Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 6 of 144
Found at i:1544351 original size:26 final size:26
Alignment explanation
Indices: 1544321--1544406 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 26
1544311 AAATAAAAAA
*
1544321 CTCATTTGCTTGATAAAACAAATTTC
1 CTCATTTGCTTGATAAAATAAATTTC
* ****
1544347 CTCATTTGGTTTGAATCAAAATAAAAAAA
1 CTCATTT-GCTTG-AT-AAAATAAATTTC
1544376 CTCATTTGCTTGATAAAATAAATTTC
1 CTCATTTGCTTGATAAAATAAATTTC
1544402 CTCAT
1 CTCAT
1544407 CTGGTTTGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
26 20 0.43
27 6 0.13
28 6 0.13
29 14 0.30
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (26 bp):
CTCATTTGCTTGATAAAATAAATTTC
Found at i:1544367 original size:29 final size:28
Alignment explanation
Indices: 1544321--1544426 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 28
1544311 AAATAAAAAA
* *
1544321 CTCATTT-GCTTG-ATAAAACAAATTTC
1 CTCATTTGGTTTGAATAAAATAAATTTC
****
1544347 CTCATTTGGTTTGAATCAAAATAAAAAAA
1 CTCATTTGGTTTGAAT-AAAATAAATTTC
*
1544376 CTCATTT-GCTTG-ATAAAATAAATTTC
1 CTCATTTGGTTTGAATAAAATAAATTTC
*
1544402 CTCATCTGGTTTGAATTAAAATAAA
1 CTCATTTGGTTTGAA-TAAAATAAA
1544427 AAAACTCATT
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
26 21 0.34
27 10 0.16
28 7 0.11
29 23 0.38
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (28 bp):
CTCATTTGGTTTGAATAAAATAAATTTC
Found at i:1544380 original size:55 final size:55
Alignment explanation
Indices: 1544310--1544449 Score: 228
Period size: 55 Copynumber: 2.6 Consensus size: 55
1544300 CATTCCTATT
*
1544310 AAAAT-AAAAAACTCATTTGCTTGATAAAACAAATTTCCTCATTTGGTTTGAATC
1 AAAATAAAAAAACTCATTTGCTTGATAAAACAAATTTCCTCATCTGGTTTGAATC
* *
1544364 AAAATAAAAAAACTCATTTGCTTGATAAAATAAATTTCCTCATCTGGTTTGAATT
1 AAAATAAAAAAACTCATTTGCTTGATAAAACAAATTTCCTCATCTGGTTTGAATC
* *
1544419 AAAATAAAAAAACTCATTTACTTCATAAAAC
1 AAAATAAAAAAACTCATTTGCTTGATAAAAC
1544450 TCAAACTAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 5 0.06
55 74 0.94
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (55 bp):
AAAATAAAAAAACTCATTTGCTTGATAAAACAAATTTCCTCATCTGGTTTGAATC
Found at i:1544434 original size:29 final size:28
Alignment explanation
Indices: 1544347--1544436 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 28
1544337 AACAAATTTC
*
1544347 CTCATTTGGTTTGAATCAAAATAAAAAAA
1 CTCA-TTGGTTTGAATTAAAATAAAAAAA
* * ****
1544376 CTCATTTGCTTG-A-TAAAATAAATTTC
1 CTCATTGGTTTGAATTAAAATAAAAAAA
1544402 CTCATCTGGTTTGAATTAAAATAAAAAAA
1 CTCAT-TGGTTTGAATTAAAATAAAAAAA
1544431 CTCATT
1 CTCATT
1544437 TACTTCATAA
Statistics
Matches: 45, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
26 13 0.29
27 6 0.13
28 8 0.18
29 18 0.40
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (28 bp):
CTCATTGGTTTGAATTAAAATAAAAAAA
Found at i:1544598 original size:20 final size:20
Alignment explanation
Indices: 1544573--1544709 Score: 80
Period size: 20 Copynumber: 6.9 Consensus size: 20
1544563 GATGATGATT
1544573 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
1544593 ATAATTTT---AT-ATTTTAAAAA
1 ATAATTTTAAAATAATTTT----A
*
1544613 ATAATTTTAAATTAATTTTA
1 ATAATTTTAAAATAATTTTA
1544633 ATAATTTT---AT-ATTTTAAAAA
1 ATAATTTTAAAATAATTTT----A
1544653 ATAATTTT--AATAATTTT-
1 ATAATTTTAAAATAATTTTA
*
1544670 ATATTTTTAAAAAATAATTTTA
1 ATAATTTT--AAAATAATTTTA
*
1544692 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
1544710 GCTGACGTAG
Statistics
Matches: 93, Mismatches: 5, Indels: 38
0.68 0.04 0.28
Matches are distributed among these distances:
16 10 0.11
17 10 0.11
20 44 0.47
21 11 0.12
22 12 0.13
23 1 0.01
24 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:1544618 original size:29 final size:29
Alignment explanation
Indices: 1544581--1544700 Score: 132
Period size: 30 Copynumber: 3.7 Consensus size: 29
1544571 TTATAATTTT
1544581 AAAATAATTTTAATAATTTTATATTTTAAAA
1 AAAATAATTTTAATAATTTTATATTTT--AA
1544612 AATAATTTTAAATTAATTTTAATAATTTTATATTTTAA
1 AA-AA---T-AATT--TT--AATAATTTTATATTTTAA
1544650 AAAATAATTTTAATAATTTTATATTTTTAA
1 AAAATAATTTTAATAATTTTATA-TTTTAA
1544680 AAAATAATTTTAATAATTTTA
1 AAAATAATTTTAATAATTTTA
1544701 AAATCATTTG
Statistics
Matches: 79, Mismatches: 0, Indels: 21
0.79 0.00 0.21
Matches are distributed among these distances:
29 12 0.15
30 27 0.34
31 4 0.05
32 2 0.03
33 4 0.05
34 1 0.01
35 1 0.01
36 4 0.05
37 2 0.03
38 6 0.08
40 16 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AAAATAATTTTAATAATTTTATATTTTAA
Found at i:1544629 original size:40 final size:39
Alignment explanation
Indices: 1544573--1544678 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 39
1544563 GATGATGATT
1544573 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
1 ATAATTTT-AAATAATTTTAATAATTTTATATTTTAAAAA
1544613 ATAATTTTAAATTAATTTTAATAATTTTATATTTTAAAAA
1 ATAATTTTAAA-TAATTTTAATAATTTTATATTTTAAAAA
*
1544653 ATAATTTT-AATAATTTT-ATATTTTTA
1 ATAATTTTAAATAATTTTAATAATTTTA
1544679 AAAAATAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
37 8 0.12
38 7 0.11
39 5 0.08
40 44 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
ATAATTTTAAATAATTTTAATAATTTTATATTTTAAAAA
Found at i:1544680 original size:30 final size:29
Alignment explanation
Indices: 1544625--1544700 Score: 143
Period size: 30 Copynumber: 2.6 Consensus size: 29
1544615 AATTTTAAAT
1544625 TAATTTTAATAATTTTATATTTTAAAAAA
1 TAATTTTAATAATTTTATATTTTAAAAAA
1544654 TAATTTTAATAATTTTATATTTTTAAAAAA
1 TAATTTTAATAATTTTATA-TTTTAAAAAA
1544684 TAATTTTAATAATTTTA
1 TAATTTTAATAATTTTA
1544701 AAATCATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 19 0.41
30 27 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATTTTAATAATTTTATATTTTAAAAAA
Found at i:1544687 original size:21 final size:22
Alignment explanation
Indices: 1544661--1544703 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1544651 AAATAATTTT
*
1544661 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
1544682 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
1544704 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:1545636 original size:24 final size:23
Alignment explanation
Indices: 1545578--1545635 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 23
1545568 TTAGTTTATT
*
1545578 GTTTTTTTTTTCGGAACATCTTC
1 GTTTTTTTTTTGGGAACATCTTC
1545601 GTTTTTTTTTTGGTGAAACATCTTC
1 GTTTTTTTTTTGG-G-AACATCTTC
1545626 GTTTTTTTTT
1 GTTTTTTTTT
1545636 GAAACAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 12 0.38
24 1 0.03
25 19 0.59
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (23 bp):
GTTTTTTTTTTGGGAACATCTTC
Found at i:1547207 original size:30 final size:30
Alignment explanation
Indices: 1547165--1547226 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1547155 ATTTCAATCA
*
1547165 TTCAACTTTGAAAATATGATAAAACAG-CC
1 TTCAACTTTGAAAATATGACAAAACAGTCC
*
1547194 TTCAACTTTTGAAAATGTGACAAAACAGTCC
1 TTCAAC-TTTGAAAATATGACAAAACAGTCC
1547225 TT
1 TT
1547227 TTCCGTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 19 0.66
31 4 0.14
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (30 bp):
TTCAACTTTGAAAATATGACAAAACAGTCC
Found at i:1548864 original size:15 final size:15
Alignment explanation
Indices: 1548840--1548890 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1548830 TTTCCAGTTT
1548840 TATA-TATATATATA
1 TATATTATATATATA
* *
1548854 TATATTATATACAAA
1 TATATTATATATATA
* *
1548869 TATATTATAAATATT
1 TATATTATATATATA
1548884 TATATTA
1 TATATTA
1548891 AAGATATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:1550528 original size:63 final size:64
Alignment explanation
Indices: 1550460--1550587 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 64
1550450 TTGAATAAAT
* * * * *
1550460 AGAATAAAATACAATTTGATTCTTAATGTAAATAATTTTA-TATAATTTTACCATGACAGTAAC
1 AGAATAAAATACAATATGATTCTTAATATAAAGAATTTTACGAGAATTTTACCATGACAGTAAC
* ** * *
1550523 AGAATAAAATGCAATATGATTCTTTGTATAAAGAATTTTACGAGAATTTTACCATGGCTGTAAC
1 AGAATAAAATACAATATGATTCTTAATATAAAGAATTTTACGAGAATTTTACCATGACAGTAAC
1550587 A
1 A
1550588 AGTGAAATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 34 0.63
64 20 0.37
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (64 bp):
AGAATAAAATACAATATGATTCTTAATATAAAGAATTTTACGAGAATTTTACCATGACAGTAAC
Found at i:1555034 original size:60 final size:60
Alignment explanation
Indices: 1554902--1555057 Score: 165
Period size: 60 Copynumber: 2.6 Consensus size: 60
1554892 GAAACCCTAG
* * * * *
1554902 AGTTCAGTTCCCAATGTAGGATAATTGCCAAGTTC-AGAGATTAACTTGGACAAAAAAAA
1 AGTTCAGATCCCAATGTAGGAAAATTACCAAGTTCAAGAGACTAAATTGGACAAAAAAAA
* *
1554961 AGTTCA-AGTCCCAATGTAGGAACAATTACCAAGTTCAAG-GCCTAAATTGGACCAAAAAAA
1 AGTTCAGA-TCCCAATGTAGGAA-AATTACCAAGTTCAAGAGACTAAATTGGACAAAAAAAA
* * * *
1555021 AGTTCAGACCCCAATATAAGAAAAGTTACTAAGTTCA
1 AGTTCAGATCCCAATGTAGGAAAA-TTACCAAGTTCA
1555058 GACCCCAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
59 21 0.26
60 57 0.70
61 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (60 bp):
AGTTCAGATCCCAATGTAGGAAAATTACCAAGTTCAAGAGACTAAATTGGACAAAAAAAA
Found at i:1558028 original size:3 final size:3
Alignment explanation
Indices: 1558015--1558050 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1558005 TTACAATCTC
1558015 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1558051 AACCCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1559102 original size:20 final size:20
Alignment explanation
Indices: 1559077--1559128 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1559067 ATAACAAAAA
* *
1559077 GTCAACTATCAAATTCAACG
1 GTCAACGATCAAAATCAACG
*
1559097 GTCAACGATCAAAATCAATG
1 GTCAACGATCAAAATCAACG
*
1559117 GTCAACGGTCAA
1 GTCAACGATCAA
1559129 CGATTAACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
GTCAACGATCAAAATCAACG
Found at i:1573794 original size:15 final size:15
Alignment explanation
Indices: 1573774--1573807 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1573764 CCAAATTTAT
1573774 AAATTTCCTTTCCTC
1 AAATTTCCTTTCCTC
1573789 AAATTTCCTTTCCTC
1 AAATTTCCTTTCCTC
1573804 AAAT
1 AAAT
1573808 ACATCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTCCTTTCCTC
Found at i:1580077 original size:18 final size:19
Alignment explanation
Indices: 1580049--1580088 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1580039 ACTAAATTAA
1580049 TCGGTTGAATCGATCTAAT
1 TCGGTTGAATCGATCTAAT
*
1580068 TCGGTT-AATCGATCTAGT
1 TCGGTTGAATCGATCTAAT
1580086 TCG
1 TCG
1580089 ATCGGAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (19 bp):
TCGGTTGAATCGATCTAAT
Found at i:1591005 original size:3 final size:3
Alignment explanation
Indices: 1590997--1591039 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1590987 GATTAAGTGG
1590997 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1591040 GAAGTGATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1592991 original size:131 final size:131
Alignment explanation
Indices: 1592757--1593017 Score: 468
Period size: 131 Copynumber: 2.0 Consensus size: 131
1592747 TACAATTTCA
* *
1592757 TTATAGGTTTAGTCATATCTGCTCTTTTTGACACAATGCCTAGAACTATCCATTGTCTCTCCTCA
1 TTATAGGTTTAGTCATATCTGCTCTTTTTGACACAATGCCTAGAACTATCCATTGCCTCTCCCCA
* *
1592822 ACTCATAAATAGGAGGCGCTTCAGTGCATTCGAACTTACGTCCTCCGATATTGACAACCATACTC
66 ACTCATAAATAGGAAGCGCTTCAATGCATTCGAACTTACGTCCTCCGATATTGACAACCATACTC
1592887 C
131 C
* *
1592888 TTATAGGTTTAGTCATATCTGCTCTTTTTGACACAATGCCTAGAATTATCTATTGCCTCTCCCCA
1 TTATAGGTTTAGTCATATCTGCTCTTTTTGACACAATGCCTAGAACTATCCATTGCCTCTCCCCA
1592953 ACTCATAAATAGGAAGCGCTTCAATGCATTCGAACTTACGTCCTCCGATATTGACAACCATACTC
66 ACTCATAAATAGGAAGCGCTTCAATGCATTCGAACTTACGTCCTCCGATATTGACAACCATACTC
1593018 ATTCCTATCG
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 124 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (131 bp):
TTATAGGTTTAGTCATATCTGCTCTTTTTGACACAATGCCTAGAACTATCCATTGCCTCTCCCCA
ACTCATAAATAGGAAGCGCTTCAATGCATTCGAACTTACGTCCTCCGATATTGACAACCATACTC
C
Found at i:1596864 original size:18 final size:18
Alignment explanation
Indices: 1596826--1596864 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1596816 ATTCTATTGC
*
1596826 TATATATATTATTATCGG
1 TATATATATTATTATCAG
* *
1596844 TATATATATTGTTGTCAG
1 TATATATATTATTATCAG
1596862 TAT
1 TAT
1596865 TGAGATGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
TATATATATTATTATCAG
Found at i:1598302 original size:12 final size:12
Alignment explanation
Indices: 1598270--1598302 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1598260 TAATTATATT
*
1598270 ATTTTAAAAATA
1 ATTTTAAAATTA
1598282 ATTTT-AAATTA
1 ATTTTAAAATTA
1598293 ATTTTAAAAT
1 ATTTTAAAAT
1598303 CATTTGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:1605344 original size:122 final size:122
Alignment explanation
Indices: 1605127--1605371 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 122
1605117 ATTAAGCAAA
* *
1605127 ACCTTCTGGATGAAGAGGAGGATGCAAGTTGGTCTGCTTAGCAGCGTCCTTGGCTACACGCAACT
1 ACCTTCTGGATGAAGAGGAGGATGCAAGTTGGTCTCCTTAGCAGCATCCTTGGCTACACGCAACT
*
1605192 CTACAATCAGTTGTTCATTATAAGTATCTTACAAGTTTAGCAAGCGTTGACATTCCT
66 CTACAACCAGTTGTTCATTATAAGTATCTTACAAGTTTAGCAAGCGTTGACATTCCT
1605249 ACCTTCTGGATGAAGAGGAGGATGCAAGTTGGTCTCCTTAGCAGCATCCTTGGCTACACGCAACT
1 ACCTTCTGGATGAAGAGGAGGATGCAAGTTGGTCTCCTTAGCAGCATCCTTGGCTACACGCAACT
1605314 CTACAACCAGTTGTTCATTATAAGTATCTTACAAGTTTAGCAAGCGTTGACATTCCT
66 CTACAACCAGTTGTTCATTATAAGTATCTTACAAGTTTAGCAAGCGTTGACATTCCT
1605371 A
1 A
1605372 TTATTCCTGA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (122 bp):
ACCTTCTGGATGAAGAGGAGGATGCAAGTTGGTCTCCTTAGCAGCATCCTTGGCTACACGCAACT
CTACAACCAGTTGTTCATTATAAGTATCTTACAAGTTTAGCAAGCGTTGACATTCCT
Found at i:1608277 original size:34 final size:35
Alignment explanation
Indices: 1608232--1608322 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 35
1608222 AATAAATGAG
* * * *
1608232 CCCAACTCTAGTTGGATTAACCAACGGTTTTG-CA
1 CCCAACGCTAGTTGGATAAACCAACGATTCTGACA
*
1608266 CCCAACGCTAGTTGGATAAACCGACGATTCTGACA
1 CCCAACGCTAGTTGGATAAACCAACGATTCTGACA
* *
1608301 CCCAATGCCTAG-CGGATAAACC
1 CCCAACG-CTAGTTGGATAAACC
1608323 GCAAAAGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 27 0.56
35 17 0.35
36 4 0.08
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (35 bp):
CCCAACGCTAGTTGGATAAACCAACGATTCTGACA
Found at i:1608505 original size:80 final size:80
Alignment explanation
Indices: 1608299--1608505 Score: 272
Period size: 80 Copynumber: 2.6 Consensus size: 80
1608289 ACGATTCTGA
* * *
1608299 CACCCAATGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTAGTATTAACCAACAAATA
1 CACCCAGTGCCTAGTGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTAGGATTAACCAACAAATA
*
1608364 TCCGTCAAATCCTGG
66 TCCGTCAAATCCTAG
* ** * * *
1608379 CACCTAGTGCCTA-TCGGATAAACCGCAAAAGTGAAACCAACTCTAGTTGGATTAACCAATAAAT
1 CACCCAGTGCCTAGT-GGATAAACCGCAAAAGTGAGCCCAGCTCTAGTAGGATTAACCAACAAAT
1608443 ATCCGTCAAATCCTAG
65 ATCCGTCAAATCCTAG
** * *
1608459 CACCCAGTGCCTAGTGGATAAACCGCAATTGTGTGCCCAGCACTAGT
1 CACCCAGTGCCTAGTGGATAAACCGCAAAAGTGAGCCCAGCTCTAGT
1608506 CAGCTAAACT
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (80 bp):
CACCCAGTGCCTAGTGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTAGGATTAACCAACAAATA
TCCGTCAAATCCTAG
Found at i:1612387 original size:36 final size:36
Alignment explanation
Indices: 1612335--1612405 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
1612325 ATCAGACCTT
*
1612335 TAATCCGTAAATGATTCATTTACTTACGATGACACC
1 TAATCCGTAAAGGATTCATTTACTTACGATGACACC
1612371 TAATCCGTAAAGGATTCATTTACTTACGATGACAC
1 TAATCCGTAAAGGATTCATTTACTTACGATGACAC
1612406 TTAGTCATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (36 bp):
TAATCCGTAAAGGATTCATTTACTTACGATGACACC
Found at i:1612431 original size:51 final size:51
Alignment explanation
Indices: 1612371--1612473 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
1612361 CGATGACACC
*
1612371 TAATCCGTAAAGGATTCATTTACTTACGATGACACTTAGTCATCGGACCTT
1 TAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTT
*
1612422 TAATCCGTAAAGGATTCATTTACTCACGATGGCACTTAGTCATCGGACCTT
1 TAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTT
1612473 T
1 T
1612474 TCGTTTATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (51 bp):
TAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTT
Found at i:1614689 original size:18 final size:18
Alignment explanation
Indices: 1614668--1614703 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
1614658 AATTTAATTC
1614668 TTTTCTTTTATTTTCTTAT
1 TTTTC-TTTATTTTCTTAT
1614687 TTTTCTTTATTTTCTTA
1 TTTTCTTTATTTTCTTA
1614704 CTCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTATTTTCTTAT
Found at i:1619860 original size:12 final size:12
Alignment explanation
Indices: 1619841--1619883 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1619831 TTTAACTTAA
1619841 ATGAACATGTTC
1 ATGAACATGTTC
* **
1619853 ACGAACAT-TAA
1 ATGAACATGTTC
1619864 ATGAACATGTTC
1 ATGAACATGTTC
1619876 ATGAACAT
1 ATGAACAT
1619884 ATAATTGAAC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (12 bp):
ATGAACATGTTC
Found at i:1619881 original size:23 final size:23
Alignment explanation
Indices: 1619797--1619899 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
1619787 TAATGTTCAC
*
1619797 GAACATGTTCATTTAACTTAAAT
1 GAACATGTTCATTGAACTTAAAT
*
1619820 GAACATGTTCATTTAACTTAAAT
1 GAACATGTTCATTGAACTTAAAT
*
1619843 GAACATGTTCA-CGAACATTAAAT
1 GAACATGTTCATTGAAC-TTAAAT
*
1619866 GAACATGTTCA-TGAACATATAATT
1 GAACATGTTCATTGAAC-T-TAAAT
1619890 GAACATGTTC
1 GAACATGTTC
1619900 CCGAACAATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
22 3 0.04
23 57 0.77
24 14 0.19
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (23 bp):
GAACATGTTCATTGAACTTAAAT
Found at i:1621748 original size:19 final size:19
Alignment explanation
Indices: 1621724--1621762 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1621714 AATAAGCTCA
1621724 TTATCAATTAGAAATTAGT
1 TTATCAATTAGAAATTAGT
1621743 TTATCAATTAGAAATTAGT
1 TTATCAATTAGAAATTAGT
1621762 T
1 T
1621763 ACAAGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
TTATCAATTAGAAATTAGT
Found at i:1626797 original size:32 final size:33
Alignment explanation
Indices: 1626754--1626833 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
1626744 TTGTCTTGAT
1626754 GGAACTGTTGCTTACTGT-TGAGT-ATCTTCCAG
1 GGAACTGTTGCTTACTGTCTGA-TCATCTTCCAG
* * *
1626786 GTAACTGTTGCTTA-TTTCTTATCATCTTCCAG
1 GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
1626818 GGAACTGTTGCTTACT
1 GGAACTGTTGCTTACT
1626834 ACTTGCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.07
32 37 0.90
33 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (33 bp):
GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
Found at i:1633831 original size:111 final size:112
Alignment explanation
Indices: 1633711--1633938 Score: 361
Period size: 118 Copynumber: 2.0 Consensus size: 112
1633701 ATATTTTTTT
*
1633711 TTCAAAAAACTCTCTTCTATCTCTCATTTTTTTTCTCATGAAATAACTTTAAATGTT-A-CAAAT
1 TTCAAAAAACTCTCTTCTATCTCTCA-TTTTTTTCTCATGAAACAACTTTAAATGTTAACCAAAT
1633774 CAAAATTCAAATTATTTTTTCTTCGATATTTGATACTAACCGTCAAAA
65 CAAAATTCAAATTATTTTTTCTTCGATATTTGATACTAACCGTCAAAA
1633822 TTCAAAAAACTCTCTTCTATCTCTCATTTTTTTCTCATGAAACAACTTTAAATGTTACAAATCCG
1 TTCAAAAAACTCTCTTCTATCTCTCATTTTTTTCTCATGAAACAACTTTAAATGTT---AA--C-
*
1633887 CAAATCAAAATTCAAATTATTTTTTCTTCGATATTTGATACTAATCGTCAAA
60 CAAATCAAAATTCAAATTATTTTTTCTTCGATATTTGATACTAACCGTCAAA
1633939 TCAATTTAAT
Statistics
Matches: 107, Mismatches: 2, Indels: 9
0.91 0.02 0.08
Matches are distributed among these distances:
110 29 0.27
111 26 0.24
114 1 0.01
118 51 0.48
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (112 bp):
TTCAAAAAACTCTCTTCTATCTCTCATTTTTTTCTCATGAAACAACTTTAAATGTTAACCAAATC
AAAATTCAAATTATTTTTTCTTCGATATTTGATACTAACCGTCAAAA
Found at i:1658365 original size:22 final size:24
Alignment explanation
Indices: 1658341--1658389 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1658331 GATTAAAACT
*
1658341 AATATATATATATTATGAAAATAATA
1 AATATATA-ATA-CATGAAAATAATA
*
1658367 AATCTATAATACATGAAAATAAT
1 AATATATAATACATGAAAATAAT
1658390 TTCTTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 3 0.14
26 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
AATATATAATACATGAAAATAATA
Found at i:1659107 original size:80 final size:80
Alignment explanation
Indices: 1658974--1659144 Score: 333
Period size: 80 Copynumber: 2.1 Consensus size: 80
1658964 TATTATCATA
1658974 TTTGTTTTTTTAAACACGTCCTCTTGCACTGATCACAACAATGCCGATATCAATCGACTAAGACT
1 TTTGTTTTTTTAAACACGTCCTCTTGCACTGATCACAACAATGCCGATATCAATCGACTAAGACT
1659039 CAATCGACATATTTC
66 CAATCGACATATTTC
1659054 TTTGTTTTTTTAAACACGTCCTCTTGCACTGATCACAACAATGCCGATATCAATCGACTAAGACT
1 TTTGTTTTTTTAAACACGTCCTCTTGCACTGATCACAACAATGCCGATATCAATCGACTAAGACT
1659119 CAATCGACATATTTC
66 CAATCGACATATTTC
*
1659134 TTTATTTTTTT
1 TTTGTTTTTTT
1659145 TAAATAGAAC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (80 bp):
TTTGTTTTTTTAAACACGTCCTCTTGCACTGATCACAACAATGCCGATATCAATCGACTAAGACT
CAATCGACATATTTC
Found at i:1660984 original size:15 final size:15
Alignment explanation
Indices: 1660964--1660993 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1660954 ATGGGTATAA
*
1660964 GAAATCTAGTTATGG
1 GAAATCGAGTTATGG
1660979 GAAATCGAGTTATGG
1 GAAATCGAGTTATGG
1660994 AAGATCAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (15 bp):
GAAATCGAGTTATGG
Found at i:1661056 original size:39 final size:39
Alignment explanation
Indices: 1661013--1661144 Score: 113
Period size: 39 Copynumber: 3.2 Consensus size: 39
1661003 TGAAAGAGAA
1661013 GAAGGATATGGAGGTAGGAGGAAATCGGATGATGAAGAT
1 GAAGGATATGGAGGTAGGAGGAAATCGGATGATGAAGAT
* * ** * * * *
1661052 GAAGGGTATAAGAAATCGAGTTATGGAAGATCAGATGA-AAGAGAA
1 GAAGGATAT-GGAGGT--AG-GA-GGAA-ATCGGATGATGA-AGAT
*
1661097 GAAGAATATGGAGGTAGGAGGAAATCGGATGATGAAGAT
1 GAAGGATATGGAGGTAGGAGGAAATCGGATGATGAAGAT
1661136 GAAGGATAT
1 GAAGGATAT
1661145 AAGAAGTCGA
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
39 27 0.40
40 8 0.12
41 1 0.01
42 4 0.06
43 1 0.01
44 8 0.12
45 18 0.27
ACGTcount: A:0.42, C:0.03, G:0.36, T:0.18
Consensus pattern (39 bp):
GAAGGATATGGAGGTAGGAGGAAATCGGATGATGAAGAT
Found at i:1661165 original size:84 final size:84
Alignment explanation
Indices: 1660979--1661158 Score: 333
Period size: 84 Copynumber: 2.1 Consensus size: 84
1660969 CTAGTTATGG
*
1660979 GAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGGATATGGAGGTAGGAGGAAATCGGATG
1 GAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATCGGATG
*
1661044 ATGAAGATGAAGGGTATAA
66 ATGAAGATGAAGGATATAA
1661063 GAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATCGGATG
1 GAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATCGGATG
1661128 ATGAAGATGAAGGATATAA
66 ATGAAGATGAAGGATATAA
*
1661147 GAAGTCGAGTTA
1 GAAATCGAGTTA
1661159 CAGAAGAAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 93 1.00
ACGTcount: A:0.43, C:0.04, G:0.34, T:0.18
Consensus pattern (84 bp):
GAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATCGGATG
ATGAAGATGAAGGATATAA
Found at i:1668117 original size:17 final size:17
Alignment explanation
Indices: 1668062--1668128 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
1668052 AAAAGTGCAT
**
1668062 AATTTTTAAAATTTTAA
1 AATTTTTAATTTTTTAA
* * *
1668079 AGTTTTTATTTTTTTCAT
1 AATTTTTAATTTTTT-AA
1668097 AATTTTTAATTTTTTAA
1 AATTTTTAATTTTTTAA
* *
1668114 AATTATAAATTTTTT
1 AATTTTTAATTTTTT
1668129 TATTTTTAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 25 0.64
18 14 0.36
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (17 bp):
AATTTTTAATTTTTTAA
Found at i:1668127 original size:35 final size:35
Alignment explanation
Indices: 1668059--1668139 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
1668049 TTTAAAAGTG
* * * *
1668059 CATAATTTTTAAAATTTTAAAGTTTTTATTTTTTT
1 CATAATTTTTAAAATTTTAAAATTATAAATTTTTT
**
1668094 CATAATTTTTAATTTTTTAAAATTATAAATTTTTT
1 CATAATTTTTAAAATTTTAAAATTATAAATTTTTT
1668129 --T-ATTTTTAAAA
1 CATAATTTTTAAAA
1668140 AGCTATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 8 0.21
33 1 0.03
35 29 0.76
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (35 bp):
CATAATTTTTAAAATTTTAAAATTATAAATTTTTT
Found at i:1669587 original size:3 final size:3
Alignment explanation
Indices: 1669579--1669603 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1669569 GACAATGGCT
1669579 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1669604 AAGGGGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1675411 original size:24 final size:24
Alignment explanation
Indices: 1675355--1675411 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
1675345 AAAGAAGAAG
*
1675355 AAAGAAAAA-AAATGAAAAATAGA
1 AAAGAAAAAGAAATGAAAAATACA
*
1675378 AAA-AATAAAGAAA-GAATTAATACA
1 AAAGAA-AAAGAAATGAA-AAATACA
1675402 AAAGAAAAAG
1 AAAGAAAAAG
1675412 GCTAATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.07
23 9 0.32
24 15 0.54
25 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.11
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAATACA
Found at i:1677746 original size:11 final size:11
Alignment explanation
Indices: 1677730--1677754 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1677720 AATAAAAAAT
1677730 TATTTTTTTTA
1 TATTTTTTTTA
1677741 TATTTTTTTTA
1 TATTTTTTTTA
1677752 TAT
1 TAT
1677755 GCATCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTTTTTA
Found at i:1681068 original size:2 final size:2
Alignment explanation
Indices: 1681061--1681086 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1681051 CATATCTTTC
1681061 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1681087 CCAAGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1684971 original size:17 final size:17
Alignment explanation
Indices: 1684948--1684987 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1684938 AAAAAGAATT
1684948 AAAATTGATAA-AAATAA
1 AAAATTG-TAATAAATAA
*
1684965 TAAATTGTAATAAATAA
1 AAAATTGTAATAAATAA
1684982 AAAATT
1 AAAATT
1684988 TAAGTCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAATTGTAATAAATAA
Found at i:1688941 original size:44 final size:43
Alignment explanation
Indices: 1688826--1688941 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
1688816 GGTTAGAAGT
* * *
1688826 TAATAATTAATATAT-TCCCATAA-TTTTTTGGTATTTTCTCA
1 TAATAATTAGTATATATACCATAATTTTTTTGGCATTTTCTCA
*
1688867 TAATAATTAGTATATATA-GATAATTCTTTTTTGGCATTTTCTCA
1 TAATAATTAGTATATATACCATAA-T-TTTTTTGGCATTTTCTCA
*
1688911 TAATAATTGGTATATATACTCATAATTTTTT
1 TAATAATTAGTATATATAC-CATAATTTTTT
1688942 GTATTGTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
41 18 0.29
42 1 0.02
44 39 0.62
45 1 0.02
46 4 0.06
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (43 bp):
TAATAATTAGTATATATACCATAATTTTTTTGGCATTTTCTCA
Found at i:1689018 original size:22 final size:22
Alignment explanation
Indices: 1688980--1689021 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1688970 AGAAATATAA
1688980 TTTTAAAATAAATAAAATTTAT
1 TTTTAAAATAAATAAAATTTAT
*
1689002 TTTTAAATATTAA-AAAATTT
1 TTTTAAA-ATAAATAAAATTT
1689022 CAATGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAAAATAAATAAAATTTAT
Found at i:1690761 original size:13 final size:13
Alignment explanation
Indices: 1690743--1690794 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1690733 AGAGTTTTTA
*
1690743 TTTTTATAATAAT
1 TTTTTATAATATT
* *
1690756 TTTTTA-ATTTTT
1 TTTTTATAATATT
1690768 TTTTTATAATATT
1 TTTTTATAATATT
*
1690781 TTTTTTTAAT-TT
1 TTTTTATAATATT
1690793 TT
1 TT
1690795 ATGTACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 13 0.41
13 19 0.59
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTATAATATT
Found at i:1690766 original size:25 final size:22
Alignment explanation
Indices: 1690737--1690796 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
1690727 TTTTAAAGAG
1690737 TTTTTATTTTTATAATAATTTTT
1 TTTTTATTTTTATAAT-ATTTTT
*
1690760 TAATTTTTTTTTTATAATATTTTT
1 T--TTTTATTTTTATAATATTTTT
*
1690784 TTTTAATTTTTAT
1 TTTTTATTTTTAT
1690797 GTACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 10 0.31
23 1 0.03
24 7 0.22
25 14 0.44
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTATTTTTATAATATTTTT
Found at i:1690767 original size:27 final size:26
Alignment explanation
Indices: 1690737--1690794 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
1690727 TTTTAAAGAG
1690737 TTTTTATTTTTATAATA-ATTTTTTAA
1 TTTTT-TTTTTATAATATATTTTTTAA
*
1690763 TTTTTTTTTTATAATATTTTTTTTTAA
1 TTTTTTTTTTATAATA-TATTTTTTAA
1690790 TTTTT
1 TTTTT
1690795 ATGTACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 5 0.17
27 13 0.45
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTTATAATATATTTTTTAA
Found at i:1692220 original size:90 final size:89
Alignment explanation
Indices: 1692067--1692264 Score: 236
Period size: 90 Copynumber: 2.2 Consensus size: 89
1692057 CGAACATTCT
* * * **
1692067 AATTTGTGGATAAACCA-TCAGTATTGCAGGTTAATACGTTGCCAGTAGTTGTGAATACACAACG
1 AATTTGTGGATAAACCACCCA-TGTTGCAGGTTAATACGCTGCCAGTAGTTGCCAATACACAACG
* ** *
1692131 GTTTTGTAGATGAAAGTTGCCAGTAA
65 GGTTTACAGATAAAAGTTGCCAGT-A
* * * *
1692157 AATTTTTGGATGAACCACCCATGTTGCAGGTTAATATGCTGCCAGTGGTTGCCAATACACAACGG
1 AATTTGTGGATAAACCACCCATGTTGCAGGTTAATACGCTGCCAGTAGTTGCCAATACACAACGG
*
1692222 GTTTACAGATAAAAGTTGTCAGTA
66 GTTTACAGATAAAAGTTGCCAGTA
*
1692246 AGTTTGTGGATAAACCACC
1 AATTTGTGGATAAACCACC
1692265 AGTGTTTGTA
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 17 0.19
90 71 0.79
91 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (89 bp):
AATTTGTGGATAAACCACCCATGTTGCAGGTTAATACGCTGCCAGTAGTTGCCAATACACAACGG
GTTTACAGATAAAAGTTGCCAGTA
Found at i:1692607 original size:86 final size:86
Alignment explanation
Indices: 1692460--1692637 Score: 311
Period size: 86 Copynumber: 2.1 Consensus size: 86
1692450 TTCATACAAT
*
1692460 TAGTAATATAGTGGTTCGAGTATCAGTAACAACTAATTAGTAATCCAATAAAAAAACGCATGTAC
1 TAGTAATATAGTGGTTCGAGTATCAGTAACAACTAATCAGTAATCCAATAAAAAAACGCATGTAC
1692525 TAATTACATACCATGCATATA
66 TAATTACATACCATGCATATA
* * * *
1692546 TAGTAATATAGTGGTTCGAGTATCAGTAACAACTACTCAGTAATCCAATCAAAGAAGGCATGTAC
1 TAGTAATATAGTGGTTCGAGTATCAGTAACAACTAATCAGTAATCCAATAAAAAAACGCATGTAC
1692611 TAATTACATACCATGCATATA
66 TAATTACATACCATGCATATA
1692632 TAGTAA
1 TAGTAA
1692638 CAATTTAGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (86 bp):
TAGTAATATAGTGGTTCGAGTATCAGTAACAACTAATCAGTAATCCAATAAAAAAACGCATGTAC
TAATTACATACCATGCATATA
Found at i:1696217 original size:31 final size:31
Alignment explanation
Indices: 1696181--1696264 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
1696171 CAAAGAAAAA
*
1696181 CACCAATACATAGCACCTGATATAATAT-AGT
1 CACCAATACATAGTACCTGATATAATATGA-T
*
1696212 CACCAATACGTAGTACCTGATATAATATGAT
1 CACCAATACATAGTACCTGATATAATATGAT
*
1696243 CACCAATACAAAGTACCTGATA
1 CACCAATACATAGTACCTGATA
1696265 CTTTTAAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (31 bp):
CACCAATACATAGTACCTGATATAATATGAT
Found at i:1699156 original size:43 final size:42
Alignment explanation
Indices: 1698996--1699162 Score: 172
Period size: 43 Copynumber: 3.9 Consensus size: 42
1698986 TATTGACACA
* * * * *
1698996 ATACTAGCACACGAGGTGCATCATCGGACAAACCGAAGCAATT
1 ATACTAGCACAC-AAGTGCATCATCGAATAAACCAAAGCAATC
* *
1699039 ATACTAGCACACAAGGTGCATCATCAAAAAAACCAAAGCAATC
1 ATACTAGCACACAA-GTGCATCATCGAATAAACCAAAGCAATC
* * * * * *
1699082 ATATTGGCATACATAGTGCATCATTGGATAAATCAAAGCAATC
1 ATACTAGCACACA-AGTGCATCATCGAATAAACCAAAGCAATC
*
1699125 ATACTAGCACACATAGTGCATCATCGAATAAAACAAAG
1 ATACTAGCACACA-AGTGCATCATCGAATAAACCAAAG
1699163 TATAAACCCA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.01
43 100 0.98
44 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (42 bp):
ATACTAGCACACAAGTGCATCATCGAATAAACCAAAGCAATC
Found at i:1701078 original size:21 final size:20
Alignment explanation
Indices: 1701053--1701091 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1701043 TGTTTTGTTC
1701053 CATAA-ATTTCATCTCATTTGT
1 CATAACATTT-ATCT-ATTTGT
1701074 CATAACATTTATCTATTT
1 CATAACATTTATCTATTT
1701092 ATAGACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.49
Consensus pattern (20 bp):
CATAACATTTATCTATTTGT
Found at i:1701721 original size:5 final size:5
Alignment explanation
Indices: 1701692--1701738 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
1701682 CGAATCCTTA
* *
1701692 CGAAT CGATT CGAGAT AGAATT CGAAT CGAAT CGAAT CGAAT CGAAT
1 CGAAT CGAAT CGA-AT CGAA-T CGAAT CGAAT CGAAT CGAAT CGAAT
1701739 ATATTTGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 29 0.81
6 7 0.19
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (5 bp):
CGAAT
Found at i:1702795 original size:18 final size:19
Alignment explanation
Indices: 1702763--1702801 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1702753 TGGGAAATAA
*
1702763 TAAAAAATATGTATTAAAT
1 TAAAAAATATATATTAAAT
*
1702782 TAAAAAAT-TATATTATAT
1 TAAAAAATATATATTAAAT
1702800 TA
1 TA
1702802 TTGGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAAATATATATTAAAT
Found at i:1704571 original size:23 final size:22
Alignment explanation
Indices: 1704532--1704581 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1704522 TTTAACTCAT
1704532 AAAAAATAATTAAATAATAATG
1 AAAAAATAATTAAATAATAATG
**
1704554 AAAATAATAATTTCATAATAA--
1 AAAA-AATAATTAAATAATAATG
1704575 AAAAAAT
1 AAAAAAT
1704582 TTTCTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 4 0.16
22 4 0.16
23 14 0.56
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAATAATTAAATAATAATG
Found at i:1705705 original size:24 final size:24
Alignment explanation
Indices: 1705677--1705763 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
1705667 AGAAATAATC
* *
1705677 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
1705701 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
1705725 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
1705749 TTTGAGTTAAACTCT
1 TTTCAATTAAACTCT
1705764 TACTAGTCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:1707711 original size:24 final size:24
Alignment explanation
Indices: 1707683--1707745 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1707673 AGAAATAATC
1707683 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
1707707 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
*
1707731 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
1707746 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:1708247 original size:18 final size:19
Alignment explanation
Indices: 1708208--1708248 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1708198 AAATAGATTG
*
1708208 ATTTTCTAGAAAAATTGTT
1 ATTTTCTAGAAAAATTGAT
1708227 ATTTTCTAGAAAAATT-AT
1 ATTTTCTAGAAAAATTGAT
1708245 ATTT
1 ATTT
1708249 ACGTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (19 bp):
ATTTTCTAGAAAAATTGAT
Found at i:1710001 original size:20 final size:20
Alignment explanation
Indices: 1709978--1710031 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1709968 AGAAGCATAC
1709978 TTGTATCGGTAGAACTGAAG
1 TTGTATCGGTAGAACTGAAG
* * *
1709998 TTGTATCGATAAAAGTGAAG
1 TTGTATCGGTAGAACTGAAG
* *
1710018 TTCTACCGGTAGAA
1 TTGTATCGGTAGAA
1710032 GTCCCAGGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGTATCGGTAGAACTGAAG
Found at i:1710416 original size:20 final size:20
Alignment explanation
Indices: 1710357--1710417 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
1710347 AAAACTTAGT
*
1710357 TTAACAATATATATATATATA
1 TTAAAAATATATATAT-TATA
*
1710378 TTAAAAATA-AGATATTATTA
1 TTAAAAATATATATATTA-TA
*
1710398 TTTCAAAATATTATATATTA
1 -TTAAAAATA-TATATATTA
1710418 ATTTTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.06
20 7 0.22
21 16 0.50
23 7 0.22
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAAAATATATATATTATA
Found at i:1711577 original size:18 final size:16
Alignment explanation
Indices: 1711546--1711589 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
1711536 GGTTTAGGGT
*
1711546 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
1711563 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
1711577 TTAAAAATTTATT
1 TTAAAAATTTATT
1711590 CTCATTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:1715090 original size:60 final size:62
Alignment explanation
Indices: 1715002--1715129 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 62
1714992 ATAATTTTTG
*
1715002 GTACTTGAACTTGACACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTT-GACCCAATTTC
1 GTACCTGAACTTGACACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACCCAATTTC
* * ** *
1715063 GTACCTGATCTTGACA-TTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTAGATTCAATTTG
1 GTACCTGAACTTGACACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACCCAATTTC
1715124 GTACCT
1 GTACCT
1715130 AAATTTATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 32 0.53
61 28 0.47
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (62 bp):
GTACCTGAACTTGACACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACCCAATTTC
Found at i:1715314 original size:31 final size:30
Alignment explanation
Indices: 1715276--1715468 Score: 107
Period size: 31 Copynumber: 6.4 Consensus size: 30
1715266 TGTTAAAAAA
1715276 TTAGGTACCAAATTAAGAAAAAGAGTCAAGT
1 TTAGGTACCAAATTAAGAAAAA-AGTCAAGT
****
1715307 TTAGGTACCAAATTGAATCCCAAA---AAGT
1 TTAGGTACCAAATT-AAGAAAAAAGTCAAGT
* *
1715335 TTAAGTACCAACTTAA-AAAAAATGTCAAGT
1 TTAGGTACCAAATTAAGAAAAAA-GTCAAGT
* * **
1715365 TTAAGTATCAAATTAAGAAAGAGTGTCAAGT
1 TTAGGTACCAAATTAAGAAA-AAAGTCAAGT
* *
1715396 TT-GAGTACCAAATT-GGACAAAAA--AAAGGT
1 TTAG-GTACCAAATTAAGA-AAAAAGTCAA-GT
*
1715425 TTAGGTATCAAATT-AGAAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAAGAAAAAA--GTCAAGT
* *
1715456 TCAGATACCAAAT
1 TTAGGTACCAAAT
1715469 ATTATATTAA
Statistics
Matches: 122, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
26 3 0.02
27 2 0.02
28 23 0.19
29 15 0.12
30 22 0.18
31 50 0.41
32 7 0.06
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (30 bp):
TTAGGTACCAAATTAAGAAAAAAGTCAAGT
Found at i:1715367 original size:30 final size:31
Alignment explanation
Indices: 1715280--1715409 Score: 110
Period size: 31 Copynumber: 4.3 Consensus size: 31
1715270 AAAAAATTAG
*
1715280 GTACCAAATTAAGAAAAAGA-GTCAAGTTTAG
1 GTACCAAATTAAGAAAAA-ATGTCAAGTTTAA
****
1715311 GTACCAAATTGAATCCCAAA----AAGTTTAA
1 GTACCAAATT-AAGAAAAAATGTCAAGTTTAA
*
1715339 GTACCAACTTAA-AAAAAATGTCAAGTTTAA
1 GTACCAAATTAAGAAAAAATGTCAAGTTTAA
* * * *
1715369 GTATCAAATTAAGAAAGAGTGTCAAGTTTGA
1 GTACCAAATTAAGAAAAAATGTCAAGTTTAA
1715400 GTACCAAATT
1 GTACCAAATT
1715410 GGACAAAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
26 3 0.04
27 2 0.03
28 16 0.21
30 18 0.23
31 35 0.45
32 4 0.05
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAATGTCAAGTTTAA
Found at i:1715445 original size:89 final size:91
Alignment explanation
Indices: 1715284--1715456 Score: 203
Period size: 89 Copynumber: 1.9 Consensus size: 91
1715274 AATTAGGTAC
** *
1715284 CAAATTAAGAAAAAGAGTCAAGTTTAGGTACCAAATTGAATCCCAAAAAGTTTAAGTACCAACTT
1 CAAATTAAGAAAAAGAGTCAAGTTTAGGTACCAAATTGAATCAAAAAAAGTTTAAGTACCAAATT
1715349 -AAAAAAAA-TGTCAAGTTTAAGTAT
66 AAAAAAAAAGTGTCAAGTTTAAGTAT
* * * * *
1715373 CAAATTAAGAAAGAGTGTCAAGTTT-GAGTACCAAATTGGA-CAAAAAAAAGGTTTAGGTATCAA
1 CAAATTAAGAAAAAGAGTCAAGTTTAG-GTACCAAATTGAATC-AAAAAAA-GTTTAAGTACCAA
*
1715436 ATT-AGAAAAAAGTGTCAAGTT
63 ATTAAAAAAAAAGTGTCAAGTT
1715457 CAGATACCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
88 2 0.03
89 40 0.56
90 20 0.28
91 9 0.13
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (91 bp):
CAAATTAAGAAAAAGAGTCAAGTTTAGGTACCAAATTGAATCAAAAAAAGTTTAAGTACCAAATT
AAAAAAAAAGTGTCAAGTTTAAGTAT
Found at i:1717140 original size:39 final size:40
Alignment explanation
Indices: 1717086--1717184 Score: 164
Period size: 39 Copynumber: 2.5 Consensus size: 40
1717076 TATGCACTCA
1717086 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
* *
1717125 ATGGACACCTTTTGAAAAGTCATAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1717165 ATGGACACCTTTTGGAAGAG
1 ATGGACACCTTTT-GAAGAG
1717185 ACTTGTCCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 26 0.47
40 24 0.44
41 5 0.09
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
Found at i:1722419 original size:39 final size:40
Alignment explanation
Indices: 1722361--1722450 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
1722351 GCATTCAATA
*
1722361 GACACCTTTTGAAGAGTCACAACC-TTTTCATATTGGATG
1 GACACCTTTTGAAAAGTCACAACCTTTTTCATATTGGATG
*
1722400 GACTCCTTTTGAAAAGTCACAACCTTTTTCATATTGGATG
1 GACACCTTTTGAAAAGTCACAACCTTTTTCATATTGGATG
1722440 GACACCTTTTG
1 GACACCTTTTG
1722451 GAAGAGACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 22 0.47
40 25 0.53
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (40 bp):
GACACCTTTTGAAAAGTCACAACCTTTTTCATATTGGATG
Found at i:1724320 original size:32 final size:33
Alignment explanation
Indices: 1724265--1724330 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
1724255 TGAATAGATT
* *
1724265 GCTCCCCTTTAATAAAAGACATTTTGAATTTAA
1 GCTCCCCTATAATAAAAGACATTTTCAATTTAA
1724298 GCTCCCCTAT-ATAAAA-ATCATTTTCAATTTAA
1 GCTCCCCTATAATAAAAGA-CATTTTCAATTTAA
1724330 G
1 G
1724331 GCATAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 1 0.03
32 20 0.67
33 9 0.30
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (33 bp):
GCTCCCCTATAATAAAAGACATTTTCAATTTAA
Found at i:1725601 original size:30 final size:30
Alignment explanation
Indices: 1725562--1725621 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1725552 GGTGCATTTA
* * *
1725562 AGAGTTCTACTAACATTCTTCTTCGTAAGT
1 AGAGCTCTACCAACATTCTTCTTCATAAGT
*
1725592 AGAGCTCTACCACCATTCTTCTTCATAAGT
1 AGAGCTCTACCAACATTCTTCTTCATAAGT
1725622 CTTTCTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (30 bp):
AGAGCTCTACCAACATTCTTCTTCATAAGT
Found at i:1737692 original size:20 final size:20
Alignment explanation
Indices: 1737650--1737692 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1737640 ATTTTTTGAT
* * *
1737650 AAAAATATTAAAAAATCATA
1 AAAAAAATTAAAAAATAAAA
*
1737670 AAAAAAATTAAAAACTAAAA
1 AAAAAAATTAAAAAATAAAA
1737690 AAA
1 AAA
1737693 TATAAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAAAAATTAAAAAATAAAA
Found at i:1737784 original size:10 final size:9
Alignment explanation
Indices: 1737770--1737966 Score: 68
Period size: 9 Copynumber: 21.3 Consensus size: 9
1737760 ATTTAAACTT
1737770 TTATAAAAA
1 TTATAAAAA
1737779 TATATAAAAA
1 T-TATAAAAA
1737789 TCT-TAAAAA
1 T-TATAAAAA
1737798 GTTATAAAAA
1 -TTATAAAAA
*
1737808 TCAT-AAAA
1 TTATAAAAA
1737816 TTCATTAAAAA
1 TT-A-TAAAAA
*
1737827 -CATAAGAAA
1 TTATAA-AAA
*
1737836 TTATAAAAC
1 TTATAAAAA
*
1737845 TTATCAAAA
1 TTATAAAAA
1737854 -T-T-AAAA
1 TTATAAAAA
*
1737860 TGTATTAAAA
1 T-TATAAAAA
*
1737870 TTGATATAAGCA
1 TT-ATA-AA-AA
*
1737882 -TATAAATA
1 TTATAAAAA
*
1737890 TTAAAAAAA
1 TTATAAAAA
1737899 TTAT-AAAA
1 TTATAAAAA
* *
1737907 TTCTAATAAT
1 TTATAA-AAA
1737917 TTATAAAAA
1 TTATAAAAA
** *
1737926 AAATTAAAA
1 TTATAAAAA
1737935 TTAATAAGAAA
1 TT-ATAA-AAA
* * *
1737946 TCATCAAAC
1 TTATAAAAA
*
1737955 TTAAAAAAA
1 TTATAAAAA
1737964 TTA
1 TTA
1737967 AAATTGATAT
Statistics
Matches: 137, Mismatches: 31, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
8 18 0.13
9 57 0.42
10 45 0.33
11 11 0.08
12 1 0.01
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1737797 original size:19 final size:19
Alignment explanation
Indices: 1737772--1737843 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
1737762 TTAAACTTTT
1737772 ATAAAAA-TATATAAAAATC
1 ATAAAAAGT-TATAAAAATC
*
1737791 TTAAAAAGTTATAAAAATC
1 ATAAAAAGTTATAAAAATC
1737810 AT-AAAA-TTCATTAAAAA-C
1 ATAAAAAGTT-A-TAAAAATC
1737828 ATAAGAAA-TTATAAAA
1 ATAA-AAAGTTATAAAA
1737844 CTTATCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.04
18 13 0.28
19 25 0.54
20 6 0.13
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (19 bp):
ATAAAAAGTTATAAAAATC
Found at i:1737802 original size:29 final size:29
Alignment explanation
Indices: 1737770--1737826 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1737760 ATTTAAACTT
*
1737770 TTATAAAAATATATAAAAATC-TTAAAAAG
1 TTATAAAAAT-CATAAAAATCATTAAAAAG
*
1737799 TTATAAAAATCATAAAATTCATTAAAAA
1 TTATAAAAATCATAAAAATCATTAAAAA
1737827 CATAAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (29 bp):
TTATAAAAATCATAAAAATCATTAAAAAG
Found at i:1737926 original size:100 final size:100
Alignment explanation
Indices: 1737793--1737997 Score: 254
Period size: 100 Copynumber: 2.0 Consensus size: 100
1737783 TAAAAATCTT
* * * * *
1737793 AAAAAGTTATAAAAATCATAAAATTCATTAAAAACATAAGAAATT-ATAA-AACTTATCAAAATT
1 AAAAAATTATAAAAATCATAAAATTCATAAAAAAAATAA-AAATTAATAAGAAATCATCAAAATT
**
1737856 AAAATGTATTAAAATTGATATAAGCATATAAATATTA
65 AAAA-AAATTAAAATTGATATAAGCATATAAATATTA
* * * *
1737893 AAAAAATTATAAAATTC-TAATAATTTATAAAAAAAATTAAAATTAATAAGAAATCATCAAACTT
1 AAAAAATTATAAAAATCATAA-AATTCATAAAAAAAATAAAAATTAATAAGAAATCATCAAAATT
1737957 AAAAAAATTAAAATTGATATAAGCATATAAATATTA
65 AAAAAAATTAAAATTGATATAAGCATATAAATATTA
*
1737993 TAAAA
1 AAAAA
1737998 TTCTATTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
99 8 0.09
100 67 0.74
101 15 0.17
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (100 bp):
AAAAAATTATAAAAATCATAAAATTCATAAAAAAAATAAAAATTAATAAGAAATCATCAAAATTA
AAAAAATTAAAATTGATATAAGCATATAAATATTA
Found at i:1738081 original size:30 final size:29
Alignment explanation
Indices: 1738014--1738109 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 29
1738004 TAATTTATAA
*
1738014 AATAAA-TTTACAAAACTAATAAAT-ATAT
1 AATAAATTTTA-AAAACTTATAAATAATAT
*
1738042 ATTTAAAATTTTATAAAACTTATAAATAATAT
1 A-AT-AAATTTTA-AAAACTTATAAATAATAT
* *
1738074 AATAAATTCTAATAAA-TTATAAACAAT-T
1 AATAAATTTTAA-AAACTTATAAATAATAT
1738102 -ATAAATTT
1 AATAAATTT
1738110 ATTAAAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.12
28 2 0.04
29 12 0.21
30 13 0.23
31 17 0.30
32 5 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
AATAAATTTTAAAAACTTATAAATAATAT
Found at i:1738243 original size:27 final size:27
Alignment explanation
Indices: 1738213--1738276 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1738203 GATCGTCCCC
* *
1738213 TAAAATAATAGGAACTTATAAATATT-A
1 TAAAATAATAAGAAATTATAAA-ATTAA
*
1738240 TAAAA-ATATAATAAATTATAAAATTAA
1 TAAAATA-ATAAGAAATTATAAAATTAA
1738267 TAAAATAATA
1 TAAAATAATA
1738277 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.13
27 26 0.84
28 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
TAAAATAATAAGAAATTATAAAATTAA
Found at i:1738267 original size:16 final size:18
Alignment explanation
Indices: 1738236--1738270 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1738226 ACTTATAAAT
1738236 ATTATAAAAATATAATAA
1 ATTATAAAAATATAATAA
1738254 ATTAT-AAAAT-TAATAA
1 ATTATAAAAATATAATAA
1738270 A
1 A
1738271 ATAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTATAAAAATATAATAA
Found at i:1738273 original size:21 final size:21
Alignment explanation
Indices: 1738244--1738285 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1738234 ATATTATAAA
*
1738244 AATATAATAA-ATTATAAAATT
1 AATAAAATAATATT-TAAAATT
1738265 AATAAAATAATATTTAAAATT
1 AATAAAATAATATTTAAAATT
1738286 TTATAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAAAATAATATTTAAAATT
Found at i:1741976 original size:68 final size:69
Alignment explanation
Indices: 1741861--1741996 Score: 193
Period size: 68 Copynumber: 2.0 Consensus size: 69
1741851 ACTTAATCAC
* * * * * * *
1741861 TTTAATATTAAGTTAATAGAATAGTTATCAAGATAAATATTATATTAAATTTAATATTTAAACAA
1 TTTAATATTAAATTAATAAAATAGCTATCAAAATAAATATAAAATTAAATTTAATATTAAAACAA
1741926 TTAT
66 TTAT
*
1741930 TTTAATATTAAATTAATAAAAT-GCTATCAAAATAAATATAAAATTAAATTTAATATTAAAACTA
1 TTTAATATTAAATTAATAAAATAGCTATCAAAATAAATATAAAATTAAATTTAATATTAAAACAA
1741994 TTA
66 TTA
1741997 AAATAATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 39 0.66
69 20 0.34
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (69 bp):
TTTAATATTAAATTAATAAAATAGCTATCAAAATAAATATAAAATTAAATTTAATATTAAAACAA
TTAT
Found at i:1744054 original size:17 final size:17
Alignment explanation
Indices: 1744012--1744076 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
1744002 GCCCAGCTTA
* *
1744012 GATTTTAATTTAAGTTT
1 GATTTAAATTTAAATTT
* *
1744029 GAATTAATTTTAAATTT
1 GATTTAAATTTAAATTT
1744046 -ATTTAAATTTAAATTT
1 GATTTAAATTTAAATTT
*
1744062 GTTTTAAATTTAAAT
1 GATTTAAATTTAAAT
1744077 ACATTTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.35
17 26 0.65
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
GATTTAAATTTAAATTT
Found at i:1744055 original size:33 final size:33
Alignment explanation
Indices: 1744013--1744085 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1744003 CCCAGCTTAG
* * * **
1744013 ATTTTAATTTAAGTTTGAATTAATTTTAAATTT
1 ATTTAAATTTAAATTTGAATTAAATTTAAATAC
**
1744046 ATTTAAATTTAAATTTGTTTTAAATTTAAATAC
1 ATTTAAATTTAAATTTGAATTAAATTTAAATAC
1744079 ATTTAAA
1 ATTTAAA
1744086 ATAATTTGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (33 bp):
ATTTAAATTTAAATTTGAATTAAATTTAAATAC
Found at i:1744060 original size:27 final size:27
Alignment explanation
Indices: 1744019--1744092 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1744009 TTAGATTTTA
* *
1744019 ATTTAAGTTTGAATTAATTTTAAATTT
1 ATTTAAATTTAAATTAATTTTAAATTT
**
1744046 ATTTAAATTTAAATTTGTTTTAAATTT
1 ATTTAAATTTAAATTAATTTTAAATTT
** * *
1744073 AAATACATTTAAAATAATTT
1 ATTTAAATTTAAATTAATTT
1744093 GAAACTTAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTAAATTTAAATTAATTTTAAATTT
Found at i:1744085 original size:16 final size:16
Alignment explanation
Indices: 1744032--1744085 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1744022 TAAGTTTGAA
* *
1744032 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
1744048 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
1744065 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
1744081 TTAAA
1 TTAAA
1744086 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:1744851 original size:20 final size:20
Alignment explanation
Indices: 1744778--1744851 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
1744768 TATAATAATG
* *
1744778 ATAATAATAATTATAGCATTA
1 ATAATAATAATGA-AACATTA
* *
1744799 ATAACCACTAACTGAAACATTA
1 ATAA-TAATAA-TGAAACATTA
* * *
1744821 ATAGTATTAATGAAATATTA
1 ATAATAATAATGAAACATTA
1744841 ATAATAATAAT
1 ATAATAATAAT
1744852 TATTAATAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
20 18 0.44
21 8 0.20
22 13 0.32
23 2 0.05
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (20 bp):
ATAATAATAATGAAACATTA
Found at i:1744858 original size:13 final size:13
Alignment explanation
Indices: 1744837--1744874 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1744827 TTAATGAAAT
*
1744837 ATTAATAATAATA
1 ATTATTAATAATA
1744850 ATTATTAATAATA
1 ATTATTAATAATA
1744863 ACTTATTAATAA
1 A-TTATTAATAA
1744875 AAAAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTATTAATAATA
Found at i:1748800 original size:40 final size:39
Alignment explanation
Indices: 1748750--1748845 Score: 156
Period size: 39 Copynumber: 2.4 Consensus size: 39
1748740 TGGGACAAGT
1748750 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAAGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATG-AAAAGGTTGTGA
* *
1748791 CTTTTCAAAAGGAGTCCATCCAATATGAAAAGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGTTGTGA
1748830 CTCTTCAAAAGGTGTC
1 CTCTTCAAAAGGTGTC
1748846 TATTGAGTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 26 0.51
40 21 0.41
41 4 0.08
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (39 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGTTGTGA
Found at i:1759327 original size:9 final size:9
Alignment explanation
Indices: 1759308--1759336 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1759298 ACCGTTATGG
1759308 ATTTA-TTT
1 ATTTATTTT
1759316 ATTTATTTT
1 ATTTATTTT
1759325 ATTTATTTT
1 ATTTATTTT
1759334 ATT
1 ATT
1759337 AGGTGTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTATTTT
Found at i:1759979 original size:17 final size:17
Alignment explanation
Indices: 1759957--1759990 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1759947 TAAGTGAACG
1759957 TCTAACTCCTTTAAACC
1 TCTAACTCCTTTAAACC
*
1759974 TCTAACTCTTTTAAACC
1 TCTAACTCCTTTAAACC
1759991 CTCATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAACTCCTTTAAACC
Found at i:1761259 original size:12 final size:12
Alignment explanation
Indices: 1761239--1761272 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1761229 AAAATATAGA
*
1761239 GGTCACGGTCAC
1 GGTCGCGGTCAC
1761251 GGTCGCGGTCAC
1 GGTCGCGGTCAC
*
1761263 GGTCGTGGTC
1 GGTCGCGGTC
1761273 GTGAATGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.29, G:0.41, T:0.21
Consensus pattern (12 bp):
GGTCGCGGTCAC
Found at i:1764119 original size:18 final size:18
Alignment explanation
Indices: 1764091--1764134 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1764081 AGTGAAATTT
1764091 ATATGAAAATCCCAGAAGG
1 ATAT-AAAATCCCAGAAGG
* *
1764110 ATTTAAAATCCCTGAAGG
1 ATATAAAATCCCAGAAGG
1764128 ATATAAA
1 ATATAAA
1764135 GTTTCTCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:1765562 original size:17 final size:17
Alignment explanation
Indices: 1765540--1765573 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1765530 TAAGTGGATG
1765540 TCTAACTCATTTAAACC
1 TCTAACTCATTTAAACC
*
1765557 TCTAACTCCTTTAAACC
1 TCTAACTCATTTAAACC
1765574 CTCATTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
TCTAACTCATTTAAACC
Found at i:1766496 original size:19 final size:19
Alignment explanation
Indices: 1766474--1766598 Score: 53
Period size: 19 Copynumber: 6.5 Consensus size: 19
1766464 TAAAATTTTA
1766474 TAAAATTGTATAAAAATAT
1 TAAAATTGTATAAAAATAT
*
1766493 TAAAA-AGT-TATAAAATCAT
1 TAAAATTGTATA-AAAAT-AT
* **
1766512 TACAATCAT-TAAAAATAT
1 TAAAATTGTATAAAAATAT
*** *
1766530 ATAAAAAAATCATAAAATTAT
1 -TAAAATTGT-ATAAAAATAT
*
1766551 TAAAATTGATATAAACATA-
1 TAAAATTG-TATAAAAATAT
* *
1766570 TAAAAATG-ATAAAAAAAT
1 TAAAATTGTATAAAAATAT
*
1766588 AAAATATTGTA
1 TAAA-ATTGTA
1766599 AATATTATAA
Statistics
Matches: 78, Mismatches: 18, Indels: 19
0.68 0.16 0.17
Matches are distributed among these distances:
17 9 0.12
18 12 0.15
19 32 0.41
20 16 0.21
21 9 0.12
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (19 bp):
TAAAATTGTATAAAAATAT
Found at i:1766555 original size:30 final size:32
Alignment explanation
Indices: 1766504--1766565 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1766494 AAAAAGTTAT
*
1766504 AAAATCATTACAATCATTAAAAAT-ATATAAA
1 AAAATCATTAAAATCATTAAAAATGATATAAA
* *
1766535 AAAATCA-TAAAATTATTAAAATTGATATAAA
1 AAAATCATTAAAATCATTAAAAATGATATAAA
1766566 CATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (32 bp):
AAAATCATTAAAATCATTAAAAATGATATAAA
Found at i:1766571 original size:39 final size:39
Alignment explanation
Indices: 1766406--1766575 Score: 118
Period size: 39 Copynumber: 4.4 Consensus size: 39
1766396 AAAAAGTCTA
* * *
1766406 ATAAAC-TCTAAAAAAATATAATATCTATATAAAATTAAT
1 ATAAACATATAAAAAAATATAAAAT-TATATAAAATTGAT
* * * *
1766445 AT-AACATATTTAAAATATTTAAAATTTTATAAAATTG-T
1 ATAAACATA-TAAAAAAATATAAAATTATATAAAATTGAT
* ** * * *
1766483 ATAAAAATATTAAAAAGTTATAAAATCAT-TACAA-TCATT
1 ATAAACATA-TAAAAAAATATAAAATTATATAAAATTGA-T
* *
1766522 AAAAATATATAAAAAAATCATAAAATTAT-TAAAATTGAT
1 ATAAACATATAAAAAAAT-ATAAAATTATATAAAATTGAT
1766561 ATAAACATATAAAAA
1 ATAAACATATAAAAA
1766576 TGATAAAAAA
Statistics
Matches: 99, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
37 1 0.01
38 17 0.17
39 67 0.68
40 14 0.14
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (39 bp):
ATAAACATATAAAAAAATATAAAATTATATAAAATTGAT
Found at i:1767165 original size:18 final size:18
Alignment explanation
Indices: 1767142--1767176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1767132 GTTCAATTAA
* *
1767142 ATAAAATATTAAAAATAG
1 ATAAAAAATAAAAAATAG
1767160 ATAAAAAATAAAAAATA
1 ATAAAAAATAAAAAATA
1767177 AAAAATTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAAAAATAAAAAATAG
Found at i:1767469 original size:22 final size:23
Alignment explanation
Indices: 1767412--1767471 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
1767402 GGGGTCGAAG
*
1767412 TTAAATTATAATTTTTATAATAA
1 TTAAATTATAATTTTTATAAGAA
* * *
1767435 TAAAAATATAATTTTTA-AAGGA
1 TTAAATTATAATTTTTATAAGAA
*
1767457 TTAAATTAAAATTTT
1 TTAAATTATAATTTT
1767472 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
TTAAATTATAATTTTTATAAGAA
Found at i:1767479 original size:30 final size:30
Alignment explanation
Indices: 1767445--1767502 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1767435 TAAAAATATA
*
1767445 ATTTTTAAAGGATTAAATTAAAATTTTATT
1 ATTTTTAAAGGATCAAATTAAAATTTTATT
* * *
1767475 ATTTTTAATGGGTCAAATTATAATTTTA
1 ATTTTTAAAGGATCAAATTAAAATTTTA
1767503 CTTTTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.50
Consensus pattern (30 bp):
ATTTTTAAAGGATCAAATTAAAATTTTATT
Found at i:1769696 original size:25 final size:24
Alignment explanation
Indices: 1769650--1769696 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1769640 CGTGCTTATT
*
1769650 TTTTAAATTTATTAAATAATATAA
1 TTTTAAATTTATAAAATAATATAA
1769674 TTTTATAATTT-TAAAATATATAT
1 TTTTA-AATTTATAAAATA-ATAT
1769697 TACTAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAAATTTATAAAATAATATAA
Found at i:1769770 original size:36 final size:36
Alignment explanation
Indices: 1769728--1769806 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
1769718 TCTAATTTAT
1769728 AATAAAAGTCTATTAATTTTGATAAATAATTTAGAG
1 AATAAAAGTCTATTAATTTTGATAAATAATTTAGAG
1769764 AATAAAAGTCTATTAATTTTGATAAATAATTTAGAG
1 AATAAAAGTCTATTAATTTTGATAAATAATTTAGAG
1769800 AATAAAA
1 AATAAAA
1769807 TATTTTAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (36 bp):
AATAAAAGTCTATTAATTTTGATAAATAATTTAGAG
Found at i:1776122 original size:16 final size:16
Alignment explanation
Indices: 1776091--1776145 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1776081 ATATTATAAA
1776091 TAAAAACATAAAAAATTT
1 TAAAAA-AT-AAAAATTT
*
1776109 TAAAAAATAAAAATAT
1 TAAAAAATAAAAATTT
* *
1776125 GAAAAATTAAAAATCTT
1 TAAAAAATAAAAAT-TT
1776142 TAAA
1 TAAA
1776146 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 19 0.61
17 6 0.19
18 6 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAAAATAAAAATTT
Found at i:1777169 original size:20 final size:21
Alignment explanation
Indices: 1777135--1777176 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1777125 TAACATTGAA
1777135 TTTAAGAATCATTTTAT-ATT
1 TTTAAGAATCATTTTATGATT
1777155 TTTAA-AATCATTTTTATGATT
1 TTTAAGAATCA-TTTTATGATT
1777176 T
1 T
1777177 ATTTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAAGAATCATTTTATGATT
Found at i:1777177 original size:19 final size:20
Alignment explanation
Indices: 1777134--1777177 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1777124 ATAACATTGA
1777134 ATTTAAGAATCATTTTATAT
1 ATTTAAGAATCATTTTATAT
*
1777154 TTTTAA-AATCATTTT-TAT
1 ATTTAAGAATCATTTTATAT
1777172 GATTTA
1 -ATTTA
1777178 TTTTTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 13 0.62
20 5 0.24
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTAAGAATCATTTTATAT
Found at i:1785352 original size:26 final size:27
Alignment explanation
Indices: 1785306--1785370 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
1785296 AAAATAAAAG
*
1785306 AAATTAAATAAAATATGTTT-A-TTTGA
1 AAATTTAATAAAATATGTTTAAGTTT-A
*
1785332 AAATTTAATAATAAT-TTTTTAAGTTTA
1 AAATTTAATAA-AATATGTTTAAGTTTA
*
1785359 AATTTTAATAAA
1 AAATTTAATAAA
1785371 GGATTAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 15 0.45
27 15 0.45
28 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (27 bp):
AAATTTAATAAAATATGTTTAAGTTTA
Found at i:1789379 original size:22 final size:22
Alignment explanation
Indices: 1789354--1789402 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1789344 TTTTAAAATT
1789354 TGGTTTATGTTCATTTGATGAA
1 TGGTTTATGTTCATTTGATGAA
1789376 TGGTTTATGTTCATTTGATGAA
1 TGGTTTATGTTCATTTGATGAA
1789398 TGGTT
1 TGGTT
1789403 AATTCAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.51
Consensus pattern (22 bp):
TGGTTTATGTTCATTTGATGAA
Found at i:1791335 original size:18 final size:17
Alignment explanation
Indices: 1791293--1791335 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1791283 GTTTTAAGCT
*
1791293 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
1791310 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
1791328 TATAATTT
1 TATAATTT
1791336 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:1800125 original size:22 final size:20
Alignment explanation
Indices: 1800078--1800175 Score: 94
Period size: 22 Copynumber: 4.8 Consensus size: 20
1800068 ATTATATTGT
1800078 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGGTGCTTTTTTTAC
* *
1800098 TCTTTTGGTTGCTGTTTTTTGC
1 TGTTTTGG-TGCT-TTTTTTAC
*
1800120 TGTTTTGGTGTTATTTTTTTAC
1 TGTTTTGGTG--CTTTTTTTAC
1800142 TGTTTT-G-G-TTTTTTTAC
1 TGTTTTGGTGCTTTTTTTAC
*
1800159 TGTTTTGTTGCTGTTTT
1 TGTTTTGGTGCT-TTTT
1800176 GATGCGGTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
17 15 0.23
19 1 0.02
20 9 0.14
21 11 0.17
22 27 0.42
23 1 0.02
ACGTcount: A:0.04, C:0.08, G:0.20, T:0.67
Consensus pattern (20 bp):
TGTTTTGGTGCTTTTTTTAC
Found at i:1800155 original size:17 final size:17
Alignment explanation
Indices: 1800133--1800165 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1800123 TTTGGTGTTA
1800133 TTTTTTTACTGTTTTGG
1 TTTTTTTACTGTTTTGG
1800150 TTTTTTTACTGTTTTG
1 TTTTTTTACTGTTTTG
1800166 TTGCTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.73
Consensus pattern (17 bp):
TTTTTTTACTGTTTTGG
Found at i:1800231 original size:15 final size:15
Alignment explanation
Indices: 1800208--1800264 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1800198 TTTTTGTTGC
*
1800208 TATTTTTGCTATTAT
1 TATTGTTGCTATTAT
1800223 TATTGTTGCTATTAT
1 TATTGTTGCTATTAT
* *
1800238 TGTTGTTTTGCTGTTAT
1 TATTG--TTGCTATTAT
*
1800255 TTTTGTTGCT
1 TATTGTTGCT
1800265 GTTTTGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 23 0.64
17 13 0.36
ACGTcount: A:0.12, C:0.07, G:0.16, T:0.65
Consensus pattern (15 bp):
TATTGTTGCTATTAT
Found at i:1800255 original size:32 final size:32
Alignment explanation
Indices: 1800211--1800287 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1800201 TTGTTGCTAT
*
1800211 TTTTGCTATTATTATTGTTGCTATTATT-GTTG
1 TTTTGCTGTTATTATTGTTGCTATT-TTGGTTG
* *
1800243 TTTTGCTGTTATTTTTGTTGCTGTTTTGGTTG
1 TTTTGCTGTTATTATTGTTGCTATTTTGGTTG
* *
1800275 TTTGGATGTTATT
1 TTTTGCTGTTATT
1800288 TTTATGCGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.10, C:0.05, G:0.21, T:0.64
Consensus pattern (32 bp):
TTTTGCTGTTATTATTGTTGCTATTTTGGTTG
Found at i:1800473 original size:21 final size:21
Alignment explanation
Indices: 1800431--1800474 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1800421 ATTTGTTTAT
* *
1800431 TTTTTAATGTTTTTTTTAATA
1 TTTTTAATGTTTATTTGAATA
1800452 TTTTTAA-GTTTATTTGATATA
1 TTTTTAATGTTTATTTGA-ATA
1800473 TT
1 TT
1800475 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATA
Found at i:1801249 original size:21 final size:19
Alignment explanation
Indices: 1801204--1801249 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1801194 ACTTTTATTA
* *
1801204 AATAAATTATATCCAAATT
1 AATAATTTATATCCAAAAT
1801223 AATAATTTATATCCACAAAT
1 AATAATTTATATCCA-AAAT
1801243 AACTAAT
1 AA-TAAT
1801250 AGAAAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 5 0.22
21 4 0.17
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAATTTATATCCAAAAT
Found at i:1802557 original size:27 final size:28
Alignment explanation
Indices: 1802500--1802559 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
1802490 TAAAAAAATG
* *
1802500 TTTTTATATTTTTTAATAAATTTAATGA
1 TTTTTATATTTTTAAATAAATTTAATAA
** *
1802528 TTTTTA-ATTTTTAAATAGTTTTTATAA
1 TTTTTATATTTTTAAATAAATTTAATAA
1802555 TTTTT
1 TTTTT
1802560 TTGAAGTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTATATTTTTAAATAAATTTAATAA
Found at i:1806480 original size:21 final size:21
Alignment explanation
Indices: 1806454--1806495 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1806444 AAAAAATAAA
*
1806454 ACTAAGTCCTT-GAGAGATTTG
1 ACTAAGT-CTTAGAAAGATTTG
1806475 ACTAAGTCTTAGAAAGATTTG
1 ACTAAGTCTTAGAAAGATTTG
1806496 TTAGCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTAAGTCTTAGAAAGATTTG
Found at i:1816413 original size:24 final size:24
Alignment explanation
Indices: 1816385--1816438 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1816375 ATTGAGGAGA
1816385 TTGAGGTTCGTCCTGACTTGAGTT
1 TTGAGGTTCGTCCTGACTTGAGTT
1816409 TTGAGGTTCGTCCTGACTTGAGTT
1 TTGAGGTTCGTCCTGACTTGAGTT
1816433 TTGAGG
1 TTGAGG
1816439 AAGAACCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.13, C:0.15, G:0.31, T:0.41
Consensus pattern (24 bp):
TTGAGGTTCGTCCTGACTTGAGTT
Found at i:1817477 original size:23 final size:23
Alignment explanation
Indices: 1817441--1817498 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1817431 TCGTTGATCT
*
1817441 ACCCGTTCACCGACCCGAACCCG
1 ACCCGTTGACCGACCCGAACCCG
*
1817464 ACCCGTTGATCGACCCGAACCCG
1 ACCCGTTGACCGACCCGAACCCG
*
1817487 ACCCATTGACCG
1 ACCCGTTGACCG
1817499 TTGGCCGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.47, G:0.19, T:0.12
Consensus pattern (23 bp):
ACCCGTTGACCGACCCGAACCCG
Found at i:1817531 original size:13 final size:13
Alignment explanation
Indices: 1817513--1817537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1817503 CCGTTGATAG
1817513 TTGACCATTGACT
1 TTGACCATTGACT
1817526 TTGACCATTGAC
1 TTGACCATTGAC
1817538 CATTGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:1825079 original size:124 final size:126
Alignment explanation
Indices: 1824844--1825080 Score: 318
Period size: 124 Copynumber: 1.9 Consensus size: 126
1824834 GACCTTTGGT
* *
1824844 TAAAAGCTTTCCCCAATCTAGTTACACCAACATAAAAAAAAAGATAAAACTCATTCTTCAAGATC
1 TAAAAGCTTTCCCCAATCTAGTTACACCAACAT-AAAAAAAAGATAAAACCCATTCTTCAAGAAC
* * *
1824909 AAATCTAAAAGACCCTTGAAGCGGAATCTTCCATCCAAGATTAAGTCTCAAATAACCTTGCA
65 AAATCTAAAAGACCCTTGAAGCAGAATCGTCCATCCAAGATAAAGTCTCAAATAACCTTGCA
** * *
1824971 TAAAAGCTTTTTCCAATCTAGTTGCACCAAC-T-CAAAAAAGATAAAACCCATTCTTCAAGAACA
1 TAAAAGCTTTCCCCAATCTAGTTACACCAACATAAAAAAAAGATAAAACCCATTCTTCAAGAACA
* * * *
1825034 AGTTTAGAAGACCCTTGGAGCAGAATCGTCCATCCCAA-ATAAAGTCT
66 AATCTAAAAGACCCTTGAAGCAGAATCGTCCAT-CCAAGATAAAGTCT
1825081 TGACTACCTT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
124 63 0.66
125 4 0.04
126 1 0.01
127 28 0.29
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (126 bp):
TAAAAGCTTTCCCCAATCTAGTTACACCAACATAAAAAAAAGATAAAACCCATTCTTCAAGAACA
AATCTAAAAGACCCTTGAAGCAGAATCGTCCATCCAAGATAAAGTCTCAAATAACCTTGCA
Done.