Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013683.1 Kokia drynarioides strain JFW-HI SEQ_128711, 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: 41814
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:680 original size:17 final size:17
Alignment explanation
Indices: 658--696 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
648 TTTAATTCAT
658 TTTAAA-TTCAATTTAAA
1 TTTAAACTT-AATTTAAA
675 TTTAAACTTAATTTAAA
1 TTTAAACTTAATTTAAA
692 TTTAA
1 TTTAA
697 GCTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAACTTAATTTAAA
Found at i:1146 original size:97 final size:97
Alignment explanation
Indices: 973--1166 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 97
963 AACTTTGGAA
*
973 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
*
1038 GAATAAAAAAT-AAAGAAACATTGCCTCGATTT
66 AAATAAAAAATAAAAG-AACATTGCCTCGATTT
* * * * * * * *
1070 AAGGGTATTCTATTATTTCGATTTGAGGAAAAATTGCACCTCGTAAGTTAAGGTACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
** *
1135 AAACT-CGAAATAAAAGAATATTGCCTCGATTT
66 AAA-TAAAAAATAAAAGAACATTGCCTCGATTT
1167 TAAAATTTTC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
97 77 0.94
98 5 0.06
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATAAAAAATAAAAGAACATTGCCTCGATTT
Found at i:1539 original size:29 final size:27
Alignment explanation
Indices: 1509--1934 Score: 123
Period size: 29 Copynumber: 14.5 Consensus size: 27
1499 AATCGTGCTA
**
1509 AAAAATGGAATTTTGGAACTTCAGGGGT
1 AAAAATGGAATTTTGGAAAATCA-GGGT
*
1537 -AAAATGGTAATTTTTGGAAAAATCGAGGTT
1 AAAAATGG-AA-TTTTGG-AAAATC-AGGGT
* *
1567 AAAAATGGAATTTTTGGAAGTATGAGGGT
1 AAAAATGGAA-TTTTGGAA-AATCAGGGT
1596 -AAAATGGTAATTTTGGAAAAATCAGGGT
1 AAAAATGG-AATTTTGG-AAAATCAGGGT
* * *
1624 CAAAAATGGAATTTTGGATTTTGGAAGTTC-GAGA
1 -AAAAATGGAATTTTGGA------AA-ATCAGGGT
**
1658 AAAAATGGTAATTTTTGGAAAAATTGGGGT
1 AAAAATGG-AA-TTTTGG-AAAATCAGGGT
**
1688 CAAAAATGGAATTTTTGGAAGTTCAGGGGT
1 -AAAAATGGAA-TTTTGGAAAATCA-GGGT
1718 -AAAA-GGTAATGTTTGGAAAAATC-GAGGT
1 AAAAATGG-AAT-TTTGG-AAAATCAG-GGT
** ** *
1746 CAAAAATAAAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAA-TTTTGGAAAATCA-GGGT
** *
1776 -AAAATGGTAATTTTTGGGAAGTTTAGGGGT
1 AAAAATGG-AA-TTTT-GGAAAATCA-GGGT
* * *
1806 -AAAATGTAATTTTGGAAAAATTAGGATT
1 AAAAATGGAATTTTGG-AAAATCAGG-GT
* * * *
1834 AAAAATGAAATTTTAGAAAGTTAGATGGT
1 AAAAATGGAATTTTGGAAAATCAG--GGT
* *
1863 AAAAATGTAATTTTTGGAAAAATCGGGGT
1 AAAAATGGAA-TTTTGG-AAAATCAGGGT
* *
1892 TAAAATGGAATTTTGGAAAGTTCATGGGT
1 AAAAATGGAATTTTGGAAA-ATCA-GGGT
1921 -AAAATGGTAATTTT
1 AAAAATGG-AATTTT
1935 TATAGTTTAT
Statistics
Matches: 308, Mismatches: 45, Indels: 89
0.70 0.10 0.20
Matches are distributed among these distances:
27 18 0.06
28 74 0.24
29 88 0.29
30 82 0.27
31 23 0.07
33 8 0.03
34 6 0.02
35 8 0.03
36 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (27 bp):
AAAAATGGAATTTTGGAAAATCAGGGT
Found at i:1575 original size:58 final size:59
Alignment explanation
Indices: 1476--1792 Score: 351
Period size: 58 Copynumber: 5.4 Consensus size: 59
1466 AGATATCCGA
*** * * * *
1476 GGGTAAAATGGTAA-TTTAAAAAAAATCGTGCTAAAAAATGGAA-TTTTGGAACTTCAG
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCAG
* *
1533 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTATGA-
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGT-TCAG
1592 GGGTAAAATGGTAA-TTTTGGAAAAATC-AGGGTCAAAAATGGAATTTTGGATTTTGGAAGTTC-
1 GGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAATGGAA---T---TTTTGGAAGTTCA
1654 G
59 G
* ** * *
1655 AGAAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCAG
* ** *
1714 GGGTAAAA-GGTAATGTTTGGAAAAATCGAGGTCAAAAATAAAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCAG
1772 GGGTAAAATGGTAATTTTTGG
1 GGGTAAAATGGTAATTTTTGG
1793 GAAGTTTAGG
Statistics
Matches: 220, Mismatches: 25, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
57 15 0.07
58 113 0.51
59 40 0.18
60 2 0.01
61 2 0.01
63 12 0.05
64 36 0.16
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCAG
Found at i:1579 original size:30 final size:30
Alignment explanation
Indices: 1537--1910 Score: 133
Period size: 29 Copynumber: 12.6 Consensus size: 30
1527 CTTCAGGGGT
1537 AAAATGGTAATTTTTGGAAAAATCGAGGTTA
1 AAAATGG-AATTTTTGGAAAAATCGAGGTTA
** *
1568 AAAATGGAATTTTTGGAAGTAT-GAGGGT-
1 AAAATGGAATTTTTGGAAAAATCGAGGTTA
*
1596 AAAATGGTAA-TTTTGGAAAAATC-AGGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGA-GGTTA
** *
1626 AAAATGGAA-TTTTGGATTTTGGAAGTTCGA-G-AA
1 AAAATGGAATTTTTGGA------AAAATCGAGGTTA
* * *
1659 AAAATGGTAATTTTTGGAAAAATTGGGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGAGGTTA
** *
1690 AAAATGGAATTTTTGG-AAGTTC-AGGGGT-
1 AAAATGGAATTTTTGGAAAAATCGA-GGTTA
* *
1718 AAAA-GGTAATGTTTGGAAAAATCGAGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGAGGTTA
** *** * *
1748 AAAATAAAATTTTTGGAAGTTTAG-GGGT-
1 AAAATGGAATTTTTGGAAAAATCGAGGTTA
* * ** *
1776 AAAATGGTAATTTTTGG-GAAGTTTAGGGGT-
1 AAAATGG-AATTTTTGGAAAAATCGA-GGTTA
* *
1806 AAAATGTAA-TTTTGGAAAAAT-TAGGATTA
1 AAAATGGAATTTTTGGAAAAATCGAGG-TTA
* * ** *
1835 AAAAT-GAAATTTTAGAAAGTTAGATGG-TA
1 AAAATGGAATTTTTGGAAAAATCGA-GGTTA
* *
1864 AAAATGTAATTTTTGGAAAAATCGGGGTT-
1 AAAATGGAATTTTTGGAAAAATCGAGGTTA
1893 AAAATGGAA-TTTTGGAAA
1 AAAATGGAATTTTTGGAAA
1911 GTTCATGGGT
Statistics
Matches: 251, Mismatches: 60, Indels: 67
0.66 0.16 0.18
Matches are distributed among these distances:
27 4 0.02
28 56 0.22
29 80 0.32
30 71 0.28
31 17 0.07
33 8 0.03
34 3 0.01
35 11 0.04
36 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAATCGAGGTTA
Found at i:1608 original size:87 final size:87
Alignment explanation
Indices: 1509--1910 Score: 316
Period size: 87 Copynumber: 4.6 Consensus size: 87
1499 AATCGTGCTA
*
1509 AAAAATGG-AA-TTTTGGAACTTCAGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAA
1 AAAAATGGTAATTTTTGGAAATTCAGGGGTAAAATGGTAA-TTTTGGAAAAATCGAGGTTAAAAA
*
1572 TGGAATTTTTGGAAGTATGAGGGT
65 TGAAATTTTTGGAAGT-TGAGGGT
* **
1596 -AAAATGGTAA-TTTTGGAAAAATCA-GGGTCAAAAATGG-AATTTTGGATTTTGGAAGTTCGA-
1 AAAAATGGTAATTTTTGG-AAATTCAGGGGT--AAAATGGTAATTTTGGA------AAAATCGAG
* * *
1656 G-AAAAAATGGTAATTTTTGGAAAAATTG-GGGT
57 GTTAAAAAT-GAAATTTTTGG--AAGTTGAGGGT
* *
1688 CAAAAATGG-AATTTTTGGAAGTTCAGGGGTAAAA-GGTAATGTTTGGAAAAATCGAGGTCAAAA
1 -AAAAATGGTAATTTTTGGAAATTCAGGGGTAAAATGGTAAT-TTTGGAAAAATCGAGGTTAAAA
* *
1751 ATAAAATTTTTGGAAGTTTAGGGGT
64 ATGAAATTTTTGGAAGTTGA-GGGT
* * *
1776 -AAAATGGTAATTTTTGGGAAGTTTAGGGGTAAAAT-GTAATTTTGGAAAAAT-TAGGATTAAAA
1 AAAAATGGTAATTTTT-GGAAATTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGG-TTAAAA
* * *
1838 ATGAAATTTTAGAAAGTTAGATGGT
64 ATGAAATTTTTGGAAGTT-GAGGGT
*
1863 AAAAAT-GTAATTTTTGGAAAAATC-GGGGTTAAAATGG-AATTTTGGAAA
1 AAAAATGGTAATTTTTGG-AAATTCAGGGG-TAAAATGGTAATTTTGGAAA
1911 GTTCATGGGT
Statistics
Matches: 256, Mismatches: 27, Indels: 64
0.74 0.08 0.18
Matches are distributed among these distances:
86 27 0.11
87 95 0.37
88 50 0.20
89 13 0.05
91 8 0.03
92 22 0.09
93 21 0.08
94 20 0.08
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.32
Consensus pattern (87 bp):
AAAAATGGTAATTTTTGGAAATTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGGTTAAAAAT
GAAATTTTTGGAAGTTGAGGGT
Found at i:1759 original size:122 final size:122
Alignment explanation
Indices: 1537--1760 Score: 346
Period size: 122 Copynumber: 1.8 Consensus size: 122
1527 CTTCAGGGGT
* *
1537 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTATGAGGGTAAAATG
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTATCAGGGTAAAATG
**
1602 GTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGGATTTTGGAAGTTCGAGAA
66 GTAATTTTGGAAAAATCAGGGTCAAAAATAAAATTTTGGATTTTGGAAGTTCGAGAA
* *
1659 AAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGT-TCAGGGGTAAAA-
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTATCA-GGGTAAAAT
1722 GGTAATGTTTGGAAAAATC-GAGGTCAAAAATAAAATTTT
65 GGTAAT-TTTGGAAAAATCAG-GGTCAAAAATAAAATTTT
1761 TGGAAGTTTA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
121 9 0.10
122 84 0.90
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (122 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTATCAGGGTAAAATG
GTAATTTTGGAAAAATCAGGGTCAAAAATAAAATTTTGGATTTTGGAAGTTCGAGAA
Found at i:1817 original size:58 final size:59
Alignment explanation
Indices: 1509--1935 Score: 210
Period size: 58 Copynumber: 7.3 Consensus size: 59
1499 AATCGTGCTA
* * * * *
1509 AAAAATGGAA-TTTTGG-AACTTCAGGGGTAAAATGGTAATTTTTGGAAA-AATCGAGGTT
1 AAAAATGTAATTTTTGGAAAATT-AGGGGTAAAATGGTAATTTTTGGAAAGATTAG-GGGT
* * * * *
1567 AAAAATGGAATTTTTGGAAGTATGA-GGGTAAAATGGTAA-TTTTGGAAAAATCA-GGGT
1 AAAAATGTAATTTTTGGAA-AATTAGGGGTAAAATGGTAATTTTTGGAAAGATTAGGGGT
* * * * ** *
1624 CAAAAATGGAA-TTTTGGATTTTGGAAGTTCGAGAAAAAATGGTAATTTTTGGAAAAATT-GGGG
1 -AAAAATGTAATTTTTGGA------AAATTAGGGGTAAAATGGTAATTTTTGGAAAGATTAGGGG
1687 T
59 T
* * * * * *
1688 CAAAAATGGAATTTTTGG-AAGTTCAGGGGTAAAA-GGTAATGTTTGGAAA-AATCGAGGT
1 -AAAAATGTAATTTTTGGAAAATT-AGGGGTAAAATGGTAATTTTTGGAAAGATTAGGGGT
** ** * *
1746 CAAAAATAAAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGGAAGTTTAGGGGT
1 -AAAAATGTAATTTTTGGAAAATTAGGGGTAAAATGGTAATTTTTGGAAAGATTAGGGGT
** * * *
1806 -AAAATGTAA-TTTTGGAAAAATTAGGATTAAAAAT-G-AAATTTTAGAAAG-TTAGATGGT
1 AAAAATGTAATTTTTGG-AAAATTAGGGGT-AAAATGGTAATTTTTGGAAAGATTAG-GGGT
* * *
1863 AAAAATGTAATTTTTGGAAAAATCGGGGTTAAAATGG-AA-TTTTGGAAAG-TTCATGGGT
1 AAAAATGTAATTTTTGGAAAATTAGGGG-TAAAATGGTAATTTTTGGAAAGATT-AGGGGT
1921 -AAAATGGTAATTTTT
1 AAAAAT-GTAATTTTT
1936 ATAGTTTATG
Statistics
Matches: 291, Mismatches: 49, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
56 4 0.01
57 36 0.12
58 138 0.47
59 59 0.20
60 7 0.02
61 1 0.00
62 1 0.00
63 12 0.04
64 27 0.09
65 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAAATTAGGGGTAAAATGGTAATTTTTGGAAAGATTAGGGGT
Found at i:3089 original size:16 final size:15
Alignment explanation
Indices: 3068--3143 Score: 52
Period size: 15 Copynumber: 5.0 Consensus size: 15
3058 ATACTAATAT
3068 TTATCATTAATATTTA
1 TTATCATTAATA-TTA
*
3084 TTATCATTATTATTA
1 TTATCATTAATATTA
*
3099 TTA--ATTAAT-TAA
1 TTATCATTAATATTA
3111 TTAATGCCATTAATATTA
1 TT-AT--CATTAATATTA
*
3129 TTCAT-ATTATTATTA
1 TT-ATCATTAATATTA
3144 ATATTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
15 15 0.31
16 11 0.23
17 6 0.12
18 6 0.12
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (15 bp):
TTATCATTAATATTA
Found at i:3148 original size:9 final size:9
Alignment explanation
Indices: 3073--3189 Score: 53
Period size: 9 Copynumber: 12.3 Consensus size: 9
3063 AATATTTATC
3073 ATTAATATTT
1 ATTAATA-TT
3083 ATT-ATCATT
1 ATTAAT-ATT
*
3092 ATTATTATT
1 ATTAATATT
*
3101 AATTAAT-TA
1 -ATTAATATT
***
3110 ATTAATGCC
1 ATTAATATT
3119 ATTAATATT
1 ATTAATATT
3128 ATTCATATTATT
1 ATT-A-A-TATT
3140 ATTAATATT
1 ATTAATATT
* *
3149 ATTATTAGT
1 ATTAATATT
3158 ATTAA-ACTT
1 ATTAATA-TT
3167 ATTTAATA-T
1 A-TTAATATT
3176 ATTTAATATGT
1 A-TTAATAT-T
3187 ATT
1 ATT
3190 TAATGCGGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
8 7 0.08
9 46 0.55
10 18 0.22
11 5 0.06
12 7 0.08
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (9 bp):
ATTAATATT
Found at i:3154 original size:12 final size:12
Alignment explanation
Indices: 3124--3161 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3114 ATGCCATTAA
*
3124 TATTATTCATAT
1 TATTATTAATAT
3136 TATTATTAATAT
1 TATTATTAATAT
*
3148 TATTATTAGTAT
1 TATTATTAATAT
3160 TA
1 TA
3162 AACTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:7925 original size:28 final size:25
Alignment explanation
Indices: 7874--7948 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 25
7864 TCCAAATTTA
*
7874 ATTTACATAAATGAACCCAAAAAATT
1 ATTTACATAAATG-ACCCAAAAAACT
7900 ATTTACATAAATGACCCAAGTTAAAACT
1 ATTTACATAAATGACCCAA---AAAACT
* * *
7928 ATTCACCTAAATGACCTAAAA
1 ATTTACATAAATGACCCAAAA
7949 TAAACAGTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.19
26 13 0.31
28 21 0.50
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (25 bp):
ATTTACATAAATGACCCAAAAAACT
Found at i:9202 original size:30 final size:29
Alignment explanation
Indices: 9180--9499 Score: 285
Period size: 30 Copynumber: 10.8 Consensus size: 29
9170 TTTCAAGGTC
*
9180 AAAAATGGAATTTTTGGAAGTTTGGGGGGT
1 AAAAATGGAATTTTTGGAAGTTT-CGGGGT
* *
9210 AAAAAT-GAGATTTTTAGAAGTTTTGGGGTT
1 AAAAATGGA-ATTTTTGGAAGTTTCGGGG-T
*
9240 AAAAATGGAATTTTTGGAAGTTT-GAGAGT
1 AAAAATGGAATTTTTGGAAGTTTCG-GGGT
*
9269 AAAAATGGAATTTTTGGAAGTCTT-AGGGT
1 AAAAATGGAATTTTTGGAAGT-TTCGGGGT
* *
9298 CAAAATGGAATTTTTGGAAGTTTCGAGGAT
1 AAAAATGGAATTTTTGGAAGTTTCG-GGGT
* * *
9328 GAAAATGAAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGGGG-T
* * * *
9358 GAAAATGGAATTTTTAGAAGTTTTGGGGAC
1 AAAAATGGAATTTTTGGAAGTTTCGGGG-T
**
9388 AAAAATAAAATTTTTGGAAG-TTCGAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTC--GGGGT
9418 AAAAATGGAATTTTTGGAAGTTTC-GGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGT
* *
9446 CGAAAATGGAATTTTCT-AAAG-TTCGGGGGT
1 -AAAAATGGAATTTT-TGGAAGTTTC-GGGGT
* *
9476 AAAAATGAAATTTTTTGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
9500 AGGGACCTCT
Statistics
Matches: 242, Mismatches: 30, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
28 10 0.04
29 85 0.35
30 136 0.56
31 11 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGT
Found at i:9210 original size:60 final size:57
Alignment explanation
Indices: 9144--9440 Score: 201
Period size: 60 Copynumber: 5.0 Consensus size: 57
9134 TTAGACATTC
* *
9144 GGGGGTAAAAGGGGTAATTTTGAG-AGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAA-AGG-AATTTTGAGAAGTTT-AGGGTCAAAAATGGAATTTTTGGAAGTTT
* * * *
9203 GGGGGGTAAAAATGAGATTTTTAGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTT
1 -GGGGGTAAAAAGGA-ATTTTGAGAAG-TTTAGGGTCAAAAATGGAATTTTTGGAAGTTT
* *
9263 GAGAGTAAAAATGGAATTTTTG-GAAGTCTTAGGGTC-AAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAAA-GGAA-TTTTGAGAAGT-TTAGGGTCAAAAATGGAATTTTTGGAAGTTT
* * * * * ** *
9321 CGAGGATGAAAATGAAATTTTTG-GAAGTTTTGGGGTTGAAAATGGAATTTTTAGAAGTTTT
1 -GGGGGT-AAAAAGGAA-TTTTGAGAAG-TTTAGGGTCAAAAATGGAATTTTTGGAAG-TTT
** ** *
9382 GGGGACAAAAATAAAATTTTTG-GAAGTTCGAGGGGT-AAAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAAA-GGAA-TTTTGAGAAGTT-TA-GGGTCAAAAATGGAATTTTTGGAAGTTT
9441 CGGGTCGAAA
Statistics
Matches: 196, Mismatches: 27, Indels: 29
0.78 0.11 0.12
Matches are distributed among these distances:
58 24 0.12
59 60 0.31
60 102 0.52
61 10 0.05
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (57 bp):
GGGGGTAAAAAGGAATTTTGAGAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTT
Found at i:9252 original size:89 final size:89
Alignment explanation
Indices: 9073--9499 Score: 347
Period size: 89 Copynumber: 4.8 Consensus size: 89
9063 AAAATGATAA
* * * * * * *
9073 TTTTGG-ATTTTCGAGGGC-AAAATGGTAATTTTGGGAAAATTTGAGGTTAAAAAGGAAATTTTT
1 TTTTGGAAGTTTCGAGGTCAAAAATGG-AATTTTTGG-AAGTTTGGGGGTAAAAATGAAATTTTT
* * **
9136 AGACA--TTCGGGGGTAAAAGGGGTAA-
64 GGA-AGTTTCGGGGATAAAAATGG-AAT
* *
9161 TTTT-GAGAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGGTAAAAATGAGATTTTT
1 TTTTGGA-AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTT-GGGGGTAAAAATGAAATTTTT
* * *
9225 AGAAGTTTTGGGGTTAAAAATGGAAT
64 GGAAGTTTCGGGGATAAAAATGGAAT
* * *
9251 TTTTGGAAGTTT-GAGAGT-AAAAATGGAATTTTTGGAAGTCTT-AGGGTCAAAATGGAATTTTT
1 TTTTGGAAGTTTCGAG-GTCAAAAATGGAATTTTTGGAAGT-TTGGGGGTAAAAATGAAATTTTT
* * *
9313 GGAAGTTTCGAGGATGAAAATGAAAT
64 GGAAGTTTCGGGGATAAAAATGGAAT
* * ** * ** *
9339 TTTTGGAAGTTTTGGGGTTGAAAATGGAATTTTTAGAAGTTTTGGGGACAAAAATAAAATTTTTG
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTTGGGGGTAAAAATGAAATTTTTG
*
9404 GAAG-TTCGAGGGGTAAAAATGGAAT
65 GAAGTTTCG-GGGATAAAAATGGAAT
* * * *
9429 TTTTGGAAGTTTCG-GGTCGAAAATGGAATTTTCT-AAAGTTCGGGGGTAAAAATGAAATTTTTT
1 TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTT-TGGAAGTTTGGGGGTAAAAATGAAATTTTTG
9492 GATAGTTT
65 GA-AGTTT
9500 AGGGACCTCT
Statistics
Matches: 276, Mismatches: 45, Indels: 34
0.78 0.13 0.10
Matches are distributed among these distances:
87 1 0.00
88 82 0.30
89 110 0.40
90 81 0.29
91 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (89 bp):
TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGG
AAGTTTCGGGGATAAAAATGGAAT
Found at i:11463 original size:13 final size:13
Alignment explanation
Indices: 11445--11470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11435 GGGTCCAAGA
11445 TTTGTAATTGGAC
1 TTTGTAATTGGAC
11458 TTTGTAATTGGAC
1 TTTGTAATTGGAC
11471 ATTATTTAAA
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:18470 original size:30 final size:30
Alignment explanation
Indices: 18434--18841 Score: 375
Period size: 30 Copynumber: 13.7 Consensus size: 30
18424 GTTCGGGGGT
* *
18434 AAAATGGAATTTTTGAAAATTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
18464 AAAATGGAATTTTTGGAAG-TTCGATGGT-A
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTCA
* * * * *
18493 AAAATGGAATTTATAGAAGTTTCGCGATCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* **
18523 AAAATGAAATTTTTGGAAGTTCAGGGGGT-A
1 AAAATGGAATTTTTGGAAGTT-TTGGGGTCA
* * * *
18553 AAAATGGGATTTTTAGAAGTTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
**
18583 AAAATGGAATTTTTGGAAGTTCGGGGGT--
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
18611 AATATGGAATTTTTGGAAGTTTTGAGGTCGA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTC-A
** * *
18642 AAAA-GGAATTTTTGGAAGTTTTAACGTTGA
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTCA
* *
18672 AAAA-GGAATTTTTGGAAGTTTTGAGGTCG
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* * *
18701 AAAATGGAAATTTTGGAAATTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
*
18731 AAAATGGGATTTTTGGAA-TTTTAGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTCA
* * * *
18760 AAAATGGGATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* * *
18790 AAAATGGAATTTTTGGAAGTTTCGAGGTCG
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
18820 AAAATGGAATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
18842 AGGGACCTCT
Statistics
Matches: 315, Mismatches: 50, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
28 24 0.08
29 61 0.19
30 222 0.70
31 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCA
Found at i:18586 original size:60 final size:59
Alignment explanation
Indices: 18288--18840 Score: 444
Period size: 59 Copynumber: 9.4 Consensus size: 59
18278 CCCGGGGGGT
** * * ** * *
18288 AAAATGGTAA-TTTTGGATTTTCGAGGGT-AAAATGGTAATTTTGGGAAAATTCAAGGTTA
1 AAAATGG-AATTTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTCA
* * ** * *
18347 AAAA-GGAAATTTTTAGACA-TTCAGGGGTAAAAGGGGTAA-TTTT-GAGAGTTTCAAGGTCG
1 AAAATGG-AATTTTTGGA-AGTTCGGGGGTAAAAATGG-AATTTTTGGA-AGTTTCGAGGTCA
* * * * * * *
18406 AAAATGAAATTTTCGGAGGTTCGGGGGT-AAAATGGAATTTTTGAAAATTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
** * * * *
18464 AAAATGGAATTTTTGGAAGTTCGATGGTAAAAATGGAATTTATAGAAGTTTCGCGATCA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * * *
18523 AAAATGAAATTTTTGGAAGTTCAGGGGGTAAAAATGGGATTTTTAGAAGTTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTC-GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* *
18583 AAAATGGAATTTTTGGAAGTTCGGGGGT-AATATGGAATTTTTGGAAGTTTTGAGGTCGA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC-A
**** * * *
18642 AAAA-GGAATTTTTGGAAGTTTTAACGTTGAAAAA-GGAATTTTTGGAAGTTTTGAGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * * * * * *
18701 AAAATGGAAATTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAATTTTAGGGGT-A
1 AAAATGGAATTTTTGG-AAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * *
18760 AAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
18820 AAAATGGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
18841 TAGGGACCTC
Statistics
Matches: 395, Mismatches: 80, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
57 2 0.01
58 85 0.22
59 166 0.42
60 137 0.35
61 5 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
Found at i:18594 original size:119 final size:118
Alignment explanation
Indices: 18298--18840 Score: 439
Period size: 119 Copynumber: 4.6 Consensus size: 118
18288 AAAATGGTAA
* * ** * *
18298 TTTTGG-ATTTTCGAGGGT-AAAATGGTAATTTTGGGAAAATTCAAGGTTAAAAA-GGAAATTTT
1 TTTTGGAAGTTTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGG-AATTTT
* ** *
18360 TAGACA-TTCAGGGGTAAAAGGGGTAA-TTTT-GAGAGTTTCA-AGGTCGAAAATGAAAT
64 TGGA-AGTTC-GGGGTAAAAATGG-AATTTTTGGA-AGTTT-AGAGGTCAAAAATGAAAT
* * * * * * *
18416 TTTCGG-AGGTTCGGGGGT-AAAATGGAATTTTTGAAAATTTTGGGGTCAAAAATGGAATTTTTG
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTG
* * * * * *
18479 GAAGTTCGATGGTAAAAATGGAATTTATAGAAGTTTCGCGATCAAAAATGAAAT
66 GAAGTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGAAAT
* * * * *
18533 TTTTGGAAG-TTCAGGGGGTAAAAATGGGATTTTTAGAAGTTTCGGGGTAAAAAATGGAATTTTT
1 TTTTGGAAGTTTC-GAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTT
* * *
18597 GGAAGTTCGGGGGT-AATATGGAATTTTTGGAAGTTTTGAGGTCGAAAAA-GGAAT
65 GGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTAGAGGTC-AAAAATGAAAT
** * * * * *
18651 TTTTGGAAGTTTTAACGTTGAAAAA-GGAATTTTTGGAAGTTTTGAGGTCGAAAATGGAAATTTT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTT
* * * * * **
18715 GGAAATTTTGGGGTTAAAAATGGGATTTTTGGAATTTTAGGGGT-AAAAATGGGAT
65 GG-AAGTTCGGGG-TAAAAATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGAAAT
* *
18770 TTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATGGAATTTTTG
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTG
18835 GAAGTT
66 GAAGTT
18841 TAGGGACCTC
Statistics
Matches: 346, Mismatches: 61, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
116 4 0.01
117 70 0.20
118 123 0.36
119 125 0.36
120 24 0.07
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (118 bp):
TTTTGGAAGTTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTG
GAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGAAAT
Found at i:20818 original size:6 final size:6
Alignment explanation
Indices: 20807--20864 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
20797 ATTATTTAAA
* * *
20807 TAAATT TAAATT TAAATT TAAATT TAAA-A TAAACT T-AATT TGAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT
20853 TAAATT TAAATT
1 TAAATT TAAATT
20865 CTGTTGGGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 11 0.26
6 30 0.70
7 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:20844 original size:17 final size:17
Alignment explanation
Indices: 20807--20864 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
20797 ATTATTTAAA
*
20807 TAAATTTAAATTTAAATT
1 TAAATTTAAA-ATAAATT
*
20825 TAAATTTAAAATAAACT
1 TAAATTTAAAATAAATT
20842 T-AATTTGAAAATAAATT
1 TAAATTT-AAAATAAATT
20859 TAAATT
1 TAAATT
20865 CTGTTGGGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.14
17 16 0.46
18 14 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:21210 original size:114 final size:110
Alignment explanation
Indices: 20937--21211 Score: 329
Period size: 117 Copynumber: 2.5 Consensus size: 110
20927 TTTTTAGGGT
* * *
20937 TTTTTTAACTAATGGTCGACACCCA-AAAATACGAAT-AATTTTTTTTTTTTGTGTTTGGCAACC
1 TTTTTCAACTAATGGCCGACACCCATAAAACACGAATAAATTTTTTTTTTTTGTGTTTGGCAACC
* * ***
21000 AATGACCGAGACCATCTTTCCCAACACTTTAAAATTTTTTCCCAC
66 AATGACCGACACCACCTTTCCCAACACAAAAAAATTTTTTCCCAC
* * *
21045 TTTTTCAACTAATGGCCGACACCTATAAAACACGAATAAAAAAATTCTTTTTTTTGGTGTTTGGC
1 TTTTTCAACTAATGGCCGACACCCATAAAACACGAAT----AAATTTTTTTTTTTTGTGTTTGGC
** * *
21110 AACCAATGGTCGACACCACCTTTCTCAACACCCAAAAATAATTTTTTCTCAC
62 AACCAATGACCGACACCACCTTTCCCAACA--CAAAAA-AATTTTTTCCCAC
*
21162 TTTTTCAACTAATGGCCAACACCCATAAAACACGAATAAATTTTTTTTTT
1 TTTTTCAACTAATGGCCGACACCCATAAAACACGAATAAATTTTTTTTTT
21212 GGAGTTTTAC
Statistics
Matches: 140, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
108 22 0.16
109 10 0.07
113 12 0.09
114 46 0.33
116 3 0.02
117 47 0.34
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (110 bp):
TTTTTCAACTAATGGCCGACACCCATAAAACACGAATAAATTTTTTTTTTTTGTGTTTGGCAACC
AATGACCGACACCACCTTTCCCAACACAAAAAAATTTTTTCCCAC
Found at i:21358 original size:68 final size:68
Alignment explanation
Indices: 21276--21412 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
21266 TTCCCTGGTT
21276 TTATCCTTATTGATGGTTGGCACCAACTTTATCAAATTAACAAAAAATTGGTGTATGGCAACCAA
1 TTATCCTTATTGATGGTTGGCACCAACTTTATCAAATTAACAAAAAATTGGTGTATGGCAACCAA
21341 TGG
66 TGG
21344 TTATCCTTATTGATGGTTGGCACCAACTTTATCAAATTAACAAAAAATTGGTGTATGGCAACCAA
1 TTATCCTTATTGATGGTTGGCACCAACTTTATCAAATTAACAAAAAATTGGTGTATGGCAACCAA
21409 TGG
66 TGG
21412 T
1 T
21413 CGACACCAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (68 bp):
TTATCCTTATTGATGGTTGGCACCAACTTTATCAAATTAACAAAAAATTGGTGTATGGCAACCAA
TGG
Found at i:22773 original size:37 final size:37
Alignment explanation
Indices: 22723--22797 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
22713 CGCCATCGAT
22723 TGCCTTCTGGTACAAGCTACTTCAAGACTATCATATA
1 TGCCTTCTGGTACAAGCTACTTCAAGACTATCATATA
22760 TGCCTTCTGGTACAAGCTACTTCAAGACTATCATATA
1 TGCCTTCTGGTACAAGCTACTTCAAGACTATCATATA
22797 T
1 T
22798 TGTCCTTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (37 bp):
TGCCTTCTGGTACAAGCTACTTCAAGACTATCATATA
Found at i:23397 original size:163 final size:163
Alignment explanation
Indices: 23127--23455 Score: 613
Period size: 163 Copynumber: 2.0 Consensus size: 163
23117 ATAAGGCATC
* *
23127 CACAAAAATTGCATAGTATAAATAACACGAGTTTAGTTAATTTTAACGTTCTTGCATGGTAGATA
1 CACAAAAACTGCATAGTATAAACAACACGAGTTTAGTTAATTTTAACGTTCTTGCATGGTAGATA
*
23192 ATGTCCATTTACGTTGGATTTCTGGGGAGATGTTGAAAGTTTTCTTTTAACCACGTAAATTTTAA
66 ATGTCCATTTACGTTGGATTTCTGGAGAGATGTTGAAAGTTTTCTTTTAACCACGTAAATTTTAA
23257 CATGGTTAATCTTCCGTTTTTATCGTTCGGGGG
131 CATGGTTAATCTTCCGTTTTTATCGTTCGGGGG
23290 CACAAAAACTGCATAGTATAAACAACACGAGTTTAGTTAATTTTAACGTTCTTGCATGGTAGATA
1 CACAAAAACTGCATAGTATAAACAACACGAGTTTAGTTAATTTTAACGTTCTTGCATGGTAGATA
*
23355 ATGTCCATTTATGTTGGATTTCTGGAGAGATGTTGAAAGTTTTCTTTTAACCACGTAAATTTTAA
66 ATGTCCATTTACGTTGGATTTCTGGAGAGATGTTGAAAGTTTTCTTTTAACCACGTAAATTTTAA
*
23420 CATGGTTAATCTTCTGTTTTTATCGTTCGGGGG
131 CATGGTTAATCTTCCGTTTTTATCGTTCGGGGG
23453 CAC
1 CAC
23456 CCTACCCAGT
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 161 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (163 bp):
CACAAAAACTGCATAGTATAAACAACACGAGTTTAGTTAATTTTAACGTTCTTGCATGGTAGATA
ATGTCCATTTACGTTGGATTTCTGGAGAGATGTTGAAAGTTTTCTTTTAACCACGTAAATTTTAA
CATGGTTAATCTTCCGTTTTTATCGTTCGGGGG
Found at i:24063 original size:20 final size:20
Alignment explanation
Indices: 24020--24063 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
24010 GAGGTTATCG
* *
24020 GACGGTGAAATATAGTGGAT
1 GACGGTGAAATATAGCGGAA
* *
24040 GACGGTGGAATATGGCGGAA
1 GACGGTGAAATATAGCGGAA
24060 GACG
1 GACG
24064 ACGGTGGTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (20 bp):
GACGGTGAAATATAGCGGAA
Found at i:24217 original size:18 final size:18
Alignment explanation
Indices: 24192--24232 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24182 TTAAAAAATT
24192 ATTT-AAATTGTTT-TTTA
1 ATTTAAAATT-TTTATTTA
24209 ATTTAAAATTTTTATTTA
1 ATTTAAAATTTTTATTTA
24227 AGTTTA
1 A-TTTA
24233 TTTAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.33
18 10 0.48
19 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTAAAATTTTTATTTA
Found at i:24308 original size:17 final size:17
Alignment explanation
Indices: 24283--24355 Score: 94
Period size: 17 Copynumber: 4.3 Consensus size: 17
24273 AGTTTAGTTT
24283 AATTTCATTTAAATTTC
1 AATTTCATTTAAATTTC
* *
24300 AAATTCATTTCAATTT-
1 AATTTCATTTAAATTTC
*
24316 AATTTCAATTTCAATTTC
1 AATTTC-ATTTAAATTTC
*
24334 AATTTAATTTAAATTTC
1 AATTTCATTTAAATTTC
24351 AATTT
1 AATTT
24356 GAACTTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 5 0.10
17 39 0.80
18 5 0.10
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTCATTTAAATTTC
Found at i:24317 original size:23 final size:22
Alignment explanation
Indices: 24284--24396 Score: 90
Period size: 23 Copynumber: 5.0 Consensus size: 22
24274 GTTTAGTTTA
24284 ATTTC-ATTTAAATTTCAAATTC
1 ATTTCAATTT-AATTTCAAATTC
*
24306 ATTTCAATTTAATTTCAATTTC
1 ATTTCAATTTAATTTCAAATTC
24328 AATTTCAATTTAATTT-AAATTTC
1 -ATTTCAATTTAATTTCAAA-TTC
* * * *
24351 AATTTGAACTTAATTTTAAACTTT
1 -ATTTCAATTTAATTTCAAA-TTC
*
24375 A-TT-AATCTAAATTTCAAATTC
1 ATTTCAAT-TTAATTTCAAATTC
24396 A
1 A
24397 AAATTAAAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
21 5 0.07
22 29 0.38
23 37 0.49
24 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.50
Consensus pattern (22 bp):
ATTTCAATTTAATTTCAAATTC
Found at i:24366 original size:17 final size:17
Alignment explanation
Indices: 24291--24363 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
24281 TTAATTTCAT
* * *
24291 TTAAATTTCAAATTCAT
1 TTAAATTTCAATTTAAC
* *
24308 TTCAATTT-AATTTCAAT
1 TTAAATTTCAATTT-AAC
* *
24325 TTCAATTTCAATTTAAT
1 TTAAATTTCAATTTAAC
24342 TTAAATTTCAATTTGAAC
1 TTAAATTTCAATTT-AAC
24360 TTAA
1 TTAA
24364 TTTTAAACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.08
17 33 0.69
18 11 0.23
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (17 bp):
TTAAATTTCAATTTAAC
Found at i:24410 original size:7 final size:6
Alignment explanation
Indices: 24289--24478 Score: 104
Period size: 6 Copynumber: 31.7 Consensus size: 6
24279 GTTTAATTTC
* * * * *
24289 ATTTAA ATTTCAA A-TT-C ATTTCA ATTT-A ATTTCA ATTTCA ATTTCA
1 ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * *
24335 ATTT-A ATTTAA ATTTCA ATTTGA ACTTAA TTTTAA ACTTTATTA ATCTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A-TTTA--A ATTTAA
* * * * *
24385 ATTTCAA ATTCAA AATTAA AGTTTAA TTTTAA ATTTAA TTTTAA TTTTAA
1 ATTT-AA ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * *
24435 TTTTAA A-TTAA ATTT-C ATTTAA ATTAAA AATTAA ATTTTA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
24479 TTAACCTTAT
Statistics
Matches: 146, Mismatches: 26, Indels: 24
0.74 0.13 0.12
Matches are distributed among these distances:
4 1 0.01
5 21 0.14
6 103 0.71
7 16 0.11
8 3 0.02
9 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:24415 original size:6 final size:6
Alignment explanation
Indices: 24406--24553 Score: 73
Period size: 6 Copynumber: 23.3 Consensus size: 6
24396 AAAATTAAAG
* * * *
24406 TTTAAT TTTAAA TTTAAT TTTAAT TTTAAT TTTAA- ATTAAA TTTCAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
* ** * * *
24453 TTAAAT TAAAAA TTAAAT TTTAATT TTTAACCT TATTAAT TTTAAAC TTTATAT
1 TTTAAT TTTAAT TTTAAT TTTAA-T TTTAA--T T-TTAAT TTT-AAT TTTA-AT
* * * * *
24507 TATTAAAC TTTAAT TTTAAA TTTAAA TTTCAT TTTCAAT TTCAAT TT
1 T-TT-AAT TTTAAT TTTAAT TTTAAT TTTAAT TTT-AAT TTTAAT TT
24554 GAACTTAATT
Statistics
Matches: 110, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
5 4 0.04
6 74 0.67
7 21 0.19
8 6 0.05
9 5 0.05
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAT
Found at i:24432 original size:65 final size:65
Alignment explanation
Indices: 24360--24505 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 65
24350 CAATTTGAAC
* * *
24360 TTAATTTTAAACTTTATTAATCTAAATTTCAAATTCAAAATT-AAAGTTTAATTTTAA-ATTTAA
1 TTAATTTTAAACTTTATAAAT-TAAATTTC--ATT-AAAATTAAAAATTAAATTTTAATATTTAA
24423 -TT-
62 CTTA
* *
24425 TTAATTTT-AA-TTT-TAAATTAAATTTCATTTAAATTAAAAATTAAATTTTAATTTTTAACCTT
1 TTAATTTTAAACTTTATAAATTAAATTTCATTAAAATTAAAAATTAAATTTTAATATTTAA-CTT
24487 A
65 A
24488 TTAATTTTAAACTTTATA
1 TTAATTTTAAACTTTATA
24506 TTATTAAACT
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
58 5 0.07
59 16 0.24
60 5 0.07
61 8 0.12
62 6 0.09
63 11 0.16
64 4 0.06
65 11 0.16
66 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (65 bp):
TTAATTTTAAACTTTATAAATTAAATTTCATTAAAATTAAAAATTAAATTTTAATATTTAACTTA
Found at i:24504 original size:16 final size:16
Alignment explanation
Indices: 24472--24518 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
24462 AAATTAAATT
* *
24472 TTAATTTTTAACCTTA
1 TTAATTTTAAACTTTA
24488 TTAATTTTAAACTTTA
1 TTAATTTTAAACTTTA
24504 -T-ATTATTAAACTTTA
1 TTAATT-TTAAACTTTA
24519 ATTTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 3 0.11
15 11 0.39
16 14 0.50
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTTTAAACTTTA
Found at i:24512 original size:15 final size:13
Alignment explanation
Indices: 24465--24531 Score: 64
Period size: 15 Copynumber: 4.8 Consensus size: 13
24455 AAATTAAAAA
*
24465 TTAAATTTTAATTT
1 TTAAACTTTAA-TT
*
24479 TTAACCTTATTAATT
1 TTAAAC-T-TTAATT
24494 TTAAACTTTATATT
1 TTAAACTTTA-ATT
24508 ATTAAACTTTAATT
1 -TTAAACTTTAATT
24522 TTAAA-TTTAA
1 TTAAACTTTAA
24532 ATTTCATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 5 0.11
13 8 0.17
14 11 0.24
15 18 0.39
16 4 0.09
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAACTTTAATT
Found at i:24816 original size:31 final size:31
Alignment explanation
Indices: 24779--24841 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
24769 CATTTAAAAT
* *
24779 AATTTGAACTTGTATTTTAATTTTGAATTTA
1 AATTTGAACTTATATTGTAATTTTGAATTTA
24810 AATTTGAACTTATATTGTAATTTTGAATTTA
1 AATTTGAACTTATATTGTAATTTTGAATTTA
24841 A
1 A
24842 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (31 bp):
AATTTGAACTTATATTGTAATTTTGAATTTA
Found at i:27987 original size:114 final size:114
Alignment explanation
Indices: 27865--28085 Score: 309
Period size: 114 Copynumber: 1.9 Consensus size: 114
27855 TAAACTAGTT
* * * *
27865 AAAAAAA-TTCGGGTGTTGGAAAAGGTGGTGTAGGCCATTTGTTGCCAAACACCAAAAAAATAAT
1 AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAAT-AT
* * *
27929 TTTTTTAATTTGTGTTTTATGGGTGTTGGCCATTGGTTGAAAAGGTGGGA
65 TTTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAAGGTGGGA
* * * *
27979 AAAAAAATTTCGGGTGTTGGGAAAGGTGATGTTGACCATTGGTTACCAAACACCCAAACAATATT
1 AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAATATT
* *
28044 TTTTTTATTTGTATTTTTTGGGTGTCGGCCATTAGTTGAAAA
66 TTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAA
28086 ATACCCCAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 47 0.51
115 46 0.49
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (114 bp):
AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAATATT
TTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAAGGTGGGA
Found at i:28097 original size:115 final size:115
Alignment explanation
Indices: 27865--28103 Score: 277
Period size: 115 Copynumber: 2.1 Consensus size: 115
27855 TAAACTAGTT
* * * *
27865 AAAAAAA-TTCGGGTGTTGGAAAAGGTGGTGTAGGCCATTTGTTGCCAAACACCAAAAAAATAAT
1 AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAATAAT
* * * * ***
27929 TTTTTTAATTTGTGTTTTATGGGTGTTGGCCATTGGTTGAAAAGGTGGGA
66 TTTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAAGATCCCA
* * * *
27979 AAAAAAATTTCGGGTGTTGGGAAAGGTGATGTTGACCATTGGTTACCAAACACCCAAACAAT-AT
1 AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAATAAT
* *
28043 TTTTTTTATTTGTATTTTTTGGGTGTCGGCCATTAGTTGAAAA-ATACCCCA
66 TTTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAAGAT--CCCA
*
28094 AAAAATATTT
1 AAAAAAATTT
28104 TTTAATCTAG
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
113 1 0.01
114 47 0.45
115 56 0.54
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (115 bp):
AAAAAAATTTCGGGTGTTGGAAAAGGTGATGTAGACCATTGGTTACCAAACACCAAAAAAATAAT
TTTTTTAATTTGTATTTTATGGGTGTCGGCCATTAGTTGAAAAGATCCCA
Found at i:36246 original size:50 final size:50
Alignment explanation
Indices: 36180--36282 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
36170 GGCACCATTA
* *
36180 CACAATTCTTTCTTTTTTTTATCTTGGTTCCATTACACACTTCTTGACTT
1 CACAATTCTTTCTTTTTTTTATCTTGGTTCCATTACACAATTCTTGAATT
36230 CACAATTCTTTCTTTTTTTTATCTTGGTTCCATTACACAATTCTTGAATT
1 CACAATTCTTTCTTTTTTTTATCTTGGTTCCATTACACAATTCTTGAATT
36280 CAC
1 CAC
36283 CCCTACGGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.50
Consensus pattern (50 bp):
CACAATTCTTTCTTTTTTTTATCTTGGTTCCATTACACAATTCTTGAATT
Found at i:38701 original size:2 final size:2
Alignment explanation
Indices: 38689--38719 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38679 AATCATTAAA
*
38689 AT AT TT 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
38720 AAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:39322 original size:27 final size:27
Alignment explanation
Indices: 39265--39339 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
39255 TGGACTAATA
*
39265 AAGATATCTACTTA-AA-AAAAACGGTT
1 AAGATATC-ACTTATAACAAAAACGGTG
*
39291 TAGATATCACTTATAACAAAAACGGTG
1 AAGATATCACTTATAACAAAAACGGTG
*
39318 AAGATATCACTTGTAACAAAAA
1 AAGATATCACTTATAACAAAAA
39340 AAATTTTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 5 0.12
26 9 0.21
27 29 0.67
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (27 bp):
AAGATATCACTTATAACAAAAACGGTG
Found at i:40510 original size:29 final size:28
Alignment explanation
Indices: 40465--40713 Score: 161
Period size: 29 Copynumber: 8.6 Consensus size: 28
40455 GGACATTCAT
* *
40465 GGGT-AAAATGGTAAATTTTGAAAGTTTCA
1 GGGTAAAAATGG--AATTTTGGAAGTTTCG
*
40494 AGGTCAAAAATGGAATTTTGGAAG-TTCGG
1 GGGT-AAAAATGGAATTTTGGAAGTTTC-G
** *
40523 GGGT-AAAATGGTAATTTTTAAAAGTTTTG
1 GGGTAAAAATGG-AA-TTTTGGAAGTTTCG
40552 GGGTCAAAAATGGAATTATTGGAAGTTT-G
1 GGGT-AAAAATGGAATT-TTGGAAGTTTCG
* * * *
40581 AGGGTAAAAATGTATTTTTTTGAAGTTTTG
1 -GGGTAAAAATGGA-ATTTTGGAAGTTTCG
* *
40611 GGGTTAAAATGGAATTCATGGAAG-TTCGG
1 GGGTAAAAATGGAATT-TTGGAAGTTTC-G
* * *
40640 GGGTAAAAATGTAATTTTTGAAGTTTCA
1 GGGTAAAAATGGAATTTTGGAAGTTTCG
* *
40668 AGGTAAAAAATGGAATTTTTTGAAG-TTCG
1 GGGT-AAAAATGGAA-TTTTGGAAGTTTCG
*
40697 GGGT-AAAATGTAATTTT
1 GGGTAAAAATGGAATTTT
40714 CAGAAGCTTA
Statistics
Matches: 175, Mismatches: 28, Indels: 37
0.73 0.12 0.15
Matches are distributed among these distances:
26 4 0.02
27 15 0.09
28 17 0.10
29 97 0.55
30 28 0.16
31 14 0.08
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTGGAAGTTTCG
Found at i:40533 original size:58 final size:57
Alignment explanation
Indices: 40465--40713 Score: 263
Period size: 58 Copynumber: 4.3 Consensus size: 57
40455 GGACATTCAT
*
40465 GGGTAAAATGGTAAATTTTGAAAGTTTCAAGGTCAAAAATGGAATT-TTGGAAGTTCGG
1 GGGTAAAAT-GTAATTTTTG-AAGTTTCAAGGTCAAAAATGGAATTATTGGAAGTTCGG
* *** * *
40523 GGGTAAAATGGTAATTTTTAAAAGTTTTGGGGTCAAAAATGGAATTATTGGAAGTTTGA
1 GGGTAAAAT-GTAATTTTT-GAAGTTTCAAGGTCAAAAATGGAATTATTGGAAGTTCGG
* *** *
40582 GGGTAAAAATGTATTTTTTTGAAGTTTTGGGGT-TAAAATGGAATTCA-TGGAAGTTCGG
1 GGGT-AAAATGTA-ATTTTTGAAGTTTCAAGGTCAAAAATGGAATT-ATTGGAAGTTCGG
* * *
40640 GGGTAAAAATGTAATTTTTGAAGTTTCAAGGTAAAAAATGGAATTTTTTGAAGTTC-G
1 GGGT-AAAATGTAATTTTTGAAGTTTCAAGGTCAAAAATGGAATTATTGGAAGTTCGG
40697 GGGTAAAATGTAATTTT
1 GGGTAAAATGTAATTTT
40714 CAGAAGCTTA
Statistics
Matches: 165, Mismatches: 19, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
56 13 0.08
57 20 0.12
58 92 0.56
59 30 0.18
60 10 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGAAGTTTCAAGGTCAAAAATGGAATTATTGGAAGTTCGG
Found at i:40561 original size:117 final size:116
Alignment explanation
Indices: 40440--40708 Score: 264
Period size: 117 Copynumber: 2.3 Consensus size: 116
40430 AATCGAGATA
* *
40440 AAAAATGGCATTTTTGGACA-TTCATGGGT-AAAATGGTA-AATTTTGAAAGTTTCAAGGTCAAA
1 AAAAATGGAATTATTGGA-AGTTCA-GGGTAAAAAT-GTATAATTTTG-AAGTTTCAAGGT-AAA
*
40502 AATGGAATT-TTGGAAGTTCGGGGGT-AAAATGGTAATTTTTAAAAGTTTTGGGGTC
61 AATGGAATTCATGGAAGTTCGGGGGTAAAAAT-GTAATTTTTAAAAGTTTTGGGGTC
* ** *** *
40557 AAAAATGGAATTATTGGAAGTTTGAGGGTAAAAATGTATTTTTTTGAAGTTTTGGGGTTAAAATG
1 AAAAATGGAATTATTGGAAG-TTCAGGGTAAAAATGTATAATTTTGAAGTTTCAAGGTAAAAATG
* *** *
40622 GAATTCATGGAAGTTCGGGGGTAAAAATGTAATTTTT-GAAGTTTCAAGGTA
65 GAATTCATGGAAGTTCGGGGGTAAAAATGTAATTTTTAAAAGTTTTGGGGTC
* * *
40673 AAAAATGGAATTTTTTGAAGTTCGGGGT-AAAATGTA
1 AAAAATGGAATTATTGGAAGTTCAGGGTAAAAATGTA
40709 ATTTTCAGAA
Statistics
Matches: 127, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
114 8 0.06
115 6 0.05
116 39 0.31
117 56 0.44
118 18 0.14
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (116 bp):
AAAAATGGAATTATTGGAAGTTCAGGGTAAAAATGTATAATTTTGAAGTTTCAAGGTAAAAATGG
AATTCATGGAAGTTCGGGGGTAAAAATGTAATTTTTAAAAGTTTTGGGGTC
Found at i:40592 original size:87 final size:87
Alignment explanation
Indices: 40469--40733 Score: 261
Period size: 87 Copynumber: 3.0 Consensus size: 87
40459 ATTCATGGGT
* * *
40469 AAAATGGTAAATTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGG
1 AAAATGG--AATTTTGGAAGTTTCAAGGTAAAAAATGGAATTTTTGAAGTTCGGGGGTAAAATGG
* *
40534 TAATTTTTAAAAGTTTTGGGGTCA
64 TAATTTTTAGAAGTTTAGGGGTCA
* * * * * *
40558 AAAATGGAATTATTGGAAGTTTGAGGGT-AAAAATGTATTTTTTTGAAGTTTTGGGGTTAAAATG
1 AAAATGGAATT-TTGGAAGTTTCAAGGTAAAAAATGGA-ATTTTTGAAG-TTCGGGGGTAAAATG
** * **
40622 G-AATTCATGGAAGTTCGGGGGT-A
63 GTAATTTTTAGAAGTTTAGGGGTCA
* *
40645 AAAATGTAATTTTTGAAGTTTCAAGGTAAAAAATGGAATTTTTTGAAGTTC-GGGGTAAAAT-GT
1 AAAATGGAATTTTGGAAGTTTCAAGGTAAAAAATGGAA-TTTTTGAAGTTCGGGGGTAAAATGGT
* *
40708 AATTTTCAGAAGCTTAGGGGTCA
65 AATTTTTAGAAGTTTAGGGGTCA
40731 AAA
1 AAA
40734 TATAATTTCT
Statistics
Matches: 140, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
84 1 0.01
85 23 0.16
86 19 0.14
87 40 0.29
88 36 0.26
89 21 0.15
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (87 bp):
AAAATGGAATTTTGGAAGTTTCAAGGTAAAAAATGGAATTTTTGAAGTTCGGGGGTAAAATGGTA
ATTTTTAGAAGTTTAGGGGTCA
Found at i:41760 original size:3 final size:3
Alignment explanation
Indices: 41747--41806 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
41737 TTTTTTATAT
* * * * *
41747 TTA TTA ATA TTA TTA TAA TTA TTA ATA -TA TTA TTA TTTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
41792 TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
41807 ATGTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Done.