCCACTAT
* * * *
89771 AGAACATGGTCTTTAACGGCTCATTTT-CCATAAACACTGCTAA
1 AGAACATGGTCTTTAGCGGCGC-TTTTACCACAAACACCGCTAA
* * **
89814 AGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
* * *** * *
89857 ATAACATGGTCTTTAGCGGTGCTTTTTGTACAAACGCCACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
* * * *
89900 AAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
* * * *
89943 AGAACATGGTTTTTAGCAGCGCTTTTATCAAAAACACCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
* * * * **
89986 AGAACATGGTCTTTAGGTGGTGCTTTTACGATAAATGCCGCTAA
1 AGAACATGGTCTTTA-GCGGCGCTTTTACCACAAACACCGCTAA
* ** * *
90030 AGAACATTGTCTTTAGCGGCGCTTTT-CTCACAAATGCCACTAT
1 AGAACATGGTCTTTAGCGGCGCTTTTAC-CACAAACACCGCTAA
* ** * * * *
90073 AGAACATGGTCTTTAGCAGTTCTTTTATCACAAACGCCTCTAT
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
* ** *
90116 AGAACATGTTCTTTAGCGGCATTTTTCCCACAAA
1 AGAACATGGTCTTTAGCGGCGCTTTTACCACAAA
90150 TGCTGCTAAC
Statistics
Matches: 276, Mismatches: 56, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
42 5 0.02
43 237 0.86
44 34 0.12
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGCTTTTACCACAAACACCGCTAA
Found at i:89922 original size:86 final size:86
Alignment explanation
Indices: 89810--90135 Score: 357
Period size: 86 Copynumber: 3.8 Consensus size: 86
89800 ATAAACACTG
* * * * *
89810 CTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAATAACATGGTCTTTAGCG
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCG
* *
89875 GTGCTTTT-TGTACAAACGCCA
66 GCGCTTTTAT-CACAAACGCCA
* * * *
89896 CTAAAAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAACATGGTTTTTAGCA
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCG
* * *
89961 GCGCTTTTATCAAAAACACCG
66 GCGCTTTTATCACAAACGCCA
** * * * * *
89982 CTAAAGAACATGGTCTTTAGGTGGTGCTTTTACGATAAATGCCGCTAAAGAACATTGTCTTTAGC
1 CTAAAGAACATGGTCTTTA-GCAGCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGC
* *
90047 GGCGCTTTTCTCACAAATGCCA
65 GGCGCTTTTATCACAAACGCCA
* ** * * * *
90069 CTATAGAACATGGTCTTTAGCAGTTCTTTTATCACAAACGCCTCTATAGAACATGTTCTTTAGCG
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCG
90134 GC
66 GC
90136 ATTTTTCCCA
Statistics
Matches: 196, Mismatches: 42, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
86 125 0.64
87 71 0.36
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (86 bp):
CTAAAGAACATGGTCTTTAGCAGCGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCG
GCGCTTTTATCACAAACGCCA
Found at i:90045 original size:87 final size:84
Alignment explanation
Indices: 89771--90135 Score: 352
Period size: 86 Copynumber: 4.2 Consensus size: 84
89761 ATGCCACTAT
* * * * ** *
89771 AGAACATGGTCTTTAACGGCTCATTTTCCATAAACACTGCTAAAGAACATGATCTTTAGCGGCGC
1 AGAACATGGTCTTTAGCGGCGC-TTTTTCACAAACACCACTAAAGAACATGGTCTTTAGCGGCGC
* *
89836 TTTTCCCACAAACGTCGCTAA
65 TTTT-ACACAAACGCCGCTAA
* * * * * *
89857 ATAACATGGTCTTTAGCGGTGCTTTTTGTACAAACGCCACTAAAAAACATGGTCTTTAGCAGCGC
1 AGAACATGGTCTTTAGCGGCGCTTTTT-CACAAACACCACTAAAGAACATGGTCTTTAGCGGCGC
89922 TTTTATCACAAACGCCGCTAA
65 TTTTA-CACAAACGCCGCTAA
* * * * * *
89943 AGAACATGGTTTTTAGCAGCGCTTTTATCAAAAACACCGCTAAAGAACATGGTCTTTAGGTGGTG
1 AGAACATGGTCTTTAGCGGCGCTTTT-TCACAAACACCACTAAAGAACATGGTCTTTA-GCGGCG
* *
90008 CTTTTACGATAAATGCCGCTAA
64 CTTTTAC-ACAAACGCCGCTAA
* ** * * **
90030 AGAACATTGTCTTTAGCGGCGCTTTTCTCACAAATGCCACTATAGAACATGGTCTTTAGCAGTTC
1 AGAACATGGTCTTTAGCGGCGCTTTT-TCACAAACACCACTAAAGAACATGGTCTTTAGCGGCGC
* *
90095 TTTTATCACAAACGCCTCTAT
65 TTTTA-CACAAACGCCGCTAA
*
90116 AGAACATGTTCTTTAGCGGC
1 AGAACATGGTCTTTAGCGGC
90136 ATTTTTCCCA
Statistics
Matches: 226, Mismatches: 47, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
85 4 0.02
86 150 0.66
87 72 0.32
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (84 bp):
AGAACATGGTCTTTAGCGGCGCTTTTTCACAAACACCACTAAAGAACATGGTCTTTAGCGGCGCT
TTTACACAAACGCCGCTAA
Found at i:90077 original size:130 final size:130
Alignment explanation
Indices: 89810--90131 Score: 387
Period size: 130 Copynumber: 2.5 Consensus size: 130
89800 ATAAACACTG
* * ** * *
89810 CTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAATAACATGGTCTTTA-GC
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAACATGGTCTTTAGGC
* *
89874 GGTGCTTTTTGTACAAACGCCACTAAAAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCG
66 GGTGCTTTTCGTACAAACGCCACTAAAAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCA
* * * *
89939 CTAAAGAACATGGTTTTTAGCAGCGCTTTTATCAAAAACACCGCTAAAGAACATGGTCTTTAGGT
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAACATGGTCTTTAGGC
* * * * * * * *
90004 GGTGCTTTTACG-ATAAATGCCGCTAAAGAACATTGTCTTTAGCGGCGCTTTTCTCACAAATGCC
66 GGTGCTTTT-CGTACAAACGCCACTAAAAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCC
90068 A
130 A
* ** * * *
90069 CTATAGAACATGGTCTTTAGCAGTTCTTTTATCACAAACGCCTCTATAGAACATGTTCTTTAG
1 CTAAAGAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAACATGGTCTTTAG
90132 CGGCATTTTT
Statistics
Matches: 162, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
129 53 0.33
130 108 0.67
131 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (130 bp):
CTAAAGAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCGCTAAAGAACATGGTCTTTAGGC
GGTGCTTTTCGTACAAACGCCACTAAAAAACATGGTCTTTAGCAGCGCTTTTATCACAAACGCCA
Found at i:95273 original size:241 final size:241
Alignment explanation
Indices: 94849--95331 Score: 785
Period size: 241 Copynumber: 2.0 Consensus size: 241
94839 AAAATCATAA
* * *
94849 TAATGATAAAATATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTTATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAGTAGTAACTT
94914 TTAGGCTTTTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAG
66 TTA-GCTTTTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAG
* *
94979 AATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAGATCTCTAATTTAAGTTTTAAATTA
130 AATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAAATA
* *
95044 GATAAGTTTGGTGAACACGTTTTAGTCAAGTTACAAGTAAATCGGAG
195 GATAAGTTTGGTGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
95091 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAGTAGT-A-TT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAGTAGTAACTT
**
95154 TT-TTTTTAGATTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGATA-GTATTTTAC
66 TTAGCTTT---TTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGA-AGGTATTTTAC
*
95217 TAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTTTAATTTAAGTTTTAAA
127 TAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAA
* *
95282 ATAGATAAGTTTGGTGAACACGTCTTAGTCAAATTACTAGTAAATTGGAG
192 ATAGATAAGTTTGGTGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
95332 GCATTTTTGG
Statistics
Matches: 225, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
238 3 0.01
240 4 0.02
241 160 0.71
242 58 0.26
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (241 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAGTAGTAACTT
TTAGCTTTTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGA
ATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAAATAG
ATAAGTTTGGTGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
Found at i:101935 original size:11 final size:11
Alignment explanation
Indices: 101919--101946 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
101909 GAAAGCGAAT
101919 AAAAAAAACAA
1 AAAAAAAACAA
101930 AAAAAAAACAA
1 AAAAAAAACAA
101941 AAAAAA
1 AAAAAA
101947 TAAAGGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:102583 original size:41 final size:41
Alignment explanation
Indices: 102499--102583 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
102489 TAAATCAAGA
*
102499 AAAAAATACAAAAAAAAAAAGAAGGAAAGAGAAGAAAATAG
1 AAAAAATACAAAAAAAAAAAGAAAGAAAGAGAAGAAAATAG
* * * *
102540 AAAAAATAGAAAAAAAAATAGAAAGAGAGAGCAAGATAA-AG
1 AAAAAATACAAAAAAAAAAAGAAAGAAAGAG-AAGAAAATAG
102581 AAA
1 AAA
102584 TTATATTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 32 0.84
42 6 0.16
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (41 bp):
AAAAAATACAAAAAAAAAAAGAAAGAAAGAGAAGAAAATAG
Found at i:103025 original size:42 final size:42
Alignment explanation
Indices: 102965--103489 Score: 707
Period size: 42 Copynumber: 12.5 Consensus size: 42
102955 AAAGAAAGCA
*
102965 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
103007 TTCATTGCATTCCA-AGGCCTAGGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATT-TAGAGGCCTAGGTGTGGAGGTC-CATTTACTT
* * *
103049 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * * * *
103091 TTCATTGAATTCAAAGGCCCAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
103133 TTCATTGCATTCAGAGGCCTCGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
103175 TTCATTGCGTTGAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
103217 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
103259 TTCATGGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
103301 TTCATT-AATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
103342 TTCATTGCATTTAGAGGCCAAGGTGTGGGGGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGT-GGAGGTCCATTTACTT
*
103385 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA-TT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
** *
103426 TTCCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTCACTT
1 TT-CATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
103469 TTCATTGCAATTAGAGGCCTA
1 TTCATTGCATTTAGAGGCCTA
103490 AGCATAGAGG
Statistics
Matches: 430, Mismatches: 45, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
41 45 0.10
42 339 0.79
43 46 0.11
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:103872 original size:3 final size:3
Alignment explanation
Indices: 103864--103914 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
103854 AAGGGCCCAA
* * * * *
103864 ATT ATT ATT ATT ATC ATC ATT ATT ATT CTT ATT CTT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
103912 ATT
1 ATT
103915 TTAATTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.