Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006179.1 Kokia drynarioides strain JFW-HI SEQ_120744, 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: 22936
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:596 original size:15 final size:16
Alignment explanation
Indices: 578--607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
568 CTTCCCTATT
578 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
593 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
608 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:600 original size:22 final size:22
Alignment explanation
Indices: 573--633 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
563 TTCGACTTCC
573 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
595 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
617 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
634 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:623 original size:21 final size:22
Alignment explanation
Indices: 587--633 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
577 TTTCTATTTC
*
587 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
609 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
630 TTTT
1 TTTT
634 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:982 original size:21 final size:22
Alignment explanation
Indices: 940--982 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
930 AATTTAGAAT
* * *
940 TGTGTTGACTTCTATCGGTACA
1 TGTGTTGACATCTACCGATACA
962 TGTGTT-ACATCTACCGATACA
1 TGTGTTGACATCTACCGATACA
983 AGTCTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (22 bp):
TGTGTTGACATCTACCGATACA
Found at i:3958 original size:13 final size:13
Alignment explanation
Indices: 3940--3975 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3930 TTTTTCGAAA
3940 AAAGTCAACGGTC
1 AAAGTCAACGGTC
**
3953 AAAGTCAATAGTC
1 AAAGTCAACGGTC
3966 AAAGTCAACG
1 AAAGTCAACG
3976 ATTAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:6493 original size:30 final size:31
Alignment explanation
Indices: 6428--6494 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
6418 GTTCGAAGGC
* * *
6428 AAAAAAGGTAATTTTTAGACACTCGAGGGTG
1 AAAAATGGTAATTTTTAAACACTCGAGGGGG
6459 -AAAATGGTAATTTTTAAACACTCG-GGGGG
1 AAAAATGGTAATTTTTAAACACTCGAGGGGG
6488 AAAAATG
1 AAAAATG
6495 TGACTTTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAATGGTAATTTTTAAACACTCGAGGGGG
Found at i:6531 original size:29 final size:29
Alignment explanation
Indices: 6499--6947 Score: 285
Period size: 29 Copynumber: 15.3 Consensus size: 29
6489 AAAATGTGAC
* *
6499 TTTTCGAAGTTTGGGGGTAAAATGATAAT
1 TTTTGGAAGTTTAGGGGTAAAATGATAAT
** * * *
6528 TTTTGGAA-CCTCGGGAGCAAAACGATAAT
1 TTTTGGAAGTTTAGGG-GTAAAATGATAAT
* * *
6557 TTTTGGACAATTTAGGGTTAAAAATAAT-AT
1 TTTTGGA-AGTTTAGGGGT-AAAATGATAAT
*
6587 TTTTGGAAG-TTCGAGGGTAAAAT-AGTAATT
1 TTTTGGAAGTTTAG-GGGTAAAATGA-TAA-T
* ** *
6617 TTTTGGAAGTTCGAGGGCAAAAATG-TGATT
1 TTTTGGAAGTT-TAGGGGTAAAATGAT-AAT
* *
6647 TTTTGGAAG-TTCGAGGGTAAAATGGTAAT
1 TTTTGGAAGTTTAG-GGGTAAAATGATAAT
*** *
6676 TTTCAAAAGTTTAGGGGTAAAAATG-TCAT
1 TTTTGGAAGTTTAGGGGT-AAAATGATAAT
*
6705 TTTTGGAAGTTTAGGGGTAAAATGATATT
1 TTTTGGAAGTTTAGGGGTAAAATGATAAT
* * * ** **
6734 TTTTAGAAGTTCA-AGGTAAAAAAAGTGTT
1 TTTTGGAAGTTTAGGGGTAAAATGA-TAAT
* *
6763 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGG-AAGTTTAGGGGTAAAATGATAAT
* *
6793 TTTTGGAAATTTAGGGGTAAAAATG-TATT
1 TTTTGGAAGTTTAGGGGT-AAAATGATAAT
*
6822 TTTTGGAAAATTTAGGGGTAAAATGATAA-
1 TTTTGG-AAGTTTAGGGGTAAAATGATAAT
* *
6851 TTTTGGAATTTTAAGGGTAAAAATG-TAAT
1 TTTTGGAAGTTTAGGGGT-AAAATGATAAT
* *
6880 TTTTAGAAAGTTTAAGGGTGAAAATG-TAAT
1 TTTT-GGAAGTTTAGGGGT-AAAATGATAAT
*
6910 TTTTATGAAGTTTAGGGGTCAAAAT-ATAAT
1 TTTT-GGAAGTTTAGGGGT-AAAATGATAAT
6940 TTTTGGAA
1 TTTTGGAA
6948 AGTTCGATGG
Statistics
Matches: 328, Mismatches: 65, Indels: 54
0.73 0.15 0.12
Matches are distributed among these distances:
27 1 0.00
28 41 0.12
29 134 0.41
30 125 0.38
31 26 0.08
32 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTAAAATGATAAT
Found at i:6616 original size:59 final size:56
Alignment explanation
Indices: 6553--6974 Score: 253
Period size: 59 Copynumber: 7.2 Consensus size: 56
6543 AGCAAAACGA
6553 TAATTTTTGGACAATTTAGGGTTAAAAATAAT-ATTTTTGGAAGTTCGAGGGTAAAATAG
1 TAATTTTTGGA-AATTTAGGG-TAAAAAT-ATGATTTTTGGAAGTTCGAGGGTAAAAT-G
* * * *
6612 TAATTTTTTGGAAGTTCGAGGGCAAAAATGTGATTTTTTGGAAGTTCGAGGGTAAAATGG
1 TAA-TTTTTGGAAATT-TAGGGTAAAAATATGA-TTTTTGGAAGTTCGAGGGTAAAAT-G
** * * *
6672 TAA-TTTTCAAAAGTTTAGGGGTAAAAATGTCATTTTTGGAAGTT-TAGGGGTAAAATG
1 TAATTTTTGGAAA-TTTA-GGGTAAAAATATGATTTTTGGAAGTTCGA-GGGTAAAATG
* * * * * * * * *
6729 ATATTTTTTAGAAGTTCAAGGTAAAAAAAGTGTTTTTTGGAAAGTTTGGGGGTAAAATGG
1 -TAATTTTTGGAAATTTAGGGTAAAAATA-TGATTTTTGG-AAGTTCGAGGGTAAAAT-G
* * *
6789 TAATTTTTGGAAATTTAGGGGTAAAAATGT-ATTTTTTGGAAAATT-TAGGGGTAAAATG
1 TAATTTTTGGAAATTTA-GGGTAAAAATATGA-TTTTTGG-AAGTTCGA-GGGTAAAATG
* * * * **
6847 ATAA-TTTTGGAATTTTAAGGGTAAAAATGTAATTTTTAGAAAGTTTAAGGGTGAAAATG
1 -TAATTTTTGGAAATTT-AGGGTAAAAATATGATTTTT-GGAAGTTCGAGGGT-AAAATG
* * * * * *
6906 TAATTTTTATGAAGTTTAGGGGTCAAAATATAATTTTTGGAAAGTTCGATGGTCAAAATA
1 TAATTTTT-GGAAATTTA-GGGTAAAAATATGATTTTTGG-AAGTTCGAGGGT-AAAATG
*
6966 TATTTTTTG
1 TAATTTTTG
6975 AACAATTCAA
Statistics
Matches: 286, Mismatches: 51, Indels: 52
0.74 0.13 0.13
Matches are distributed among these distances:
57 10 0.03
58 82 0.29
59 101 0.35
60 93 0.33
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (56 bp):
TAATTTTTGGAAATTTAGGGTAAAAATATGATTTTTGGAAGTTCGAGGGTAAAATG
Found at i:6669 original size:88 final size:87
Alignment explanation
Indices: 6556--6974 Score: 281
Period size: 88 Copynumber: 4.7 Consensus size: 87
6546 AAAACGATAA
* *
6556 TTTTTGGACAATTTAGGGTTAAAAATAAT-ATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTT
1 TTTTTGGA-AGTTTAGGGGT-AAAATAATAATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTT
* *
6620 TGGAAGTTCGAGGGCAAAAATGTGAT
64 TGGAAGTT-TAGGGTAAAAATGT-AT
* ** *** * *
6646 TTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTCAAAAGTT-TAGGGGTAAAA-ATGTCA-TTT
1 TTTTTGGAAGTTTAG-GGGTAAAATAATAATTTTTGGAAGTTCGA-GGGTAAAATA-GTAATTTT
6707 TTGGAAGTTTAGGGGT-AAAATGATAT
63 TTGGAAGTTTA-GGGTAAAAATG-TAT
* * * * ** * * *
6733 TTTTTAGAAGTTCA-AGGTAAAAAAAGTGTTTTTTGGAAAGTTTGGGGGTAAAATGGTAA-TTTT
1 TTTTTGGAAGTTTAGGGGTAAAATAA-TAATTTTTGG-AAGTTCGAGGGTAAAATAGTAATTTTT
*
6796 TGGAAATTTAGGGGTAAAAATGTAT
64 TGGAAGTTTA-GGGTAAAAATGTAT
* * * **
6821 TTTTTGGAAAATTTAGGGGTAAAATGATAA-TTTTGGAATTTTAAGGGTAAAA-ATGTAATTTTT
1 TTTTTGG-AAGTTTAGGGGTAAAATAATAATTTTTGGAAGTTCGAGGGTAAAATA-GTAATTTTT
* * *
6884 AGAAAGTTTAAGGGTGAAAATGTAAT
64 TGGAAGTTT-AGGGTAAAAATGT-AT
*
6910 TTTTAT-GAAGTTTAGGGGTCAAAAT-ATAATTTTTGGAAAGTTCGATGGTCAAAATA-T-ATTT
1 TTTT-TGGAAGTTTAGGGGT-AAAATAATAATTTTTGG-AAGTTCGAGGGT-AAAATAGTAATTT
6971 TTTG
62 TTTG
6975 AACAATTCAA
Statistics
Matches: 254, Mismatches: 51, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
86 7 0.03
87 40 0.16
88 113 0.44
89 63 0.25
90 26 0.10
91 4 0.02
92 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (87 bp):
TTTTTGGAAGTTTAGGGGTAAAATAATAATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTTG
GAAGTTTAGGGTAAAAATGTAT
Found at i:6678 original size:30 final size:29
Alignment explanation
Indices: 6556--6974 Score: 199
Period size: 30 Copynumber: 14.2 Consensus size: 29
6546 AAAACGATAA
* *
6556 TTTTTGGACAATTTAGGGTTAAAAA--TAAT
1 TTTTTGGA-AGTTGAGGG-TAAAAATGTAAT
6585 ATTTTTGGAAGTTCGAGGGT-AAAATAGTAAT
1 -TTTTTGGAAGTT-GAGGGTAAAAAT-GTAAT
* *
6616 TTTTTGGAAGTTCGAGGGCAAAAATGTGAT
1 TTTTTGGAAGTT-GAGGGTAAAAATGTAAT
6646 TTTTTGGAAGTTCGAGGGT-AAAATGGTAA-
1 TTTTTGGAAGTT-GAGGGTAAAAAT-GTAAT
*** * *
6675 TTTTCAAAAGTTTAGGGGTAAAAATGTCA-
1 TTTTTGGAAGTTGA-GGGTAAAAATGTAAT
*
6704 TTTTTGGAAGTTTAGGGGT-AAAATG-ATAT
1 TTTTTGGAAGTTGA-GGGTAAAAATGTA-AT
* * * * *
6733 TTTTTAGAAGTTCAAGGTAAAAAAAGT-GT
1 TTTTTGGAAGTTGAGGGT-AAAAATGTAAT
*
6762 TTTTTGGAAAGTTTGGGGGT-AAAATGGTAA-
1 TTTTTGG-AAG-TTGAGGGTAAAAAT-GTAAT
* *
6792 TTTTTGGAAATTTAGGGGTAAAAATGT-AT
1 TTTTTGGAAGTTGA-GGGTAAAAATGTAAT
* *
6821 TTTTTGGAAAATTTAGGGGT-AAAATGATAA-
1 TTTTTGG-AAGTTGA-GGGTAAAAATG-TAAT
* *
6851 -TTTTGGAATTTTAAGGGTAAAAATGTAAT
1 TTTTTGGAA-GTTGAGGGTAAAAATGTAAT
* * * *
6880 TTTTAGAAAGTTTAAGGGTGAAAATGTAAT
1 TTTTTGGAAG-TTGAGGGTAAAAATGTAAT
* * *
6910 TTTTAT-GAAGTTTAGGGGTCAAAATATAA-
1 TTTT-TGGAAGTTGA-GGGTAAAAATGTAAT
* * *
6939 TTTTTGGAAAGTTCGATGGTCAAAATAT-AT
1 TTTTTGG-AAGTT-GAGGGTAAAAATGTAAT
6969 TTTTTG
1 TTTTTG
6975 AACAATTCAA
Statistics
Matches: 313, Mismatches: 42, Indels: 68
0.74 0.10 0.16
Matches are distributed among these distances:
28 28 0.09
29 109 0.35
30 160 0.51
31 16 0.05
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTTGGAAGTTGAGGGTAAAAATGTAAT
Found at i:7641 original size:16 final size:17
Alignment explanation
Indices: 7620--7656 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
7610 AAAAACCTCT
7620 TTTTTCATTTT-TTTCA
1 TTTTTCATTTTATTTCA
*
7636 TTTTTCTTTTTATTTCA
1 TTTTTCATTTTATTTCA
7653 TTTT
1 TTTT
7657 AAAACCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCATTTTATTTCA
Found at i:8829 original size:17 final size:17
Alignment explanation
Indices: 8807--8892 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
8797 ATTTTTTTAT
*
8807 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
8824 TAAATTTAAA-CTAGAAA
1 TAAATTTAAATTTA-AAA
* *
8841 TTAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
8858 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
8875 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
8892 T
1 T
8893 TTGGGCTTGG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
16 7 0.12
17 48 0.84
18 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:8830 original size:11 final size:11
Alignment explanation
Indices: 8814--8867 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
8804 TATTAAATTC
8814 AAATTTAAAAT
1 AAATTTAAAAT
*
8825 AAATTTAAACT
1 AAATTTAAAAT
* **
8836 AGAAATTAATTT
1 A-AATTTAAAAT
*
8848 AAATTTATAAT
1 AAATTTAAAAT
8859 AAATTTAAA
1 AAATTTAAA
8868 CTTAAAATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:8852 original size:34 final size:33
Alignment explanation
Indices: 8809--8892 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 33
8799 TTTTTTATTA
*
8809 AATTCAAATTTAAAATAAATTTAAAC-TAGAAATT
1 AATTTAAATTTAAAATAAATTTAAACTTA-AAA-T
*
8843 AATTTAAATTTATAATAAATTTAAACTTAAAAT
1 AATTTAAATTTAAAATAAATTTAAACTTAAAAT
8876 AATTTAAAATTTAAAAT
1 AATTT-AAATTTAAAAT
8893 TTGGGCTTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 6 0.13
34 37 0.82
35 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (33 bp):
AATTTAAATTTAAAATAAATTTAAACTTAAAAT
Found at i:9618 original size:209 final size:208
Alignment explanation
Indices: 9252--10271 Score: 1267
Period size: 209 Copynumber: 4.9 Consensus size: 208
9242 TTTTACTAGA
* * * * * *
9252 AAGACGGATTTGGATCACTTTTC--TACGTCTCGTTAGGAAGGTGATCATTTTATTGCTTCGACC
1 AAGACGGATTTGGTTCACTTCTCAGTA--TCTCATCAGGAAGCTGACCATTTTATTGCTTCGACC
* ** * * * * *
9315 TGCTTCTCCCTATCTCATCGGGAAGCTGGGGTTCGAAGTTTCACTCATATCGAGCTTTGTTTCAT
64 TGCTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCAT
* * * * *
9380 TTATTTGGTCTACTTCTCAATAACTCATCAGGAAGATAACCGCATCACATGTTTTAATCCGCTTC
129 TGAGTTGGTCTACTTCTC-ATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTC
9445 TCTGTATCTCATCAAG
193 TCTGTATCTCATCAAG
*
9461 AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTACTTCGACCTG
1 AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTG
* * *
9526 CTTCTCAGTATCTCATCAGGAAGTTAGGGTTCAAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
66 CTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
* * * * * *
9591 AGCTAGTCTACTTATCAGTATCTCATCAGGAAGATGACTGCATCACATGTTTTACTCCGCTTCTC
131 AGTTGGTCTACTTCTCA-TATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTC
*
9656 TGTATCTCATTAAG
195 TGTATCTCATCAAG
* * * *
9670 AAGACGAATTTGATTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTG
1 AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTG
* * *
9735 CTTTTCAGCATCTCATCAGGAAGCTAGGGTTTGAAGTTTCGCTCACATTGAGCTTTGTTTCATGG
66 CTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
* * * *
9800 AGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTATTTTGATCCGCTTCTT
131 AGTTGGTCTACTTCTCA-TATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTC
*
9865 TGTATCTCA-CTAGTG
195 TGTATCTCATC-A-AG
* * ** *
9880 AAGACAGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGAC-GACCATTTTATTACTTCGACCT
1 AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAG-CTGACCATTTTATTGCTTCGACCT
* * *
9944 GCTTTTCAGTATCTCATCAGGAAG-TTGGGATTCGAAGTTTCTCTCATATTGAGCTTTGTTTCAT
65 GCTTTTCAGTATCTCATCAGGAAGCTAGGG-TTCGAAGTTTCGCTCACATTGAGCTTTGTTTCAT
* * * * ** * *
10008 TGAGTTGATATACTTCTCTATATCTCATCAGGAAGATGACCACCTCACTTACTTCAATCTGCTTC
129 TGAGTTGGTCTACTTCTC-ATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTC
* *
10073 TCTGTATCTAATCAGG
193 TCTGTATCTCATCAAG
*** * *
10089 AAGATAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTG
1 AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTG
* *
10154 CTTTTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCATTGAGCTTTGTTTCATTG
66 CTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
* * * *
10219 AGTTGGTATACTTCTCTATATCTCATCAAGAAGACGACCGCCTCACTTGTTTT
131 AGTTGGTCTACTTCTC-ATATCTCATCAGGAAGATGACCGCATCACTTGTTTT
10272 GAATAACTGC
Statistics
Matches: 707, Mismatches: 93, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
208 2 0.00
209 525 0.74
210 175 0.25
211 5 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (208 bp):
AAGACGGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTG
CTTTTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
AGTTGGTCTACTTCTCATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCT
GTATCTCATCAAG
Found at i:10074 original size:419 final size:417
Alignment explanation
Indices: 9297--10273 Score: 1327
Period size: 419 Copynumber: 2.3 Consensus size: 417
9287 GGAAGGTGAT
* * * *
9297 CATTTTATTGCTTCGACCTGCTTCTC-CCTATCTCATCGGGAAGCTGGGGTTCGAAGTTTCACTC
1 CATTTTATTGCTTCGACCTGCTTTTCAGC-ATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTC
* * * * * *
9361 ATATCGAGCTTTGTTTCATTTATTTGGTCTACTTCTCAATAACTCATCAGGAAGATAACCGCATC
65 ACATTGAGCTTTGTTTCATTGAGTTGGTCTACTTCTC-ATATCTCATCAGGAAGATGACCGCATC
* * * *
9426 ACATGTTTTAATCCGCTTCTCTGTATCTCATCAAGAAGACGGATTTGGTTCACTTCTCAGTATCT
129 ACTTGTTTTGATCCGCTTCTCTGTATCTCATCAAGAAGACAGATTTGGTCCACTTCTCAGTATCT
9491 CATCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGT
194 CATCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGT
*
9556 TCAAAGTTTCGCTCACATTGAGCTTTGTTTCATTGAGCTAGTCTACTTATCAGTATCTCATCAGG
259 TCAAAGTTTCGCTCACATTGAGCTTTGTTTCATTGAGCTAGTATACTTATCAGTATCTCATCAGG
** ** * * * * * *
9621 AAGATGACTGCATCACATGTTTTACTCCGCTTCTCTGTATCTCATTAAGAAGACGAATTTGATTC
324 AAGATGACCACATCACATACTTCAATCCGCTTCTCTGTATCTAATCAAGAAGACAAATTTGATCC
*
9686 ACTTCTCAGTATCTCATCAGGAAGCTAAC
389 ACTTCTCAGTATCTCATCAAGAAGCTAAC
* * *
9715 CATTTTATTGCTTCAACCTGCTTTTCAGCATCTCATCAGGAAGCTAGGGTTTGAAGTTTCGCTCA
1 CATTTTATTGCTTCGACCTGCTTTTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCA
* *
9780 CATTGAGCTTTGTTTCATGGAGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCA
66 CATTGAGCTTTGTTTCATTGAGTTGGTCTACTTCTCA-TATCTCATCAGGAAGATGACCGCATCA
* * * **
9845 CTTATTTTGATCCGCTTCTTTGTATCTCA-CTAGTGAAGACAGATTTGGTCCACTTCTTTGTATC
130 CTTGTTTTGATCCGCTTCTCTGTATCTCATC-A-AGAAGACAGATTTGGTCCACTTCTCAGTATC
*
9909 TCATCAGGAAGAC-GACCATTTTATTACTTCGACCTGCTTTTCAGTATCTCATCAGGAAGTT-GG
193 TCATCAGGAAG-CTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGG
* * * * *
9972 GATTCGAAGTTTCTCTCATATTGAGCTTTGTTTCATTGAG-TTGATATACTTCTCTA-TATCTCA
257 G-TTCAAAGTTTCGCTCACATTGAGCTTTGTTTCATTGAGCTAG-TATACTTATC-AGTATCTCA
* * * * *
10035 TCAGGAAGATGACCACCTCACTTACTTCAATCTGCTTCTCTGTATCTAATCAGGAAGATAAATTT
319 TCAGGAAGATGACCACATCACATACTTCAATCCGCTTCTCTGTATCTAATCAAGAAGACAAATTT
* *
10100 GGTCCACTTCTCAGTATCTCATCAAGAAGCTGAC
384 GATCCACTTCTCAGTATCTCATCAAGAAGCTAAC
* *
10134 CATTTTATTGCTTCGACCTGCTTTTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCG
1 CATTTTATTGCTTCGACCTGCTTTTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCA
* * * *
10199 CATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTATATCTCATCAAGAAGACGACCGCCTCA
66 CATTGAGCTTTGTTTCATTGAGTTGGTCTACTTCTC-ATATCTCATCAGGAAGATGACCGCATCA
10264 CTTGTTTTGA
130 CTTGTTTTGA
10274 ATAACTGCAA
Statistics
Matches: 489, Mismatches: 61, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
417 2 0.00
418 142 0.29
419 342 0.70
420 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (417 bp):
CATTTTATTGCTTCGACCTGCTTTTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCA
CATTGAGCTTTGTTTCATTGAGTTGGTCTACTTCTCATATCTCATCAGGAAGATGACCGCATCAC
TTGTTTTGATCCGCTTCTCTGTATCTCATCAAGAAGACAGATTTGGTCCACTTCTCAGTATCTCA
TCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTC
AAAGTTTCGCTCACATTGAGCTTTGTTTCATTGAGCTAGTATACTTATCAGTATCTCATCAGGAA
GATGACCACATCACATACTTCAATCCGCTTCTCTGTATCTAATCAAGAAGACAAATTTGATCCAC
TTCTCAGTATCTCATCAAGAAGCTAAC
Found at i:10416 original size:39 final size:39
Alignment explanation
Indices: 10373--10543 Score: 152
Period size: 39 Copynumber: 4.4 Consensus size: 39
10363 CTACCTCTAT
*
10373 CTCGGGGTAAAAGATTGGTTAATGATGATCTGCCTCAGG
1 CTCGGGGTAAGAGATTGGTTAATGATGATCTGCCTCAGG
* *
10412 CTCGGGGTAAGAGATTAGTTAAT-AGTGATCTGCCCCAGG
1 CTCGGGGTAAGAGATTGGTTAATGA-TGATCTGCCTCAGG
* * * *
10451 CTCGGTGTAAAAGA-TCG--AATGGTTGTAATCTGCCTCAGG
1 CTCGGGGTAAGAGATTGGTTAAT-GATG--ATCTGCCTCAGG
* ** * ** *
10490 CTCGGTGTAAGAGATTGACTGATGATGATAGGCCTCAGA
1 CTCGGGGTAAGAGATTGGTTAATGATGATCTGCCTCAGG
10529 CTCGGGGTAAGAGAT
1 CTCGGGGTAAGAGAT
10544 GAGAATCTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
36 3 0.03
37 2 0.02
38 3 0.03
39 93 0.87
40 1 0.01
41 3 0.03
42 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.26
Consensus pattern (39 bp):
CTCGGGGTAAGAGATTGGTTAATGATGATCTGCCTCAGG
Found at i:10533 original size:78 final size:78
Alignment explanation
Indices: 10400--10543 Score: 175
Period size: 78 Copynumber: 1.8 Consensus size: 78
10390 GTTAATGATG
* ** * *
10400 ATCTGCCTCAGGCTCGGGGTAAGAGATTAGTTAATAGTGATCTGCCCCAGGCTCGGTGTAAAAGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTAATAGTGATAGGCCCCAGACTCGGGGTAAAAGA
10465 TCGAATGGTTGTA
66 TCGAATGGTTGTA
* * * *
10478 ATCTGCCTCAGGCTCGGTGTAAGAGATT-GACTGAT-GATGATAGGCCTCAGACTCGGGGTAAGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTAG-CTAATAG-TGATAGGCCCCAGACTCGGGGTAAAA
10541 GAT
64 GAT
10544 GAGAATCTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
77 2 0.04
78 53 0.96
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (78 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTAATAGTGATAGGCCCCAGACTCGGGGTAAAAGA
TCGAATGGTTGTA
Found at i:10591 original size:41 final size:42
Alignment explanation
Indices: 10533--10628 Score: 142
Period size: 41 Copynumber: 2.3 Consensus size: 42
10523 CTCAGACTCG
* * *
10533 GGGTAAGAGA-TGAGAATCTTCATTCTGCCCTTATTGATTAA
1 GGGTAAAAGACTGAGAATCTTCAATATGCCCTTATTGATTAA
*
10574 GGGTAAAAGACTG-GAATCTTCAATATGCCCTTCTTGATTAA
1 GGGTAAAAGACTGAGAATCTTCAATATGCCCTTATTGATTAA
10615 GGGTAAAAGACTGA
1 GGGTAAAAGACTGA
10629 ATGATGATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 47 0.96
42 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (42 bp):
GGGTAAAAGACTGAGAATCTTCAATATGCCCTTATTGATTAA
Found at i:10842 original size:49 final size:49
Alignment explanation
Indices: 10784--11102 Score: 238
Period size: 49 Copynumber: 6.5 Consensus size: 49
10774 CCATCTTGTT
* * * *
10784 TTCTAAGGTACCGGGTTCGTCATTACGGCCTCAA-CATTTCCTTCATATC
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCCTTCAAATC
* * * *
10833 TTCTGAGGTACTAGGTTTGTCGTTGCGGCCTCAA-CCTTTCCCTTAAAATC
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCCTTT-CCTTCAAATC
* * ** * ** *
10883 TTC-ATGGTACCAGTTTCGCCATTGCAACCTCAACCTTTTTTTTCATATC
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCCTTCAAATC
* * * *
10932 TTTTAAGGTACCAGGTTCGTTATTACGGCCTCAACCCTTCCCTT-AAATC
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCCTTCAAATC
* * * * *
10981 TTC-ATGGTACCAGATTCGCCATTGCAGCCTCAA-CGTTTCCTTTCATATC
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCC-TTCAAATC
* * * *
11030 TTCTAAGGTACCAGGTTCGCCATTGCGACCTCAACCTTTTCCTTAAAATC
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCCTTCAAATC
*
11080 TTC-ATGGTACCGGGTTCGTCATT
1 TTCTA-GGTACCAGGTTCGTCATT
11103 ATGACTTCAA
Statistics
Matches: 208, Mismatches: 50, Indels: 24
0.74 0.18 0.09
Matches are distributed among these distances:
47 6 0.03
48 27 0.13
49 90 0.43
50 77 0.37
51 8 0.04
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (49 bp):
TTCTAGGTACCAGGTTCGTCATTGCGGCCTCAACCCTTTCCTTCAAATC
Found at i:10966 original size:50 final size:50
Alignment explanation
Indices: 10787--11073 Score: 240
Period size: 50 Copynumber: 5.8 Consensus size: 50
10777 TCTTGTTTTC
* * * * *
10787 TAAGGTACCGGGTTCGTCATTACGGCCTCAACATTT-CCTTCATATCTTC
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
* * * * * * *
10836 TGAGGTACTAGGTTTGTCGTTGCGGCCTCAACCTTTCCCTTAAAATC-TT
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
* * * ** ***
10885 CATGGTACCAGTTTCGCCATTGCAACCTCAACCTTTTTTTTCATATCTTT
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
** * * *
10935 TAAGGTACCAGGTTCGTTATTACGGCCTCAACCCTTCCCTT-AAATC-TT
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
* * * * * * *
10983 CATGGTACCAGATTCGCCATTGCAGCCTCAACGTTTCCTTTCATATCTTC
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
* *
11033 TAAGGTACCAGGTTCGCCATTGCGACCTCAACCTTTTCCTT
1 TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTT
11074 AAAATCTTCA
Statistics
Matches: 176, Mismatches: 58, Indels: 7
0.73 0.24 0.03
Matches are distributed among these distances:
48 33 0.19
49 70 0.40
50 73 0.41
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (50 bp):
TAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTT
Found at i:11012 original size:98 final size:99
Alignment explanation
Indices: 10812--11090 Score: 391
Period size: 98 Copynumber: 2.8 Consensus size: 99
10802 GTCATTACGG
* * * * *
10812 CCTCAACATTTCC-TTCATATCTTCTGAGGTACTAGGTTTGTCGTTGCGGCCTCAACCTTTCCCT
1 CCTCAACCTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCT
*
10876 TAAAATCTTCATGGTACCAGTTTCGCCATTGCAA
66 TAAAATCTTCATGGTACCAGATTCGCCATTGCAA
** * * * *
10910 CCTCAACCTTTTTTTTCATATCTTTTAAGGTACCAGGTTCGTTATTACGGCCTCAACCCTTCCCT
1 CCTCAACCTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCT
*
10975 T-AAATCTTCATGGTACCAGATTCGCCATTGCAG
66 TAAAATCTTCATGGTACCAGATTCGCCATTGCAA
* * * *
11008 CCTCAACGTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGCCATTGCGACCTCAACCTTTTCCT
1 CCTCAACCTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCT
11073 TAAAATCTTCATGGTACC
66 TAAAATCTTCATGGTACC
11091 GGGTTCGTCA
Statistics
Matches: 156, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
98 96 0.62
99 60 0.38
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (99 bp):
CCTCAACCTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCT
TAAAATCTTCATGGTACCAGATTCGCCATTGCAA
Found at i:11144 original size:147 final size:147
Alignment explanation
Indices: 10783--11137 Score: 347
Period size: 148 Copynumber: 2.4 Consensus size: 147
10773 TCCATCTTGT
* * ** * * *
10783 TTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACATTTCCTTCATATCTTC-TGAGGTACTAG
1 TTTC-AAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCAT--GGTACCAG
* * * * * * *
10847 GTTTGTCGTTGCGGCCTCAACCTTTCCCTTAAAATCTTCATGGTACCAGTTTCGCCATTGCAACC
63 ATTCGCCATTGCAGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACCAGGTTCGCCATTGCAACC
** * *
10912 TCAACCTTTTTTTTCATATC
128 TCAACCTTTTCCTTAAAATC
* * * *
10932 TTTTAAGGTACCAGGTTCGTTATTACGGCCTCAACCCTTCCCTTAAATCTTCATGGTACCAGATT
1 TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCATGGTACCAGATT
* * * * *
10997 CGCCATTGCAGCCTCAACGTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGCCATTGCGACCTC
66 CGCCATTGCAGCCTCAACCTTTCCCTTAAAATCTTC-AAGGTACCAGGTTCGCCATTGCAACCTC
11062 AACCTTTTCCTTAAAATC
130 AACCTTTTCCTTAAAATC
* * * * * *
11080 -TTCATGGTACCGGGTTCGTCATTATGACTTCAACCTTTCCCATCACAT-TTCATGGTAC
1 TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCC-TCAAATCTTCATGGTAC
11138 TGGATTCACC
Statistics
Matches: 168, Mismatches: 35, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
147 80 0.48
148 84 0.50
149 4 0.02
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (147 bp):
TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCATGGTACCAGATT
CGCCATTGCAGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACCAGGTTCGCCATTGCAACCTCA
ACCTTTTCCTTAAAATC
Found at i:11158 original size:147 final size:147
Alignment explanation
Indices: 10783--11215 Score: 363
Period size: 147 Copynumber: 2.9 Consensus size: 147
10773 TCCATCTTGT
* * ** * * *
10783 TTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACATTTCCTTCATATCTTC-TGAGGTACTAG
1 TTTC-AAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCAT--GGTACCAG
* *** * * *
10847 GTTTGTCGTTGCGGCCTCAACCTTTCCCTTAAAATCTTC-ATGGTACCAGTTTCGCCATTGCAAC
63 ATTCACCGTTGCGGCCTCAA-CTTTCCCTTCAAATCTTCTAAGGTACCAGGTTCGCCATTGCAAC
** * *
10911 CTCAACCTTTTTTTTCATATC
127 CTCAACCTTTTCCTTAAAATC
* * * *
10932 TTTTAAGGTACCAGGTTCGTTATTACGGCCTCAACCCTTCCCTTAAATCTTCATGGTACCAGATT
1 TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCATGGTACCAGATT
* * * * * *
10997 CGCCATTGCAGCCTCAACGTTTCCTTTCATATCTTCTAAGGTACCAGGTTCGCCATTGCGACCTC
66 CACCGTTGCGGCCTCAAC-TTTCCCTTCAAATCTTCTAAGGTACCAGGTTCGCCATTGCAACCTC
11062 AACCTTTTCCTTAAAATC
130 AACCTTTTCCTTAAAATC
* * * * * * **
11080 -TTCATGGTACCGGGTTCGTCATTATGACTTCAACCTTTCCCATCACAT-TTCATGGTACTGGAT
1 TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCC-TCAAATCTTCATGGTACCAGAT
* * * * * * **
11143 TCACCGTTACGGCCTCAATCTTTCCCATCACATCTTCTGAGGTATC-GAGTTCACCATTGCAGTC
65 TCACCGTTGCGGCCTCAA-CTTTCCCTTCAAATCTTCTAAGGTACCAG-GTTCGCCATTGCAACC
11207 TCAACCTTT
128 TCAACCTTT
11216 ACTGTCACAT
Statistics
Matches: 229, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
146 2 0.01
147 138 0.60
148 85 0.37
149 4 0.02
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (147 bp):
TTTCAAGGTACCAGGTTCGTCATTACGACCTCAACCCTTCCCTCAAATCTTCATGGTACCAGATT
CACCGTTGCGGCCTCAACTTTCCCTTCAAATCTTCTAAGGTACCAGGTTCGCCATTGCAACCTCA
ACCTTTTCCTTAAAATC
Found at i:12207 original size:17 final size:17
Alignment explanation
Indices: 12175--12206 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12165 TTCACCTCAA
12175 CCTCTCCTTTTCTTTTT
1 CCTCTCCTTTTCTTTTT
12192 CCTCT-CTTTT-TTTTT
1 CCTCTCCTTTTCTTTTT
12207 TGGTTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTCTCCTTTTCTTTTT
Found at i:12213 original size:22 final size:22
Alignment explanation
Indices: 12188--12229 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12178 CTCCTTTTCT
12188 TTTTCCTCTCT-TTTTTTTTTGG
1 TTTTCCTC-CTGTTTTTTTTTGG
*
12210 TTTTCTTCCTGTTTTTTTTT
1 TTTTCCTCCTGTTTTTTTTT
12230 ATTTTGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTCCTCCTGTTTTTTTTTGG
Found at i:18255 original size:29 final size:29
Alignment explanation
Indices: 18223--18292 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
18213 TTTTGGAGGT
* *
18223 TCGGAGGCAAAACGGTAATTTTTGGACAC
1 TCGGAGGGAAAACGGTAATTTTTGAACAC
* * *
18252 TCGGGGGTGAAAATGGTAATTTTTTAACAC
1 TCGGAGG-GAAAACGGTAATTTTTGAACAC
18282 TC-GAGGGAAAA
1 TCGGAGGGAAAA
18293 ATGCGACTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 5 0.15
29 9 0.26
30 20 0.59
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (29 bp):
TCGGAGGGAAAACGGTAATTTTTGAACAC
Found at i:18337 original size:29 final size:28
Alignment explanation
Indices: 18300--18678 Score: 166
Period size: 29 Copynumber: 13.1 Consensus size: 28
18290 AAAATGCGAC
18300 TTTTGGAAGTTTGGACGTAAAATGATAAT
1 TTTTGGAAGTTTGGA-GTAAAATGATAAT
* ** * *
18329 TTTTTGAAGCTCGGGAGCAAAACGATAAT
1 TTTTGGAAG-TTTGGAGTAAAATGATAAT
*
18358 TTTTGGAAAATTTAGG-GTCAAAATGAT-AT
1 TTTTGG-AAGTTT-GGAGT-AAAATGATAAT
* *
18387 ATTTGGAAGTTTGAGGGTAAAATGATAATT
1 TTTTGGAAGTTTG-GAGTAAAATGATAA-T
* * * * *
18417 TTTTGAAAATTCGAGGGTGAAAATG-CAA-
1 TTTTGGAAGTTTG-GAGT-AAAATGATAAT
* *
18445 TTTTGGAAGTTCGAGAGTAAAGT-AGTAATT
1 TTTTGGAAGTTTG-GAGTAAAATGA-TAA-T
* * *
18475 TTTTGGAAGTTCGAGGGTAAAAAT-ATGATT
1 TTTTGGAAGTTTG-GAGT-AAAATGAT-AAT
* * * *
18505 TTTTGGATGTTCGGGGGTAAAATGGTAA-
1 TTTTGGAAGTT-TGGAGTAAAATGATAAT
* * *
18533 TTTTGAAAGTTTGAGGGTAAAAATG-TGAT
1 TTTTGGAAGTTTG-GAGT-AAAATGATAAT
* * * *
18562 TTTTGGAAAGTTTGGGGTCAAATGGTAAA
1 TTTTGG-AAGTTTGGAGTAAAATGATAAT
* *
18591 TTTTGGAAATTTGGGGTAAAATG-TAATT
1 TTTTGGAAGTTTGGAGTAAAATGATAA-T
* * *
18619 TTTTGAAAGTTTGGAGGCAAAATGAAAAT
1 TTTTGGAAGTTTGGA-GTAAAATGATAAT
*
18648 TTTTGGAAGTTTGAGGGTAAAAATG-TAAT
1 TTTTGGAAGTTTG-GAGT-AAAATGATAAT
18677 TT
1 TT
18679 CTAGAAAGTT
Statistics
Matches: 273, Mismatches: 50, Indels: 54
0.72 0.13 0.14
Matches are distributed among these distances:
27 9 0.03
28 78 0.29
29 91 0.33
30 82 0.30
31 13 0.05
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
TTTTGGAAGTTTGGAGTAAAATGATAAT
Found at i:18414 original size:58 final size:57
Alignment explanation
Indices: 18318--18771 Score: 227
Period size: 58 Copynumber: 7.8 Consensus size: 57
18308 GTTTGGACGT
* * * * * * *
18318 AAAATGATAATTTTTTGAAGCTCGGGAGCAAAACGATAATTTTTGGAAAATTTAGGGTC
1 AAAATGATGATTTTTGGAAGTTTGGG-GTAAAATGATAATTTTTGG-AAATTTAGGGTA
* * * *
18377 AAAATGAT-ATATTTGGAAGTTTGAGGGTAAAATGATAATTTTTTGAAAATTCGAGGGTG
1 AAAATGATGATTTTTGGAAGTTTG-GGGTAAAATGATAA-TTTTTGGAAATT-TAGGGTA
* * * * *
18436 AAAATGCA--A-TTTTGGAAGTTCGAGAGTAAAGT-AGTAATTTTTTGGAAGTTCGAGGGTA
1 AAAATG-ATGATTTTTGGAAGTTTG-GGGTAAAATGA-TAA-TTTTTGGAAATT-TAGGGTA
* * *
18494 AAAAT-ATGATTTTTTGGATGTTCGGGGGTAAAATGGTAA-TTTT-GAAAGTTTGAGGGTA
1 AAAATGATGA-TTTTTGGAAGTT-TGGGGTAAAATGATAATTTTTGGAAA-TTT-AGGGTA
* * * *
18552 AAAATG-TGATTTTTGGAAAGTTTGGGGTCAAATGGTAAATTTTGGAAATTTGGGGT-
1 AAAATGATGATTTTTGG-AAGTTTGGGGTAAAATGATAATTTTTGGAAATTTAGGGTA
* * * * *
18608 AAAATG-TAATTTTTTGAAAGTTTGGAGGCAAAATGAAAATTTTTGGAAGTTTGAGGGTA
1 AAAATGATGA-TTTTTGGAAGTTTGG-GGTAAAATGATAATTTTTGGAAATTT-AGGGTA
* * * * * * * *
18667 AAAATG-TAATTTCTAGAAAGTTTAAGGGTAAAAATG-TATTTTTTATGAAGTTTAAGGGTT
1 AAAATGATGATTT-TTGGAAGTTT-GGGGT-AAAATGATAATTTTT-GGAAATTT-AGGGTA
* *
18727 AAAAT-ATAATTTTTGGAAAGTTTAGGGGTCAAAATG-TGATTTTTG
1 AAAATGATGATTTTTGG-AAGTTT-GGGGT-AAAATGATAATTTTTG
18772 AATAGTTTAG
Statistics
Matches: 317, Mismatches: 51, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
56 17 0.05
57 55 0.17
58 110 0.35
59 60 0.19
60 74 0.23
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
AAAATGATGATTTTTGGAAGTTTGGGGTAAAATGATAATTTTTGGAAATTTAGGGTA
Found at i:18433 original size:30 final size:30
Alignment explanation
Indices: 18300--18770 Score: 262
Period size: 30 Copynumber: 16.1 Consensus size: 30
18290 AAAATGCGAC
*
18300 TTTTGGAAGTTTG-GACGTAAAATGATAATT
1 TTTTGGAAGTTTGAG-GGTAAAATGATAATT
* * * *
18330 TTTT-GAAGCTCG-GGAGCAAAACGATAA-T
1 TTTTGGAAGTTTGAGG-GTAAAATGATAATT
*
18358 TTTTGGAAAATTT-AGGGTCAAAATGAT-A-T
1 TTTTGG-AAGTTTGAGGGT-AAAATGATAATT
*
18387 ATTTGGAAGTTTGAGGGTAAAATGATAATT
1 TTTTGGAAGTTTGAGGGTAAAATGATAATT
* * * *
18417 TTTTGAAAATTCGAGGGTGAAAATG-CAA--
1 TTTTGGAAGTTTGAGGGT-AAAATGATAATT
* * *
18445 TTTTGGAAGTTCGAGAGTAAAGT-AGTAATT
1 TTTTGGAAGTTTGAGGGTAAAATGA-TAATT
* *
18475 TTTTGGAAGTTCGAGGGTAAAAAT-ATGATT
1 TTTTGGAAGTTTGAGGGT-AAAATGATAATT
* * * *
18505 TTTTGGATGTTCGGGGGTAAAATGGTAA--
1 TTTTGGAAGTTTGAGGGTAAAATGATAATT
* *
18533 TTTTGAAAGTTTGAGGGTAAAAATG-TGA-T
1 TTTTGGAAGTTTGAGGGT-AAAATGATAATT
* * *
18562 TTTTGGAAAGTTTG-GGGTCAAATGGTAA-A
1 TTTTGG-AAGTTTGAGGGTAAAATGATAATT
*
18591 TTTTGGAAATTTG-GGGTAAAATG-TAATT
1 TTTTGGAAGTTTGAGGGTAAAATGATAATT
* * *
18619 TTTTGAAAGTTTG-GAGGCAAAATGA-AAAT
1 TTTTGGAAGTTTGAG-GGTAAAATGATAATT
18648 TTTTGGAAGTTTGAGGGTAAAAATG-TAATT
1 TTTTGGAAGTTTGAGGGT-AAAATGATAATT
* * * *
18678 TCTAGAAAGTTTAAGGGTAAAAATG-T-ATT
1 TTTTGGAAGTTTGAGGGT-AAAATGATAATT
* *
18707 TTTTATGAAGTTTAAGGGTTAAAAT-ATAA-T
1 TTTT-GGAAGTTTGAGGG-TAAAATGATAATT
*
18737 TTTTGGAAAGTTT-AGGGGTCAAAATG-TGATT
1 TTTTGG-AAGTTTGA-GGGT-AAAATGATAATT
18768 TTT
1 TTT
18771 GAATAGTTTA
Statistics
Matches: 349, Mismatches: 58, Indels: 67
0.74 0.12 0.14
Matches are distributed among these distances:
27 7 0.02
28 83 0.24
29 93 0.27
30 149 0.43
31 17 0.05
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
TTTTGGAAGTTTGAGGGTAAAATGATAATT
Found at i:18564 original size:88 final size:87
Alignment explanation
Indices: 18388--18678 Score: 215
Period size: 88 Copynumber: 3.3 Consensus size: 87
18378 AAATGATATA
* *
18388 TTTGGAAGTTTGAGGGTAAAATGATAATTTTTTGAAAATTCGAGGGTGAAAATGCAATTTTGGAA
1 TTTGGAAGTTCGAGGGTAAAATGATAATTTTTTGAAAATTCGAGGGTGAAAATGCAATTTTGAAA
*
18453 GTTCGAGAGTAAAGTAGTAATTT
66 GTTCGAGAGTAAAATAGTAA-TT
* * ** * *
18476 TTTGGAAGTTCGAGGGTAAAAAT-ATGATTTTTTGGATGTTCGGGGGT-AAAATGGTAATTTTGA
1 TTTGGAAGTTCGAGGGT-AAAATGATAATTTTTTGAAAATTCGAGGGTGAAAAT-GCAATTTTGA
* * *
18539 AAGTTTGAGGGTAAAA-ATGTGATT
64 AAGTTCGAGAGTAAAATA-GTAATT
* * * * * * *
18563 TTTGGAAAGTTTG-GGGTCAAATGGTAA-ATTTTGGAAATTTG-GGGT-AAAATGTAATTTTTTG
1 TTTGG-AAGTTCGAGGGTAAAATGATAATTTTTTGAAAATTCGAGGGTGAAAATGCAA--TTTTG
* * *
18624 AAAGTTTG-GAGGCAAAAT-GAAAATT
63 AAAGTTCGAGA-GTAAAATAG-TAATT
*
18649 TTTGGAAGTTTGAGGGTAAAAATG-TAATTT
1 TTTGGAAGTTCGAGGGT-AAAATGATAATTT
18679 CTAGAAAGTT
Statistics
Matches: 164, Mismatches: 26, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
84 4 0.02
85 18 0.11
86 47 0.29
87 25 0.15
88 65 0.40
89 5 0.03
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (87 bp):
TTTGGAAGTTCGAGGGTAAAATGATAATTTTTTGAAAATTCGAGGGTGAAAATGCAATTTTGAAA
GTTCGAGAGTAAAATAGTAATT
Found at i:19434 original size:9 final size:9
Alignment explanation
Indices: 19420--19457 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
19410 AAAAAACCTC
19420 TTTTTTCAT
1 TTTTTTCAT
19429 TTTTTTCA-
1 TTTTTTCAT
19437 -TTTTTCAT
1 TTTTTTCAT
19445 TTTATTTCAT
1 TTT-TTTCAT
19455 TTT
1 TTT
19458 AAAACCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.27
9 10 0.38
10 9 0.35
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:19442 original size:16 final size:17
Alignment explanation
Indices: 19421--19457 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
19411 AAAAACCTCT
19421 TTTTTCATTTT-TTTCA
1 TTTTTCATTTTATTTCA
19437 TTTTTCATTTTATTTCA
1 TTTTTCATTTTATTTCA
19454 TTTT
1 TTTT
19458 AAAACCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTTATTTCA
Found at i:20625 original size:6 final size:6
Alignment explanation
Indices: 20614--20671 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
20604 TACTTTTTAA
* * *
20614 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA- AT-AAT TTAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT
20660 TTAAAAT TTAAA
1 TT-AAAT TTAAA
20672 ATTTGGGCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 23 0.53
7 12 0.28
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:20637 original size:17 final size:17
Alignment explanation
Indices: 20615--20666 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
20605 ACTTTTTAAT
20615 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
20632 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
20649 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
20666 T
1 T
20667 TTAAAATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20662 original size:7 final size:7
Alignment explanation
Indices: 20616--20675 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
20606 CTTTTTAATT
20616 AAATTT-
1 AAATTTA
20622 AAATTTA
1 AAATTTA
20629 AAA--T-
1 AAATTTA
20633 AAATTTA
1 AAATTTA
* *
20640 AACTTAAA
1 AAATT-TA
20648 ATAATTTA
1 A-AATTTA
20656 AAATTTA
1 AAATTTA
20663 AAATTTA
1 AAATTTA
20670 AAATTT
1 AAATTT
20676 GGGCTTGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
4 3 0.07
5 1 0.02
6 7 0.16
7 26 0.59
8 4 0.09
9 3 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:22919 original size:2 final size:2
Alignment explanation
Indices: 22912--22936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22902 GACCTGAATC
22912 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.