Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005065.1 Kokia drynarioides strain JFW-HI SEQ_118865, 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: 4907
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Found at i:639 original size:27 final size:26
Alignment explanation
Indices: 542--639 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 26
532 AAAGGGGTTG
* **
542 AAAATGAAGTTTTGGAGAGTTCGAGGTT
1 AAAATGTAGTTTTGGA-AGTTC-AGGGA
* **
570 AAAATGTAATTTTGGAAAGTTTGGGGTA
1 AAAATGTAGTTTTGG-AAGTTCAGGG-A
*
598 AAAATGTGATTTTTGGAAGTTCAGGGA
1 AAAATGT-AGTTTTGGAAGTTCAGGGA
625 AAAATGTAGTGTTTG
1 AAAATGTAGT-TTTG
640 AGAAATTTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
26 2 0.04
27 14 0.25
28 32 0.57
29 8 0.14
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.35
Consensus pattern (26 bp):
AAAATGTAGTTTTGGAAGTTCAGGGA
Found at i:658 original size:29 final size:27
Alignment explanation
Indices: 542--774 Score: 110
Period size: 29 Copynumber: 8.1 Consensus size: 27
532 AAAGGGGTTG
* * * * *
542 AAAATGAAGTTTTGGAGAGTTCGAGGTT
1 AAAATGTAGTTTTGGA-AATTTGGGGTA
*
570 AAAATGTAATTTTGGAAAGTTTGGGGTA
1 AAAATGTAGTTTTGGAAA-TTTGGGGTA
* * **
598 AAAATGTGATTTTTGGAAGTTCAGGG-A
1 AAAATGT-AGTTTTGGAAATTTGGGGTA
625 AAAATGTAGTGTTTGAGAAATTTGGGGTA
1 AAAATGTAGT-TTTG-GAAATTTGGGGTA
* * *
654 AAAATGTGATTTTTGGATATTCGAGGGTA
1 AAAATGT-AGTTTTGGAAATTTG-GGGTA
* * * *
683 AAAATATAATTTT-TATAAGTTCGAGGGTAA
1 AAAATGTAGTTTTGGA-AA-TTTG-GGGT-A
* * *
713 AAAATGTGATTTTTGTAAGTTTGAGGGTA
1 AAAATGT-AGTTTTGGAAATTTG-GGGTA
* *
742 AAAATGTATTTTTTGAGAAGTTTAGGGGTA
1 AAAATGTA-GTTTTG-GAAATTT-GGGGTA
772 AAA
1 AAA
775 CCATAATTTT
Statistics
Matches: 164, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
26 2 0.01
27 14 0.09
28 53 0.32
29 55 0.34
30 31 0.19
31 7 0.04
32 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (27 bp):
AAAATGTAGTTTTGGAAATTTGGGGTA
Found at i:725 original size:30 final size:29
Alignment explanation
Indices: 559--754 Score: 142
Period size: 28 Copynumber: 6.9 Consensus size: 29
549 AGTTTTGGAG
* * *
559 AGTTCGA-GGTTAAAATGTAATTTTGGA-A
1 AGTTCGAGGGTAAAAATGTGATTTT-TATA
* **
587 AGTTTG-GGGTAAAAATGTGATTTTTGGA
1 AGTTCGAGGGTAAAAATGTGATTTTTATA
* *
615 AGTTC-AGGG-AAAAATGT-AGTGTTTGAGA
1 AGTTCGAGGGTAAAAATGTGA-T-TTTTATA
* *
643 AATTTG-GGGTAAAAATGTGATTTTTGGAT-
1 AGTTCGAGGGTAAAAATGTGATTTTT--ATA
* *
672 A-TTCGAGGGTAAAAATATAATTTTTATA
1 AGTTCGAGGGTAAAAATGTGATTTTTATA
*
700 AGTTCGAGGGTAAAAAATGTGATTTTTGTA
1 AGTTCGAGGGT-AAAAATGTGATTTTTATA
*
730 AGTTTGAGGGTAAAAATGT-ATTTTT
1 AGTTCGAGGGTAAAAATGTGATTTTT
755 TGAGAAGTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
26 1 0.01
27 11 0.08
28 52 0.39
29 44 0.33
30 27 0.20
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AGTTCGAGGGTAAAAATGTGATTTTTATA
Found at i:763 original size:30 final size:30
Alignment explanation
Indices: 570--994 Score: 244
Period size: 30 Copynumber: 14.5 Consensus size: 30
560 GTTCGAGGTT
*
570 AAAATGTAATTTTGGA-AAGTTTG-GGGTA
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
* *
598 AAAATGTGATTTTTG-GAAG-TTCAGGG-A
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
* * *
625 AAAATGTAGTGTTTGAGAAATTTG-GGGTA
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
* *
654 AAAATGTGATTTTTG-GATA-TTCGAGGGTA
1 AAAATGTAATTTTTGAGA-AGTTTGAGGGTA
* * *
683 AAAATATAATTTTT-ATAAGTTCGAGGGTAA
1 AAAATGTAATTTTTGAGAAGTTTGAGGGT-A
* *
713 AAAATGTGATTTTTG-TAAGTTTGAGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
*
742 AAAATGTATTTTTTGAGAAGTTT-AGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGA-GGGTA
*** * *
772 AAACCATAATTTTAGAGAAGTTTG-GGGTC
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
* * * *
801 GAAATG-GATTTTGGAGCAA-TTT-AGGGGTC
1 AAAATGTAATTTTTGAG-AAGTTTGA-GGGTA
* * * *
830 AAAATATAATTGTT-AGAAAGTTTAAGGGTC
1 AAAATGTAATTTTTGAG-AAGTTTGAGGGTA
* *
860 AAAATGTAATTTTT-ACAA-TATTTAGGGGCT-
1 AAAATGTAATTTTTGAGAAGT-TTGA-GGG-TA
* * *
890 AAAATGTAATTTTAGAAAAGTTT-AGGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGA-GGGTA
* * * *
920 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
* * * *
950 AAAATGTAATTTTAGAAAATTTTG-GGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTA
*
979 AAAATGTGATTTTTGA
1 AAAATGTAATTTTTGA
995 AAGAAAATAG
Statistics
Matches: 321, Mismatches: 49, Indels: 53
0.76 0.12 0.13
Matches are distributed among these distances:
27 15 0.05
28 43 0.13
29 104 0.32
30 150 0.47
31 8 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTGAGGGTA
Found at i:2816 original size:86 final size:85
Alignment explanation
Indices: 2710--2878 Score: 205
Period size: 86 Copynumber: 2.0 Consensus size: 85
2700 GAGCTTCATC
* * * * *
2710 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA-CTGCATCACTTGTTTTAATCCACTTC
1 GATTTGATCCACTTCTCTGTATCTCATCAAGAAGACGATCT-CATCA-TTGCTTTAACCCACTTC
* *
2774 TCTGTATCTTATCAGGAAGACG
64 TCTATATCTCATCAGGAAGACG
* * * * *
2796 GATTTGATCCACTTCTCTGTATTTCATCAGGAAGACGATCTCTTTATTGCTTTGACCCACTTCTC
1 GATTTGATCCACTTCTCTGTATCTCATCAAGAAGACGATCTCATCATTGCTTTAACCCACTTCTC
2861 TATATCTCATCAGGAAGA
66 TATATCTCATCAGGAAGA
2879 TGGGGTTTGA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 32 0.46
86 36 0.51
87 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
GATTTGATCCACTTCTCTGTATCTCATCAAGAAGACGATCTCATCATTGCTTTAACCCACTTCTC
TATATCTCATCAGGAAGACG
Found at i:3442 original size:204 final size:204
Alignment explanation
Indices: 2673--3426 Score: 1193
Period size: 204 Copynumber: 3.7 Consensus size: 204
2663 ATTTGTTCCT
*
2673 GATGAGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
1 GATGGGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
* * * *
2738 AAGAAGATGACTGCATCACTTGTTTTAATCCACTTCTCTGTATCTTATCAGGAAGACGGATTTGA
66 AAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
* * *
2803 TCCACTTCTCTGTATTTCATCAGGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTATATCT
131 TCCACTTCTCTATATTTCATCAAGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTGTATCT
2868 CATCAGGAA
196 CATCAGGAA
* *
2877 GATGGGGTTTGATGTTTCACTCACATTAAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATT
1 GATGGGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
* * * * *
2942 AGGAAGATGACTGCATCACTTGTTTTAATCCGCTTCTTTGTATCTCATCAGGAAGACGGATTTGG
66 AAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
* * * * *
3007 TCCACTTCTCAATATTTCATCAAGAAGACGACCTCTTTATTGCTTTGACCCATTTTTTTGTATCT
131 TCCACTTCTCTATATTTCATCAAGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTGTATCT
3072 CATCAGGAA
196 CATCAGGAA
* * *
3081 GATGGGGTTTGATGTTTCACTCACATTGATCTTCATCGATTTGGTCTACTTCTTTTTATCTCATC
1 GATGGGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
* * * *
3146 AAGAAGATTACCGTATCACTTGTTTTAATCCGCTTCTCTGTATCTTATCAGGAAGACAAATTTGA
66 AAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
*
3211 TCCACTTCTCTTTATTTCATCAAGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTGTATCT
131 TCCACTTCTCTATATTTCATCAAGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTGTATCT
*
3276 TATCAGGAA
196 CATCAGGAA
* * *
3285 GATAGGGTTTGATGCTTCACTCACATTGAGCTTCATCAATTTGGTCTACTTCTCTGTATCTCATC
1 GATGGGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
* * *
3350 AAGAAGATGACCACATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGATGAATTTGG
66 AAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
3415 TCCACTTCTCTA
131 TCCACTTCTCTA
3427 CATCTTGTCA
Statistics
Matches: 499, Mismatches: 51, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
204 499 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (204 bp):
GATGGGGTTTGATGTTTCACTCACATTGAGCTTCATCGATTTGGTCTACTTCTCTGTATCTCATC
AAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGA
TCCACTTCTCTATATTTCATCAAGAAGACGATCTCTTTATTGCTTTGACCCACTTCTCTGTATCT
CATCAGGAA
Found at i:3560 original size:39 final size:39
Alignment explanation
Indices: 3480--3583 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 39
3470 TAATCTACCC
* * * *
3480 CATGATCGAGGTAAGAGATTGGATGGCTGTGATTTGTCT
1 CATGATCGGGGTAAGAGATCGGATGGCTGTGATCTGCCT
* *
3519 CATGGTCGGGGTAAGAGATC-GAGTGGCTGTGGTCTGCCT
1 CATGATCGGGGTAAGAGATCGGA-TGGCTGTGATCTGCCT
** *
3558 CATGATCGGTATAAAAGATCGGATGG
1 CATGATCGGGGTAAGAGATCGGATGG
3584 TTGCAATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.04
39 49 0.92
40 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (39 bp):
CATGATCGGGGTAAGAGATCGGATGGCTGTGATCTGCCT
Found at i:3667 original size:78 final size:77
Alignment explanation
Indices: 3605--4208 Score: 672
Period size: 78 Copynumber: 7.8 Consensus size: 77
3595 CCCTATCGTC
* * * *
3605 GGGTAAGAGATTGGCTGATAGTGATTTGCCTCATGATCGGGGTAAAAGATCGAATGACTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
* *
3670 TGCCTTAGGCTCA
66 TGCCCTA-GCTCG
* * * * * * *
3683 GGATAAGAGATTGACTAATGGTGATCTACCTCAGGCTCGAGGTAAAAGATCGGATGACTGTAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
*
3748 TGCCCGA-CTCG
66 TGCCCTAGCTCG
* ** *
3759 AGGTAAGAGATTGGCTGATGGTGATCTGCC-CTAGGCTCGAAGTAAATGATCGAATGACTGCAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTC-AGGCTCGGGGTAAAAGATCGAATGACTGCAAT
**
3823 CTGCCCTAGGCTTA
65 CTGCCCTA-GCTCG
* * * * * * * *
3837 GTGTAAGAGATTAGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
*
3902 TGCCCTAAGCTTG
66 TGCCCT-AGCTCG
* * * *
3915 GGGTAAGAGATTAGTTGATGGTGATCTACCTCTGGCTCGGGGTAAAAGATCGAATGACTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
*
3980 TGCCCCAGGCTCG
66 TGCCCTA-GCTCG
* * * **
3993 GGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTCGGGGTAAAAGATCGGATGGCTTTAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
* *
4058 TATCCCAAGCTCG
66 T-GCCCTAGCTCG
* * * *
4071 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
*
4136 TGCCCCAAGCTCG
66 TG-CCCTAGCTCG
* * ** *
4149 GGGTAAGAGATTGGTTGATGATGATCTGCCTCAGATTTGGGGTAAAAGATCGAATGACTG
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTG
4209 TGATTTGTCC
Statistics
Matches: 442, Mismatches: 76, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.00
76 63 0.14
77 1 0.00
78 371 0.84
79 6 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (77 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAATGACTGCAATC
TGCCCTAGCTCG
Found at i:3786 original size:37 final size:38
Alignment explanation
Indices: 3686--3803 Score: 105
Period size: 37 Copynumber: 3.1 Consensus size: 38
3676 AGGCTCAGGA
* * * *
3686 TAAGAGATTGACTAATGGTGATCTACCTCAGGCTCGAGG
1 TAAGAGATTGGCTGATGGTGATCTGCC-CAGACTCGAGG
* * * *
3725 TAAAAGATCGGATGACT-GTAATCTGCCC-GACTCGAGG
1 TAAGAGATTGGCTGA-TGGTGATCTGCCCAGACTCGAGG
* *
3762 TAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAAG
1 TAAGAGATTGGCTGATGGTGATCTGCCC-AGACTCGAGG
3801 TAA
1 TAA
3804 ATGATCGAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
36 1 0.02
37 30 0.49
38 1 0.02
39 28 0.46
40 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (38 bp):
TAAGAGATTGGCTGATGGTGATCTGCCCAGACTCGAGG
Found at i:3864 original size:39 final size:39
Alignment explanation
Indices: 3821--4178 Score: 139
Period size: 39 Copynumber: 9.2 Consensus size: 39
3811 AATGACTGCA
* * *
3821 ATCTGCCCTAGGCTTAGTGTAAGAGATTAGTTGATGGTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
* * * * *
3860 ATCTGCCCCAAGCTCGGGGTAAAAGA-TCG--GATGGCTACA
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGG-T--G
3899 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
* * * * * * **
3938 ATCTACCTCT-GGCTCGGGGTAAAAGA-TCGAATGACT-GCA
1 ATCTGCC-CTAAGCTTGGGGTAAGAGATTAG-TTGA-TGGTG
* * * * *
3977 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
* * * * * *
4016 ATCTGCCTTAGGCTCGGGGTAAAAGA-TCG--GATGGCTTTA
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGG---TG
* * * *
4055 ATCTATCCC-AAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCT-GCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
* ** * * *
4094 ATCTGCCCCAAGCTCAGGGTAAAAGA-TCG--AATGGCTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGG-TG
* * * *
4131 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATG
1 --ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
4172 ATCTGCC
1 ATCTGCC
4179 TCAGATTTGG
Statistics
Matches: 244, Mismatches: 49, Indels: 52
0.71 0.14 0.15
Matches are distributed among these distances:
36 14 0.06
37 3 0.01
38 13 0.05
39 185 0.76
40 13 0.05
41 3 0.01
42 13 0.05
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (39 bp):
ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
Found at i:4626 original size:49 final size:49
Alignment explanation
Indices: 4484--4907 Score: 297
Period size: 49 Copynumber: 8.7 Consensus size: 49
4474 TAAGACTCGT
* * * *
4484 CGTTGCGGCCTCAACCTTTCCCATCATAT-TTCATGGTATCAGATTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGGTTCGC
** * * * *
4532 TATTACGGCCTCAATCCTTGT--CATC-CATCTTTTAAGGTGTCGGGTTCGC
1 CGTTGCGGCCTCAA-CCTT-TCCCATCACATC-TTCATGGTATCGGGTTCGC
* * * *
4581 CATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTA-CTGGGTTTGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATC-GGGTTCGC
* * * * * * * * * **
4630 CATTGCTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGGTTCGC
* *
4679 CGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTATCGGGTTTGC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTATCGGGTTCGC
* * * * * *
4729 CGTTGTGGCCTCAACCTTTCCCTTTAAATCTTCATGGTATCGAGTTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGGTTCGC
* * * ** *
4778 CATTACGGTCTCAACCTTTCCCATCACAT-TTCATGGTATCGAATTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGGTTCGC
* * * *
4826 CGTTGCGGCCTTAATCTTTCCCATCACATCTTTTAAGGTA-CGAGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTATCG-GGTTCGC
* * * *
4876 CGTTGTGGCCTCAATCTTTCCCTTCAAATCTT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTT
Statistics
Matches: 290, Mismatches: 71, Indels: 29
0.74 0.18 0.07
Matches are distributed among these distances:
47 3 0.01
48 60 0.21
49 147 0.51
50 80 0.28
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (49 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGGGTTCGC
Found at i:4878 original size:147 final size:146
Alignment explanation
Indices: 4489--4907 Score: 502
Period size: 147 Copynumber: 2.8 Consensus size: 146
4479 CTCGTCGTTG
* **** * **
4489 CGGCCTCAACCTTTCCCATCATATTTCATGGTATCAGATTCGTTATTACGGCCTCAATCCTTGTC
1 CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAGATTCACCGTTGCGGCCTCAATCCTTCCC
* * *
4554 ATC-CATCTTTTAAGGTGTCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGG
66 ATCACATCTTTTAAGGT-ACGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGG
* * *
4618 TACTGGGTTTGCCATTG
130 TACTGAGTTCGCCATTA
* * * * * * *
4635 CTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTACCGTTGCGGCCTCAATCCTTCC
1 CGGCCTCAACCTTTCCCATCACAT-TTCATGGTATCAGATTCACCGTTGCGGCCTCAATCCTTCC
* * *
4700 CATCACATCTTCTAAGGTATCGGGTTTGCCGTTGTGGCCTCAACCTTTCCCTTTAAATCTTCATG
65 CATCACATCTTTTAAGGTA-CGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATG
*
4765 GTA-TCGAGTTCGTCATTA
129 GTACT-GAGTTCGCCATTA
* * *
4783 CGGTCTCAACCTTTCCCATCACATTTCATGGTATC-GAATTCACCGTTGCGGCCTTAATCTTTCC
1 CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAG-ATTCACCGTTGCGGCCTCAATCCTTCC
*
4847 CATCACATCTTTTAAGGTACGAGGTTCGCCGTTGTGGCCTCAATCTTTCCCTTCAAATCTT
65 CATCACATCTTTTAAGGTACG-GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTT
Statistics
Matches: 228, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
146 21 0.09
147 124 0.54
148 83 0.36
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (146 bp):
CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAGATTCACCGTTGCGGCCTCAATCCTTCCC
ATCACATCTTTTAAGGTACGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGGT
ACTGAGTTCGCCATTA
Done.