Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005996.1 Hibiscus syriacus cultivar Beakdansim tig00014120_pilon, 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: 69187
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8778 original size:12 final size:11
Alignment explanation
Indices: 8760--8847 Score: 62
Period size: 12 Copynumber: 8.2 Consensus size: 11
8750 TTATTTATAT
8760 ATTTAAT-AT-
1 ATTTAATAATA
8769 ATTTAATAATA
1 ATTTAATAATA
8780 A--TAATAATA
1 ATTTAATAATA
8789 A--TAATAATA
1 ATTTAATAATA
*
8798 ATATTTATAATA
1 AT-TTAATAATA
*
8810 ATAATAATAATA
1 AT-TTAATAATA
*
8822 ATAATAATAATA
1 AT-TTAATAATA
*
8834 ATAATAATAATA
1 AT-TTAATAATA
8846 AT
1 AT
8848 AAATAAATCA
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
9 25 0.35
10 2 0.03
11 1 0.01
12 43 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:8780 original size:3 final size:3
Alignment explanation
Indices: 8772--8849 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
8762 TTAATATATT
* *
8772 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8820 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8850 ATAAATCAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:9393 original size:113 final size:113
Alignment explanation
Indices: 9087--9981 Score: 1295
Period size: 113 Copynumber: 8.0 Consensus size: 113
9077 AGTCATCCAA
* ** * * *
9087 AAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTCTT--TTCTTCAAATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
* * * * * * *
9148 TGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTTGAACAA
66 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
* * *
9196 AAGGGTTAAACAAGTTCTTCTCATTATGAAC-T-TTCTT--TTCTTCAGATGAGTTCTTCTCATT
1 AA-GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
* * **** * * * *
9257 ATGAACTCTCTTTGGCGCTGCTGATCCATCAAATGATGAATTCAAGCA-
65 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
* * *
9305 AAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AA-GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
** * * * * *
9370 ATGAACTTTAACTGGAAAGGCTGATCCATCAAGGGATGGATTTGAGCAA
65 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
*
9419 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
9484 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
66 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
* *
9532 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
9597 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
66 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
*
9645 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCCTTCAGATGAGTTCTTCTTATT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-CTTCAGATGAGTTCTTCTTATT
9710 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
65 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
* *
9759 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
*
9824 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAATAT
66 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
* *
9872 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
9937 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAA
66 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAA
9982 TCTTTGCTAA
Statistics
Matches: 729, Mismatches: 50, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
109 33 0.05
110 89 0.12
111 4 0.01
113 489 0.67
114 114 0.16
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACAT
Found at i:9765 original size:340 final size:339
Alignment explanation
Indices: 9084--9981 Score: 1330
Period size: 340 Copynumber: 2.7 Consensus size: 339
9074 TAGAGTCATC
* ** * *
9084 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTCTT--TTCTTCAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
* * * * * * * * *
9145 TTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTTGAACAAAAGGGTTAAACAAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAA-GGTTGAACAAA
* * *
9210 TTCTTCTCATTATGAACTTTC-T-TT--T-CTTCAGATGAGTTCTTCTCATTATGAACTCTCTTT
130 TTCTTCTCATTATGAA-TTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCT
**** * * * * *
9270 GGCGCTGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGTTCTTCTCATTATGAA
194 GGAAAAGCTGATCCATCAAGTGATGGATTTAAACAAAGGGTTAAACAAATTCTTCTCATTATGAA
*
9335 CTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAGGCTGATCCATC
259 CTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAAGCTGATCCATC
* *
9400 AAGGGATGGATTTGAG
324 AAGGGATGGATTTAAA
9416 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
9481 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACAAAT
9546 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
* *
9611 AAAAGCTGATCCATCAAGTGATGGATTTAAACATAA-GGTTGAACAAATTCTTCTCATTATGAAT
196 AAAAGCTGATCCATCAAGTGATGGATTTAAACA-AAGGGTTAAACAAATTCTTCTCATTATGAAC
* **
9675 TTCTTCTTCCTTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATC
260 TTCTCCTTCCTT-CTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAAGCTGATCCATC
*
9740 AAGTGATGGATTTAAA
324 AAGGGATGGATTTAAA
* * * *
9756 CATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
*
9821 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAATATAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACAAAT
9886 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
9951 AAAAGCTGATCCATCAAGTGATGGATTTAAA
196 AAAAGCTGATCCATCAAGTGATGGATTTAAA
9982 TCTTTGCTAA
Statistics
Matches: 515, Mismatches: 40, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
332 30 0.06
333 1 0.00
334 9 0.02
335 26 0.05
336 68 0.13
338 1 0.00
339 95 0.18
340 285 0.55
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (339 bp):
CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAACATAAGGTTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTAAACAAAGGGTTAAACAAATTCTTCTCATTATGAACT
TCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAAGCTGATCCATCAA
GGGATGGATTTAAA
Found at i:10849 original size:83 final size:83
Alignment explanation
Indices: 10683--11561 Score: 1514
Period size: 83 Copynumber: 10.6 Consensus size: 83
10673 GATTCCTACT
* * * *
10683 AAACCAGATCAGA-AACTCAAAGAACACTTCCAGACGATGCTAT--GCATATAC-TCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
10744 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
10762 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
**
10827 TCAATGATTGGTTCTATC
66 TCAATGATTGGTTCTGCC
* * *
10845 AAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
10910 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* * *
10928 AAACCAGATCAGATAACTCAAAGAACATTTCTAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
*
10993 TCAATGATTGGTTCTGTC
66 TCAATGATTGGTTCTGCC
* *
11011 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11076 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
11094 AAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11159 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
11177 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11242 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
11260 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11325 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
11343 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11408 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
11426 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATATTCTAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
11491 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
11509 AAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGAGTACATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
11562 GCATTTGTTC
Statistics
Matches: 762, Mismatches: 34, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
79 13 0.02
80 29 0.04
82 6 0.01
83 714 0.94
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
TCAATGATTGGTTCTGCC
Found at i:12322 original size:16 final size:16
Alignment explanation
Indices: 12271--12323 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
12261 AATAAAAGAG
12271 TAAATTGAATTTTTGAAAA
1 TAAATTGAA--TTTG-AAA
* *
12290 TAAATTGAATCTCAAA
1 TAAATTGAATTTGAAA
12306 TAAATTGAATTTGAAA
1 TAAATTGAATTTGAAA
12322 TA
1 TA
12324 GATAGAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 19 0.63
17 2 0.07
19 9 0.30
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAATTGAATTTGAAA
Found at i:12647 original size:1 final size:1
Alignment explanation
Indices: 12643--12708 Score: 87
Period size: 1 Copynumber: 66.0 Consensus size: 1
12633 CTTGACCCCC
* * * * *
12643 TTTTTTTTTTTTTTTTTTTTCTCTTTTCTTTTTTTTTTTTTCTTTTTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12708 T
1 T
12709 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:12673 original size:28 final size:28
Alignment explanation
Indices: 12642--12708 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
12632 TCTTGACCCC
12642 CTTTTTTTTTTTTT-TTTTTTTCTCTTTT
1 CTTTTTTTTTTTTTCTTTTTTT-TCTTTT
12670 CTTTTTTTTTTTTTCTTTTTTTTCTTTT
1 CTTTTTTTTTTTTTCTTTTTTTTCTTTT
12698 -TTTTTTTTTTT
1 CTTTTTTTTTTT
12709 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 11 0.29
28 20 0.53
29 7 0.18
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (28 bp):
CTTTTTTTTTTTTTCTTTTTTTTCTTTT
Found at i:24513 original size:3 final size:3
Alignment explanation
Indices: 24505--24580 Score: 116
Period size: 3 Copynumber: 25.0 Consensus size: 3
24495 TTAATATATT
* *
24505 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
24553 TAAA TAA TTA TAA TAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA
24581 ATAAATCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:25127 original size:113 final size:113
Alignment explanation
Indices: 24857--25825 Score: 1518
Period size: 113 Copynumber: 8.6 Consensus size: 113
24847 ACTTTCTTTT
* * * * * * *
24857 CTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
* * * *
24922 GAACAAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTTC-T-TT--T-
66 AAACATAA-GGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTC
* * * **** * * *
24967 CTTCAGATGAGTTCTTCTCATTATGAACTCTCTTTGGCGCTGCTGATCCATCAAATGATGAATTC
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
* * * * * *
25032 AAGCA-AAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTT
66 AAACATAA-GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
** * *
25080 CTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAGGTTGATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
* * * * * *
25145 GAGCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTT
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
25193 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25258 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
25306 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25371 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
25419 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25484 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
25532 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25597 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
*
25645 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25710 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
66 AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
*
25758 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTT
1 CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
25823 AAA
66 AAA
25826 TATTTGCTAA
Statistics
Matches: 808, Mismatches: 45, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
108 3 0.00
109 30 0.04
110 58 0.07
112 1 0.00
113 714 0.88
114 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
CTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
AAACATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
Found at i:26649 original size:83 final size:83
Alignment explanation
Indices: 26552--27434 Score: 1534
Period size: 83 Copynumber: 10.6 Consensus size: 83
26542 GGTTCCTACT
* * * * *
26552 AAACCAGATCAGATAACTCAAAGAACACTTTCAGACGATGCTATGAGCATATT-ACTCTTCTAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA-TCTTCCAAT
26616 TTCAATGATTGGTTCTGCC
65 TTCAATGATTGGTTCTGCC
* *
26635 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
*
26700 TCAATGATTGGTTCTGTC
66 TCAATGATTGGTTCTGCC
** *
26718 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
26783 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* * *
26801 AAACCAGATCATATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
*
26866 TCAATGATTGGTTCTGTC
66 TCAATGATTGGTTCTGCC
* *
26884 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
26949 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
26967 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
27032 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
27050 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
27115 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* * *
27133 AAACCAAATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
27198 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
27216 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
27281 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
27299 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCATCTTCTAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
27364 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
27382 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
27435 GCATTTGTTC
Statistics
Matches: 766, Mismatches: 33, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
83 765 1.00
84 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
TCAATGATTGGTTCTGCC
Found at i:28195 original size:16 final size:16
Alignment explanation
Indices: 28144--28196 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
28134 AATAAAAGAG
28144 TAAATTGAATTTTCGAAAA
1 TAAATTGAA-TTT-G-AAA
* *
28163 TAAATTGAATCTCAAA
1 TAAATTGAATTTGAAA
28179 TAAATTGAATTTGAAA
1 TAAATTGAATTTGAAA
28195 TA
1 TA
28197 GATAGAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 19 0.63
18 2 0.07
19 9 0.30
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (16 bp):
TAAATTGAATTTGAAA
Found at i:28527 original size:1 final size:1
Alignment explanation
Indices: 28517--28595 Score: 59
Period size: 1 Copynumber: 79.0 Consensus size: 1
28507 TTGACCCCTC
* * * * * * * * **
28517 TTTTTCTTTTTTTCTTTTTTCTCTTTTTTCTCTTTTTCTCTTTTCCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
28582 TTTTCTTTTTTTTT
1 TTTTTTTTTTTTTT
28596 CTTTCTTCTT
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:28530 original size:8 final size:8
Alignment explanation
Indices: 28517--28593 Score: 93
Period size: 8 Copynumber: 9.6 Consensus size: 8
28507 TTGACCCCTC
28517 TTTTTCTT
1 TTTTTCTT
28525 TTTTTC-T
1 TTTTTCTT
28532 TTTTTCTCT
1 TTTTTCT-T
*
28541 TTTTTCTC
1 TTTTTCTT
*
28549 TTTTTCTC
1 TTTTTCTT
*
28557 TTTTCCTT
1 TTTTTCTT
*
28565 TTTTTTTT
1 TTTTTCTT
*
28573 TTTTTTTT
1 TTTTTCTT
28581 TTTTTCTT
1 TTTTTCTT
28589 TTTTT
1 TTTTT
28594 TTCTTTCTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
7 7 0.11
8 46 0.75
9 8 0.13
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:28534 original size:7 final size:7
Alignment explanation
Indices: 28517--28602 Score: 81
Period size: 8 Copynumber: 12.1 Consensus size: 7
28507 TTGACCCCTC
28517 TTTTTCTT
1 TTTTTC-T
28525 TTTTTCTT
1 TTTTTC-T
28533 TTTTCTCT
1 TTTT-TCT
28541 TTTTTCT
1 TTTTTCT
28548 CTTTTTCT
1 -TTTTTCT
* *
28556 CTTTTCC
1 TTTTTCT
28563 TTTTT-T
1 TTTTTCT
28569 TTTTT-T
1 TTTTTCT
28575 TTTTT-T
1 TTTTTCT
28581 TTTTTCT
1 TTTTTCT
28588 TTTTT-T
1 TTTTTCT
28594 TTCTTTCT
1 TT-TTTCT
28602 T
1 T
28603 CTTCTCTTCA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
6 20 0.29
7 21 0.30
8 26 0.38
9 2 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:28535 original size:9 final size:9
Alignment explanation
Indices: 28517--28599 Score: 73
Period size: 9 Copynumber: 9.0 Consensus size: 9
28507 TTGACCCCTC
28517 TTTTTC-TT
1 TTTTTCTTT
28525 TTTTTCTTT
1 TTTTTCTTT
*
28534 TTTCTCTTT
1 TTTTTCTTT
*
28543 TTTCTCTTT
1 TTTTTCTTT
28552 TTCTCTT-TTCCT
1 TT-T-TTCTT--T
28564 TTTTT-TTT
1 TTTTTCTTT
*
28572 TTTTTTTTT
1 TTTTTCTTT
28581 TTTTTCTTTT
1 TTTTTC-TTT
28591 TTTTTCTTT
1 TTTTTCTTT
28600 CTTCTTCTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
8 12 0.18
9 32 0.49
10 16 0.25
11 2 0.03
12 3 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:28558 original size:40 final size:40
Alignment explanation
Indices: 28514--28605 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
28504 ATCTTGACCC
28514 CTCTTTTTCTTTTTTTCTTTTTTCTCTTTTTTCTCTTTTT
1 CTCTTTTTCTTTTTTTCTTTTTTCTCTTTTTTCTCTTTTT
* * * * *
28554 CTCTTTTCCTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 CTCTTTTTCTTTTTTTCTTTTTTCTCTTTTTTCTCTTTTT
*
28594 TTCTTTCTTCTT
1 CTCTTT-TTCTT
28606 CTCTTCAAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (40 bp):
CTCTTTTTCTTTTTTTCTTTTTTCTCTTTTTTCTCTTTTT
Found at i:30258 original size:24 final size:24
Alignment explanation
Indices: 30231--30281 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
30221 ATGAAATATT
30231 AATAATA-TATATAAATACTATAAA
1 AATAATAGTATATAAATA-TATAAA
*
30255 AATAATATGTATATATATATATAAA
1 AATAATA-GTATATAAATATATAAA
30280 AA
1 AA
30282 ATTATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAATAGTATATAAATATATAAA
Found at i:30749 original size:41 final size:42
Alignment explanation
Indices: 30694--30772 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
30684 TAAATTGTCT
* *
30694 CTATTATTAAAAAA-TAT-TCAAAATATATTTAATTTATAATC
1 CTATTATTAAAAAATTATATAAAAAAATATTT-ATTTATAATC
**
30735 CTATTATTTCAAAATTATATAAAAAAATATTTATTTAT
1 CTATTATTAAAAAATTATATAAAAAAATATTTATTTAT
30773 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 12 0.38
42 9 0.28
43 11 0.34
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (42 bp):
CTATTATTAAAAAATTATATAAAAAAATATTTATTTATAATC
Found at i:32321 original size:3 final size:3
Alignment explanation
Indices: 32313--32381 Score: 102
Period size: 3 Copynumber: 23.0 Consensus size: 3
32303 TTAATATATT
* * * *
32313 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32361 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
32382 ATAAATCAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:32618 original size:32 final size:32
Alignment explanation
Indices: 32573--32637 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
32563 ACTCCGGGCG
*
32573 ACCAAGGAGTGAGTGCGAGCTATCCATGGAGC
1 ACCAAGGAGTGAGTGCGAGCTATCCAGGGAGC
*
32605 ACCAAGGATTGAGTGCGAGCTATCCAGGGAGC
1 ACCAAGGAGTGAGTGCGAGCTATCCAGGGAGC
32637 A
1 A
32638 GTGCATGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.15
Consensus pattern (32 bp):
ACCAAGGAGTGAGTGCGAGCTATCCAGGGAGC
Found at i:33026 original size:26 final size:26
Alignment explanation
Indices: 32997--33057 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
32987 TTATTTGCTT
* * *
32997 CAACGGTCAAATTTAATTACGCTCTC
1 CAACGCTCAAATTTAATGACGCCCTC
33023 CAACGCTCAAATTTAATGACGCCCTC
1 CAACGCTCAAATTTAATGACGCCCTC
33049 CAACGCTCA
1 CAACGCTCA
33058 TTTTCTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (26 bp):
CAACGCTCAAATTTAATGACGCCCTC
Found at i:33105 original size:6 final size:6
Alignment explanation
Indices: 33094--33125 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
33084 TTTAGGGTAA
33094 AAGCAG AAGCAG AAGCAG AAGCAG AAGCAG AA
1 AAGCAG AAGCAG AAGCAG AAGCAG AAGCAG AA
33126 ACATCACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.31, T:0.00
Consensus pattern (6 bp):
AAGCAG
Found at i:33337 original size:21 final size:21
Alignment explanation
Indices: 33289--33337 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
33279 ACTAAAATTT
33289 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTTAGTATA
*
33311 AATTATTAGTTTGTTAG-ATTA
1 AGTTATTAGTTTGTTAGTA-TA
33332 AGTTAT
1 AGTTAT
33338 ATTATATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTTAGTATA
Found at i:33347 original size:28 final size:30
Alignment explanation
Indices: 33314--33376 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
33304 TAGTATAAAT
33314 TATTAGTTTGTTAGATTAAG-T-TATATTA
1 TATTAGTTTGTTAGATTAAGTTATATATTA
*
33342 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGATTAAGTTATATATTA
33372 TATTA
1 TATTA
33377 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
TATTAGTTTGTTAGATTAAGTTATATATTA
Found at i:33867 original size:17 final size:17
Alignment explanation
Indices: 33845--33901 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
33835 GATAATTTCC
33845 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
*
33862 GTTTAAAAATAT-TTAGT
1 GTTTAAAAAAATATT-GT
*
33879 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTGT
33896 GTTTAA
1 GTTTAA
33902 TTTATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:37380 original size:49 final size:49
Alignment explanation
Indices: 37245--37547 Score: 420
Period size: 49 Copynumber: 6.1 Consensus size: 49
37235 AATCATGATT
* * *
37245 TAATAATGAATTTA-TATTTAAAATTATAATAATTATT-TAGTAATGATTAG
1 TAATAATGAAATTATTA-TTAATATT-TAATGATT-TTGTAGTAATGATTAG
37295 TAATAATGAAATTATTATTATTAATATTTAATGATTTTGTAGTAATGATTAG
1 TAATAATG-AA--ATTATTATTAATATTTAATGATTTTGTAGTAATGATTAG
*
37347 TAATAATGAAATTATTATTAATATTTAATGATTTGGTAGTAATGATTAG
1 TAATAATGAAATTATTATTAATATTTAATGATTTTGTAGTAATGATTAG
*
37396 TAATAATGAAATTATTATTAATATTTAATGATTTGGTAGTAATGATTAG
1 TAATAATGAAATTATTATTAATATTTAATGATTTTGTAGTAATGATTAG
*
37445 TAATAATTAAATTATTATTAATATTTAATGA-TTTGATAGTAATGATTAG
1 TAATAATGAAATTATTATTAATATTTAATGATTTTG-TAGTAATGATTAG
* *
37494 TAATAATTAAATTATTGTTAATATTTAATGA-TTTGATAGTAATGATT--
1 TAATAATGAAATTATTATTAATATTTAATGATTTTG-TAGTAATGATTAG
37541 TAATAAT
1 TAATAAT
37548 TATTAGTAAT
Statistics
Matches: 240, Mismatches: 7, Indels: 15
0.92 0.03 0.06
Matches are distributed among these distances:
47 7 0.03
48 3 0.01
49 176 0.73
50 8 0.03
51 6 0.03
52 28 0.12
53 10 0.04
54 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (49 bp):
TAATAATGAAATTATTATTAATATTTAATGATTTTGTAGTAATGATTAG
Found at i:37776 original size:12 final size:11
Alignment explanation
Indices: 37754--38074 Score: 141
Period size: 11 Copynumber: 26.3 Consensus size: 11
37744 TAACCATAAA
37754 AATGATTTAAT
1 AATGATTTAAT
37765 AATGATTT--T
1 AATGATTTAAT
37774 AAT-ATTTAAT
1 AATGATTTAAT
*
37784 GATTTGATGATTTAGT
1 -A----ATGATTTAAT
37800 AATGATTT--T
1 AATGATTTAAT
37809 AAT-ATTTAAT
1 AATGATTTAAT
*
37819 GATTTGATGATTTAGT
1 -A----ATGATTTAAT
37835 AATGATTTTAAT
1 AATGA-TTTAAT
37847 ATTATGATTTAAT
1 A--ATGATTTAAT
37860 AATGATTTAGTAAT
1 AATGA-TT--TAAT
*
37874 AATCATTATAAT
1 AATGATT-TAAT
37886 AATGATTTAAT
1 AATGATTTAAT
37897 AATGACTTTAAT
1 AATGA-TTTAAT
37909 ATTTGATGATTTAAT
1 A----ATGATTTAAT
37924 AATGATTTTATAAT
1 AATGA--TT-TAAT
*
37938 AATCATTATAAT
1 AATGATT-TAAT
*
37950 AATAATTTAGTAAT
1 AATGA-TT--TAAT
*
37964 AATCATTATAAT
1 AATGATT-TAAT
37976 AATGATTTAAT
1 AATGATTTAAT
* **
37987 AATAACGATAAT
1 AATGA-TTTAAT
37999 AATGATTTAATAAT
1 AATGA-TT--TAAT
*
38013 AATCATTATAAT
1 AATGATT-TAAT
* *
38025 AATAATTGAATAGT
1 AATGATT---TAAT
38039 AATGATTTAAT
1 AATGATTTAAT
*
38050 AATGATTTAGT
1 AATGATTTAAT
38061 AATGATTTAAT
1 AATGATTTAAT
38072 AAT
1 AAT
38075 TATCACTTAT
Statistics
Matches: 247, Mismatches: 26, Indels: 74
0.71 0.07 0.21
Matches are distributed among these distances:
8 8 0.03
9 8 0.03
10 2 0.01
11 72 0.29
12 65 0.26
13 17 0.07
14 46 0.19
15 13 0.05
16 16 0.06
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (11 bp):
AATGATTTAAT
Found at i:37782 original size:19 final size:18
Alignment explanation
Indices: 37758--37849 Score: 79
Period size: 19 Copynumber: 5.2 Consensus size: 18
37748 CATAAAAATG
37758 ATTTAATAATGATTTTAAT
1 ATTT-ATAATGATTTTAAT
*
37777 A-TT-TAATGA-TTTGAT
1 ATTTATAATGATTTTAAT
37792 GATTTAGTAATGATTTTAAT
1 -ATTTA-TAATGATTTTAAT
*
37812 A-TT-TAATGA-TTTGAT
1 ATTTATAATGATTTTAAT
37827 GATTTAGTAATGATTTTAAT
1 -ATTTA-TAATGATTTTAAT
37847 ATT
1 ATT
37850 ATGATTTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.17
16 14 0.24
17 4 0.07
18 4 0.07
19 17 0.29
20 10 0.17
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (18 bp):
ATTTATAATGATTTTAAT
Found at i:37785 original size:16 final size:15
Alignment explanation
Indices: 37764--37860 Score: 63
Period size: 16 Copynumber: 5.9 Consensus size: 15
37754 AATGATTTAA
37764 TAATGATTTTAATATT
1 TAATGA-TTTAATATT
*
37780 TAATGATTTGATGATTT
1 TAATGATTTAAT-A-TT
37797 AGTAATGATTTTAATATT
1 --TAATGA-TTTAATATT
*
37815 TAATGATTTGATGATTT
1 TAATGATTTAAT-A-TT
37832 AGTAATGATTTTAATA-T
1 --TAATGA-TTTAATATT
37849 T-ATGATTTAATA
1 TAATGATTTAATA
37861 ATGATTTAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 23
0.71 0.04 0.24
Matches are distributed among these distances:
13 7 0.10
14 4 0.06
15 11 0.16
16 14 0.21
17 5 0.07
18 2 0.03
19 14 0.21
20 10 0.15
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TAATGATTTAATATT
Found at i:37788 original size:8 final size:8
Alignment explanation
Indices: 37764--37832 Score: 61
Period size: 8 Copynumber: 8.2 Consensus size: 8
37754 AATGATTTAA
37764 TAATGATTT
1 TAATGA-TT
37773 TAAT-ATT
1 TAATGATT
37780 TAATGATT
1 TAATGATT
*
37788 TGATGATTT
1 TAATGA-TT
37797 AGTAATGATTT
1 --TAATGA-TT
37808 TAAT-ATT
1 TAATGATT
37815 TAATGATT
1 TAATGATT
*
37823 TGATGATT
1 TAATGATT
37831 TA
1 TA
37833 GTAATGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 12 0.24
8 21 0.41
9 10 0.20
11 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:37803 original size:35 final size:35
Alignment explanation
Indices: 37755--37856 Score: 181
Period size: 35 Copynumber: 3.0 Consensus size: 35
37745 AACCATAAAA
*
37755 ATGATTTAATAATGATTTTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
37790 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
37825 ATGATTTAGTAATGATTTTAATA-TT-ATGATTT
1 ATGATTTAGTAATGATTTTAATATTTAATGATTT
37857 AATAATGATT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
33 7 0.11
34 2 0.03
35 57 0.86
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (35 bp):
ATGATTTAGTAATGATTTTAATATTTAATGATTTG
Found at i:37938 original size:64 final size:63
Alignment explanation
Indices: 37761--37963 Score: 228
Period size: 64 Copynumber: 3.3 Consensus size: 63
37751 AAAAATGATT
* * *
37761 TAATAATGATTT--TAAT-ATTTAATGATTTGATGATTTAGTAATGATTTTAATATTTAATGA-T
1 TAATAATGATTTAGTAATGATTTAAT-ATTTGATGATTTAATAATGATTTT-ATA-ATAATCATT
37822 -
63 A
*
37822 T--TGATGATTTAGTAATGATTTTAATA-TT-ATGATTTAATAATGA-TTTAGTAATAATCATTA
1 TAATAATGATTTAGTAATGA-TTTAATATTTGATGATTTAATAATGATTTTA-TAATAATCATTA
*
37882 TAATAATGATTTAATAATGACTTTAATATTTGATGATTTAATAATGATTTTATAATAATCATTA
1 TAATAATGATTTAGTAATGA-TTTAATATTTGATGATTTAATAATGATTTTATAATAATCATTA
*
37946 TAATAATAATTTAGTAAT
1 TAATAATGATTTAGTAAT
37964 AATCATTATA
Statistics
Matches: 121, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
58 6 0.05
59 14 0.12
60 15 0.12
61 7 0.06
62 24 0.20
63 8 0.07
64 43 0.36
65 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (63 bp):
TAATAATGATTTAGTAATGATTTAATATTTGATGATTTAATAATGATTTTATAATAATCATTA
Found at i:37957 original size:26 final size:26
Alignment explanation
Indices: 37850--38063 Score: 196
Period size: 26 Copynumber: 8.5 Consensus size: 26
37840 TTTTAATATT
*
37850 ATGATTTAATAATGAT--TTAGTAATA
1 ATGATTTAATAATAATCATTA-TAATA
* *
37875 ATCA-TT-ATAATAATGATT-TAATA
1 ATGATTTAATAATAATCATTATAATA
* * *
37898 ATGACTTTAATATTTGATGATT-TAATA
1 ATGA-TTTAATA-ATAATCATTATAATA
*
37925 ATGATTTTATAATAATCATTATAATA
1 ATGATTTAATAATAATCATTATAATA
* *
37951 ATAATTTAGTAATAATCATTATAATA
1 ATGATTTAATAATAATCATTATAATA
*
37977 ATGATTTAATAATAA-C--GATAATA
1 ATGATTTAATAATAATCATTATAATA
38000 ATGATTTAATAATAATCATTATAATA
1 ATGATTTAATAATAATCATTATAATA
* * * *
38026 ATAATTGAATAGTAATGATT-TAATA
1 ATGATTTAATAATAATCATTATAATA
*
38051 ATGATTTAGTAAT
1 ATGATTTAATAAT
38064 GATTTAATAA
Statistics
Matches: 155, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
23 36 0.23
24 3 0.02
25 28 0.18
26 72 0.46
27 16 0.10
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (26 bp):
ATGATTTAATAATAATCATTATAATA
Found at i:37964 original size:90 final size:88
Alignment explanation
Indices: 37799--37990 Score: 284
Period size: 90 Copynumber: 2.2 Consensus size: 88
37789 GATGATTTAG
* * *
37799 TAATGATTT--TAATATTTAATGATTTGATGATTTAGTAATGATTTTAATATTATGATTTAATAA
1 TAATGATTTAATAATATTTAATGATTTGATGATTTAATAATGATTTTAATATAATCATTTAATAA
*
37862 TGATTTAGTAATAATCATTATAA
66 TAATTTAGTAATAATCATTATAA
37885 TAATGATTTAATAATGACTTTAAT-ATTTGATGATTTAATAATGATTTT-ATAATAATCATTATA
1 TAATGATTTAATAAT-A-TTTAATGATTTGATGATTTAATAATGATTTTAAT-ATAATCATT-TA
37948 ATAATAATTTAGTAATAATCATTATAA
62 ATAATAATTTAGTAATAATCATTATAA
37975 TAATGATTTAATAATA
1 TAATGATTTAATAATA
37991 ACGATAATAA
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
86 9 0.09
88 6 0.06
89 32 0.33
90 49 0.51
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (88 bp):
TAATGATTTAATAATATTTAATGATTTGATGATTTAATAATGATTTTAATATAATCATTTAATAA
TAATTTAGTAATAATCATTATAA
Found at i:38234 original size:59 final size:56
Alignment explanation
Indices: 38159--38279 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 56
38149 TCGAATTTAT
* *
38159 TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATTATTATTAA
1 TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATGATTACTAA
*
38215 TAATGATTTATTATTAATATTTAATTATTTGATACTAATGATTTACTAATGATTACTAG
1 TAATGATTT-TTA--AATATTTAATTATTTGATACTAATGATTTACTAATGATTACTAA
38274 TAATGA
1 TAATGA
38280 AATTATAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 47 0.80
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATGATTACTAA
Found at i:38239 original size:24 final size:24
Alignment explanation
Indices: 38191--38235 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
38181 TATTTGATAC
*
38191 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
38215 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
38236 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:38242 original size:17 final size:17
Alignment explanation
Indices: 38202--38243 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
38192 AATGATTTAC
38202 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
38219 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
38236 TAATTATT
1 TAATTATT
38244 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:39180 original size:23 final size:23
Alignment explanation
Indices: 39154--39198 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39144 AAAATTACAA
*
39154 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
39177 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
39199 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:40529 original size:30 final size:30
Alignment explanation
Indices: 40495--40598 Score: 140
Period size: 30 Copynumber: 3.4 Consensus size: 30
40485 TCCCTTAAAC
40495 AACTAATAAACTATTCTTTAATATAACTTT
1 AACTAATAAACTATTCTTTAATATAACTTT
*
40525 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAACTTT
*
40555 AACTAATAAACGATT-TTTAATTATAA-TTT
1 AACTAATAAACTATTCTTTAA-TATAACTTT
*
40584 ACTACTAAAAAACTA
1 A--ACTAATAAACTA
40599 ATTAACTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.12
30 48 0.73
31 10 0.15
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:40803 original size:21 final size:21
Alignment explanation
Indices: 40779--40818 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40769 TTTCTATATG
40779 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
40800 ATATAATTTAAACTAACAA
1 ATATAACTTAAACTAACAA
40819 ACTCATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:40899 original size:18 final size:18
Alignment explanation
Indices: 40846--40900 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
40836 TTGTTTTACC
*
40846 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
40864 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
40876 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
40893 CTAATTTA
1 CTAATTTA
40901 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:40959 original size:30 final size:28
Alignment explanation
Indices: 40907--40966 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
40897 TTTAAATAAT
*
40907 TATTCTTTTATATAACTTAAACTAATAAAC
1 TATTCTTTTATATAACTAAAACT--TAAAC
*
40937 TATTTTTTTATTATAA-TAAAACTTAAAC
1 TATTCTTTTA-TATAACTAAAACTTAAAC
40965 TA
1 TA
40967 CTAATAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
30 15 0.56
31 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTCTTTTATATAACTAAAACTTAAAC
Found at i:41065 original size:27 final size:29
Alignment explanation
Indices: 41030--41094 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
41020 TATATATAAC
*
41030 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
41057 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
41085 TTAATTATTT
1 TTAAATATTT
41095 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:41149 original size:370 final size:364
Alignment explanation
Indices: 40536--41215 Score: 917
Period size: 370 Copynumber: 1.8 Consensus size: 364
40526 ACTAATAAAC
40536 TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAAACTAAT
1 TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAAACTAAT
* *
40601 TAACTAAATTTTTTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAACTAACACA
66 AAACTAAATTTTTTATATAATATAAATTCAACAAAAAAATATAACTTAACTATTTAACTAACACA
40666 AACTAATTACATATTTTTTTTATATATAACTAACGACTAACAAACTAACTAATTATTTTTATTAA
131 AACTAATTACATA------TTATATATAACTAAC-ACTAACAAACTAACTAATTATTTTTATTAA
* * * ** *
40731 TATGTAACTATCAAACATACTAATTAAATAATTTTTTATTTCTATATGATATAACTTAAACTAAC
189 TATATAACCATCAAACAAACTAATTAAATAATTTTAAATTTATATATGATATAACTTAAACTAAC
* * * * **
40796 AATAATATAATTTAAACTAACAAACTCATTATCTAATTTTTTGTTTTACCCTAATTTATAATAAT
254 AATAATAAAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTACCCTAATTTATAATAAT
40861 AAACTAATTAACTAATAATTTATAACAATAAACTAATTTAAATAAT
319 AAACTAATTAACTAATAATTTATAACAATAAACTAATTTAAATAAT
* * * *
40907 TATTCTTTTATATAACTTAAACTAATAAACTATTTTTTTATTATAATAAAACTTAAACTACTAAT
1 TATTCTTTAATATAACTTAAACTAATAAACGA-TTTTTAATTATAAT-----TT--ACTACTAAA
*
40972 AAACTAATAAACTAATTTTTTTATATAATATAAATTCAACAACCAAAATATATATAACTTAACTA
58 AAACTAATAAACTAAATTTTTTATATAATATAAATTCAAC-A--AAAA-A-ATATAACTTAACTA
* * *
41037 TTTAACTAACTACAAACTAATTA-A-A-TAT-TA-GACT-A-ACTAACACACTAATTAATTATTT
118 TTTAACTAAC-ACAAACTAATTACATATTATATATAACTAACACTAACAAACTAACTAATTATTT
41095 TT-TTAATATATAACCATCAAACAAACTAATTAAATAATTTTAAATTTATATATGATATAACTTA
182 TTATTAATATATAACCATCAAACAAACTAATTAAATAATTTTAAATTTATATATGATATAACTTA
41159 AACTAACAATAATAAAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTACC
247 AACTAACAATAATAAAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTACC
41216 TTAAACTGAC
Statistics
Matches: 273, Mismatches: 22, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
370 107 0.39
371 53 0.19
372 13 0.05
373 1 0.00
374 3 0.01
375 2 0.01
376 3 0.01
377 2 0.01
379 46 0.17
380 1 0.00
382 3 0.01
383 2 0.01
384 25 0.09
385 12 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (364 bp):
TATTCTTTAATATAACTTAAACTAATAAACGATTTTTAATTATAATTTACTACTAAAAAACTAAT
AAACTAAATTTTTTATATAATATAAATTCAACAAAAAAATATAACTTAACTATTTAACTAACACA
AACTAATTACATATTATATATAACTAACACTAACAAACTAACTAATTATTTTTATTAATATATAA
CCATCAAACAAACTAATTAAATAATTTTAAATTTATATATGATATAACTTAAACTAACAATAATA
AAACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTACCCTAATTTATAATAATAAACTAA
TTAACTAATAATTTATAACAATAAACTAATTTAAATAAT
Found at i:41202 original size:21 final size:21
Alignment explanation
Indices: 41149--41188 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41139 TTTATATATG
41149 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
41170 ATAAAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
41189 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:41231 original size:39 final size:39
Alignment explanation
Indices: 41176--41260 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
41166 AATAATAAAA
41176 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
* *
41215 CTTAAACTGACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
41254 CTTAAAC
1 CTTAAAC
41261 CATAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:41284 original size:39 final size:40
Alignment explanation
Indices: 41176--41284 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 40
41166 AATAATAAAA
*
41176 CTTAAACTAAC-AAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTCACTAAACTAATTAACTAAAATTTTGTTTTAC
*
41215 CTTAAACTGACT-AACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTCACTAAACTAATTAACTAAAATTTTGTTTTAC
**
41254 CTTAAAC-CA-TAAACTAACAAACTAATAATTT
1 CTTAAACTCACTAAACTAATTAACTAA-AATTT
41285 AAAATAATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
37 1 0.02
38 13 0.21
39 49 0.78
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.37
Consensus pattern (40 bp):
CTTAAACTCACTAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:41377 original size:23 final size:22
Alignment explanation
Indices: 41337--41381 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
41327 TGTTGTGCTA
*
41337 TCCCTTTCTTCTTCCTCCTCTTT
1 TCCCTTGCTTCTTCCTCC-CTTT
41360 TCCCTTGCTCTCTT-CTCCCTTT
1 TCCCTTGCT-TCTTCCTCCCTTT
41382 CTTTCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.53
Consensus pattern (22 bp):
TCCCTTGCTTCTTCCTCCCTTT
Found at i:45909 original size:2 final size:2
Alignment explanation
Indices: 45902--45932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45892 AAGCATTTTC
45902 AT AT AT 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 AT AT AT A
45933 ATTCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48841 original size:13 final size:13
Alignment explanation
Indices: 48823--48848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48813 TTTTCGATTT
48823 CGTATTAGAATTG
1 CGTATTAGAATTG
48836 CGTATTAGAATTG
1 CGTATTAGAATTG
48849 AGGAAGGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
CGTATTAGAATTG
Found at i:49184 original size:21 final size:21
Alignment explanation
Indices: 49160--49243 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
49150 TATGTTGTTT
49160 TTCGGGATAATTATGTGGTCC
1 TTCGGGATAATTATGTGGTCC
*
49181 TTCGGGACAATTATGTGG-CAC
1 TTCGGGATAATTATGTGGTC-C
* *
49202 TTCGGTGCA-AACCTATGTGGTCA
1 TTCGG-G-ATAA-TTATGTGGTCC
49225 TTCGGGATAATTATGTGGT
1 TTCGGGATAATTATGTGGT
49244 ACTTTGGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 6 0.11
23 13 0.25
24 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (21 bp):
TTCGGGATAATTATGTGGTCC
Found at i:49229 original size:44 final size:44
Alignment explanation
Indices: 49171--49256 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
49161 TCGGGATAAT
*
49171 TATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
* * *
49215 TATGTGGTCATTCGGGATAATTATGTGGTACTTTGGTGCAAA
1 TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAA
49257 TTACAAGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAATTATGTGGCACTTCGGTGCAAACC
Found at i:52147 original size:29 final size:29
Alignment explanation
Indices: 52088--52323 Score: 296
Period size: 29 Copynumber: 8.2 Consensus size: 29
52078 GCAGTCAACT
* * **
52088 ATTACGAAAATAACACATTTTTTTTAAATA
1 ATTACCAAAATATCAC-TTTTTTCGAAATA
** *
52118 ATTATGAAAATATCACTTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
*
52147 ATTACCAAAATATCAC-TTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
52175 ATTACCAAAATATCACTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
** *
52204 ATTACCAAGTTATCAC-TTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
*
52232 ATTACCAAAATATCATTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
**
52261 ATTAAAAAAATATCACTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
* *
52290 ATTACCAAAATATAATTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCGAAATA
*
52319 TTTAC
1 ATTAC
52324 GAAACTAACA
Statistics
Matches: 182, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
28 52 0.29
29 116 0.64
30 14 0.08
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTACCAAAATATCACTTTTTTCGAAATA
Found at i:52185 original size:57 final size:57
Alignment explanation
Indices: 52113--52323 Score: 305
Period size: 57 Copynumber: 3.7 Consensus size: 57
52103 CATTTTTTTT
** *
52113 AAATAATTATGAAAATATCACTTTTTTCAAAATAATTACCAAAATATCACTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAAATATCACTTTTTCA
**
52170 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAGTTATCACTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAAATATCACTTTTTCA
* ** *
52227 AAATAATTACCAAAATATCATTTTTTTCGAAATAATTAAAAAAATATCACTTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAAATATCAC-TTTTTCA
* * *
52285 AAATAATTACCAAAATATAATTTTTTTCGAAATATTTAC
1 AAATAATTACCAAAATATCACTTTTTTCGAAATAATTAC
52324 GAAACTAACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 97 0.70
58 42 0.30
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (57 bp):
AAATAATTACCAAAATATCACTTTTTTCGAAATAATTACCAAAATATCACTTTTTCA
Found at i:52310 original size:86 final size:85
Alignment explanation
Indices: 52094--52310 Score: 281
Period size: 86 Copynumber: 2.5 Consensus size: 85
52084 AACTATTACG
* ** ** *
52094 AAAATAACACATTTTTTTTAAATAATTATGAAAATATCACTTTTTTCAAAATAATTACCAAAATA
1 AAAATATCAC-TTTTTTCGAAATAATTACCAAAATAT-AATTTTTTCAAAATAATTACCAAAATA
**
52159 TCACTTTTTCAAAATAATTACC
64 TCACTTTTTCAAAATAATTAAA
** * *
52181 AAAATATCACTTTTTTCGAAATAATTACCAAGTTATCACTTTTTCAAAATAATTACCAAAATATC
1 AAAATATCACTTTTTTCGAAATAATTACCAAAATATAATTTTTTCAAAATAATTACCAAAATATC
* *
52246 ATTTTTTTCGAAATAATTAAA
66 A-CTTTTTCAAAATAATTAAA
52267 AAAATATCACTTTTTTCGAAATAATTACCAAAATATAATTTTTT
1 AAAATATCACTTTTTTCGAAATAATTACCAAAATATAATTTTTT
52311 TCGAAATATT
Statistics
Matches: 111, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 27 0.24
86 75 0.68
87 9 0.08
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (85 bp):
AAAATATCACTTTTTTCGAAATAATTACCAAAATATAATTTTTTCAAAATAATTACCAAAATATC
ACTTTTTCAAAATAATTAAA
Found at i:52350 original size:29 final size:29
Alignment explanation
Indices: 52315--52410 Score: 138
Period size: 29 Copynumber: 3.3 Consensus size: 29
52305 TTTTTTTCGA
** *
52315 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
* * *
52344 AGTATTTACGAAACTAATATTTTTTTAAT
1 AATATTTACGAAACTAACATTTTTTTAAC
52373 AATATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
52402 AATATTTAC
1 AATATTTAC
52411 AAAAATACCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (29 bp):
AATATTTACGAAACTAACATTTTTTTAAC
Found at i:52958 original size:20 final size:20
Alignment explanation
Indices: 52933--52991 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
52923 CACTTCATTT
52933 TATTTTATTCT-TAGTGCTAA
1 TATTTTATT-TATAGTGCTAA
*
52953 TATTTTATTTATACTGCTAA
1 TATTTTATTTATAGTGCTAA
52973 T-TATTTATTTATAGTGCTA
1 TAT-TTTATTTATAGTGCTA
52992 TAGGATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (20 bp):
TATTTTATTTATAGTGCTAA
Found at i:56504 original size:29 final size:29
Alignment explanation
Indices: 56472--56707 Score: 331
Period size: 28 Copynumber: 8.3 Consensus size: 29
56462 CATTTTTTTT
* *
56472 AAATAATTACGAAAATATCACTATTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCA
56501 AAATAATTACCAAAATATCAC--TTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCA
* *
56528 AAATAATTACCAAAATATCAC-GTTTTCG
1 AAATAATTACCAAAATATCACTTTTTTCA
*
56556 AAATAATTACCAAATTATCAC-TTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCA
*
56584 AAATAATTACCAAAATATCATTTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCA
**
56613 AAATAA-TACCAAAATATCACTTTTTTTG
1 AAATAATTACCAAAATATCACTTTTTTCA
*
56641 AAATAATTACCAAAATATCATTTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCA
*
56670 AAATAATTACCAAAATATCA-TTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTTCA
*
56698 AAATATTTAC
1 AAATAATTAC
56708 GAAACTAACA
Statistics
Matches: 189, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
27 27 0.14
28 90 0.48
29 72 0.38
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATAATTACCAAAATATCACTTTTTTCA
Found at i:56543 original size:56 final size:57
Alignment explanation
Indices: 56472--56707 Score: 334
Period size: 57 Copynumber: 4.2 Consensus size: 57
56462 CATTTTTTTT
* *
56472 AAATAATTACGAAAATATCACTATTTTCAAAATAATTACCAAAATATCAC-TTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCAAAATAATTACCAAAATATCACTTTTTCA
* * *
56528 AAATAATTACCAAAATATCAC-GTTTTCGAAATAATTACCAAATTATCACTTTTTCA
1 AAATAATTACCAAAATATCACTTTTTTCAAAATAATTACCAAAATATCACTTTTTCA
* **
56584 AAATAATTACCAAAATATCATTTTTTTCAAAATAA-TACCAAAATATCACTTTTTTTG
1 AAATAATTACCAAAATATCACTTTTTTCAAAATAATTACCAAAATATCAC-TTTTTCA
* * *
56641 AAATAATTACCAAAATATCATTTTTTTCAAAATAATTACCAAAATATCATTTTTTCG
1 AAATAATTACCAAAATATCACTTTTTTCAAAATAATTACCAAAATATCACTTTTTCA
*
56698 AAATATTTAC
1 AAATAATTAC
56708 GAAACTAACA
Statistics
Matches: 163, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
55 25 0.15
56 59 0.36
57 66 0.40
58 13 0.08
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (57 bp):
AAATAATTACCAAAATATCACTTTTTTCAAAATAATTACCAAAATATCACTTTTTCA
Found at i:56734 original size:29 final size:29
Alignment explanation
Indices: 56699--56794 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
56689 ATTTTTTCGA
56699 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACACCTTCTTAAC
* ** * *
56728 ATTATTTACGAAACTAACATTTTTTTAAT
1 AATATTTACGAAACTAACACCTTCTTAAC
* * ** *
56757 AATATTTATGAAACTAATATTTTTTTAAC
1 AATATTTACGAAACTAACACCTTCTTAAC
56786 AATATTTAC
1 AATATTTAC
56795 AAAAATACCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (29 bp):
AATATTTACGAAACTAACACCTTCTTAAC
Found at i:57355 original size:20 final size:20
Alignment explanation
Indices: 57330--57388 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
57320 CGCTTCATTT
57330 TATTTTATTCT-TAGTGCTAA
1 TATTTTATT-TATAGTGCTAA
57350 TATTTTATTTATAGTGCTAA
1 TATTTTATTTATAGTGCTAA
57370 T-TATTTATTTATAGTGCTA
1 TAT-TTTATTTATAGTGCTA
57389 TAGGATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.05
20 35 0.95
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (20 bp):
TATTTTATTTATAGTGCTAA
Found at i:63098 original size:17 final size:18
Alignment explanation
Indices: 63076--63109 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
63066 AGGATTATAT
63076 TCTTTTCATT-TTATTTA
1 TCTTTTCATTATTATTTA
*
63093 TCTTTTCTTTATTATTT
1 TCTTTTCATTATTATTT
63110 TTACCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTTCATTATTATTTA
Found at i:65798 original size:15 final size:14
Alignment explanation
Indices: 65774--65816 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
65764 TGAGTGTTTG
65774 TTTGTTTATTTTTA
1 TTTGTTTATTTTTA
65788 TTTGTTTTATTTTT-
1 TTTG-TTTATTTTTA
*
65802 TTATCTTTATTTTTA
1 TT-TGTTTATTTTTA
65817 ATATTAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTGTTTATTTTTA
Found at i:65821 original size:23 final size:23
Alignment explanation
Indices: 65778--65821 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
65768 TGTTTGTTTG
* *
65778 TTTATTTTTATTTGTTTTATTTT
1 TTTATCTTTATTTGTTATATTTT
65801 TTTATCTTTATTT-TTAATATT
1 TTTATCTTTATTTGTT-ATATT
65822 AGTTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATCTTTATTTGTTATATTTT
Found at i:67975 original size:31 final size:31
Alignment explanation
Indices: 67934--68003 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
67924 GGGTCGAGGG
*
67934 TTTACTTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
67965 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
67996 TTTACCTA
1 TTTACCTA
68004 GGTTATTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:68022 original size:31 final size:31
Alignment explanation
Indices: 67933--68026 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
67923 AGGGTCGAGG
* * * *
67933 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTAGGTTATTCGGAACATATGGACT
* * * *
67964 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTAGGTTATTCGGAACATATGGACT
*
67995 GTTTACCTAGGTTATTTGGAATC-TATGGACT
1 GTTTACCTAGGTTATTCGGAA-CATATGGACT
68026 G
1 G
68027 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTAGGTTATTCGGAACATATGGACT
Done.