Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007891.1 Hibiscus syriacus cultivar Beakdansim tig00110273_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 893409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:706269 original size:32 final size:33
Alignment explanation
Indices: 706208--706274 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
706198 CAAAATTTCA
706208 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATGGAATATGGACAG
706240 AAGAAAGAAAATGA-TAAGTAA-GGAA-ATGGACAG
1 AAGAAAG-AAATGATTAA--AATGGAATATGGACAG
706273 AA
1 AA
706275 ATGATATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
32 15 0.48
33 14 0.45
34 2 0.06
ACGTcount: A:0.58, C:0.01, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATGGAATATGGACAG
Found at i:710159 original size:16 final size:16
Alignment explanation
Indices: 710126--710174 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
710116 TAAGGTAATG
710126 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
710144 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
710160 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
710175 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:715915 original size:19 final size:20
Alignment explanation
Indices: 715874--715924 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
715864 GAAACCCCTT
*
715874 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
715894 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
715913 TGAAGATACATG
1 TGAAAATACATG
715925 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:721826 original size:19 final size:20
Alignment explanation
Indices: 721785--721835 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
721775 GAAACCCCTT
*
721785 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
721805 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
721824 TGAAGATACATG
1 TGAAAATACATG
721836 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:729744 original size:23 final size:22
Alignment explanation
Indices: 729706--729748 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
729696 CAATTCCTTT
729706 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
729728 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
729749 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:730104 original size:10 final size:10
Alignment explanation
Indices: 730089--730131 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
730079 AAACAAAAAC
730089 AAAAAAACCA
1 AAAAAAACCA
*
730099 AAAAAAGCCA
1 AAAAAAACCA
*
730109 AAAAAAAACA
1 AAAAAAACCA
*
730119 AAAAAAGCCA
1 AAAAAAACCA
730129 AAA
1 AAA
730132 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:730112 original size:20 final size:20
Alignment explanation
Indices: 730089--730131 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
730079 AAACAAAAAC
*
730089 AAAAAAACCAAAAAAAGCCA
1 AAAAAAAACAAAAAAAGCCA
730109 AAAAAAAACAAAAAAAGCCA
1 AAAAAAAACAAAAAAAGCCA
730129 AAA
1 AAA
730132 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAGCCA
Found at i:734442 original size:23 final size:22
Alignment explanation
Indices: 734404--734446 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
734394 CAATTCCTTT
734404 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
734426 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
734447 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:736783 original size:33 final size:33
Alignment explanation
Indices: 736741--736818 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
736731 GTAGCTCCTT
736741 GTGAAAAGGTACTTCTTGGAATGGCAACTCTTC
1 GTGAAAAGGTACTTCTTGGAATGGCAACTCTTC
736774 GTGAAAAGGTACTTCTTGGAATGGCAACTCTTC
1 GTGAAAAGGTACTTCTTGGAATGGCAACTCTTC
* *
736807 ATCAAAAGGTAC
1 GTGAAAAGGTAC
736819 GATTTCACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (33 bp):
GTGAAAAGGTACTTCTTGGAATGGCAACTCTTC
Found at i:736790 original size:18 final size:17
Alignment explanation
Indices: 736738--736791 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 17
736728 ATGGTAGCTC
736738 CTTGTGAAAAGGTACTT
1 CTTGTGAAAAGGTACTT
* *
736755 CTTG-G-AATGGCAAC-T
1 CTTGTGAAAAGG-TACTT
736770 CTTCGTGAAAAGGTACTT
1 CTT-GTGAAAAGGTACTT
736788 CTTG
1 CTTG
736792 GAATGGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 8 0.29
18 8 0.29
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (17 bp):
CTTGTGAAAAGGTACTT
Found at i:736806 original size:18 final size:18
Alignment explanation
Indices: 736752--736806 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
736742 TGAAAAGGTA
736752 CTTCTTGGAATGGCAACT
1 CTTCTTGGAATGGCAACT
* * * *
736770 CTTCGTGAAAAGG-TA--
1 CTTCTTGGAATGGCAACT
736785 CTTCTTGGAATGGCAACT
1 CTTCTTGGAATGGCAACT
736803 CTTC
1 CTTC
736807 ATCAAAAGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 6
0.65 0.20 0.15
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 1 0.04
18 14 0.54
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
CTTCTTGGAATGGCAACT
Found at i:739357 original size:16 final size:16
Alignment explanation
Indices: 739325--739372 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
739315 AAGGTAATGT
739325 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
739343 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
739359 AGTAAGAAAATGAA
1 AATAAGAAAATGAA
739373 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.68
17 3 0.11
18 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:739592 original size:13 final size:13
Alignment explanation
Indices: 739576--739616 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
739566 AGTCTTTTTC
739576 TTTTCTTTTTTGT
1 TTTTCTTTTTTGT
* *
739589 TTTTCTTCTTTCT
1 TTTTCTTTTTTGT
739602 TTTTCTCTTTTTGT
1 TTTTCT-TTTTTGT
739616 T
1 T
739617 GCTTTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTGT
Found at i:739612 original size:27 final size:24
Alignment explanation
Indices: 739568--739616 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
739558 GATGTAAGAG
739568 TCTTTTTCTTTTCTTTTTTGTTTT
1 TCTTTTTCTTTTCTTTTTTGTTTT
739592 TCTTCTTTCTTTTTCTCTTTTTGTT
1 TCTT-TTTC-TTTTCT-TTTTTGTT
739617 GCTTTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 6 0.27
27 8 0.36
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (24 bp):
TCTTTTTCTTTTCTTTTTTGTTTT
Found at i:743417 original size:16 final size:16
Alignment explanation
Indices: 743384--743432 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
743374 TAAGGTAATG
743384 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
743402 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
743418 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
743433 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:743662 original size:13 final size:13
Alignment explanation
Indices: 743646--743686 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
743636 AGTCTTTTTC
743646 TTTTCTTTTTTGT
1 TTTTCTTTTTTGT
* *
743659 TTTTCTTCTTTCT
1 TTTTCTTTTTTGT
743672 TTTTCTCTTTTTGT
1 TTTTCT-TTTTTGT
743686 T
1 T
743687 GCTTTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTGT
Found at i:743682 original size:27 final size:24
Alignment explanation
Indices: 743638--743686 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
743628 GATGTAGGAG
743638 TCTTTTTCTTTTCTTTTTTGTTTT
1 TCTTTTTCTTTTCTTTTTTGTTTT
743662 TCTTCTTTCTTTTTCTCTTTTTGTT
1 TCTT-TTTC-TTTTCT-TTTTTGTT
743687 GCTTTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 6 0.27
27 8 0.36
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (24 bp):
TCTTTTTCTTTTCTTTTTTGTTTT
Found at i:746072 original size:19 final size:21
Alignment explanation
Indices: 746029--746080 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
746019 GAAACCCCTT
746029 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
746050 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
746069 TGAAGATACATG
1 TGAAAATACATG
746081 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:750056 original size:19 final size:21
Alignment explanation
Indices: 750013--750064 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
750003 GAAACCCCTT
750013 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
750034 TGAAAGTACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
750053 TGAAGATACATG
1 TGAAAATACATG
750065 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:751259 original size:81 final size:81
Alignment explanation
Indices: 751124--751286 Score: 299
Period size: 81 Copynumber: 2.0 Consensus size: 81
751114 AGTATGGAAT
751124 AACTCCCTTAGAACCAGCTTTGAATAACATCCATGGTGTAATCAAGTCATGGAGAAAATTGGAGC
1 AACTCCCTTAGAACCAGCTTTGAATAACATCCATGGTGTAATCAAGTCATGGAGAAAATTGGAGC
*
751189 TAGATAGGATCACATC
66 TAGACAGGATCACATC
* *
751205 AACTCCCTTAGAACTAGCTTTGAATAACATCCATGGTGTGATCAAGTCATGGAGAAAATTGGAGC
1 AACTCCCTTAGAACCAGCTTTGAATAACATCCATGGTGTAATCAAGTCATGGAGAAAATTGGAGC
751270 TAGACAGGATCACATC
66 TAGACAGGATCACATC
751286 A
1 A
751287 TTTTCCCCTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (81 bp):
AACTCCCTTAGAACCAGCTTTGAATAACATCCATGGTGTAATCAAGTCATGGAGAAAATTGGAGC
TAGACAGGATCACATC
Found at i:756209 original size:16 final size:16
Alignment explanation
Indices: 756169--756217 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
756159 AAAGGTAAAG
*
756169 GAATAAGAATAGATAAAA
1 GAATAAGAA-A-ATGAAA
756187 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* *
756203 GAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
756218 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:756371 original size:17 final size:17
Alignment explanation
Indices: 756349--756383 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
756339 ACTTTGCAAC
756349 TTTGCTTCAAATTTTCT
1 TTTGCTTCAAATTTTCT
**
756366 TTTGCTTTGAATTTTCT
1 TTTGCTTCAAATTTTCT
756383 T
1 T
756384 CTTTTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (17 bp):
TTTGCTTCAAATTTTCT
Found at i:756455 original size:13 final size:13
Alignment explanation
Indices: 756439--756479 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
756429 AGTCTTTTTC
756439 TTTTCTTTTTTGT
1 TTTTCTTTTTTGT
* *
756452 TTTTCTTCTTTCT
1 TTTTCTTTTTTGT
756465 TTTTCTCTTTTTGT
1 TTTTCT-TTTTTGT
756479 T
1 T
756480 GCTATTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTGT
Found at i:756475 original size:27 final size:24
Alignment explanation
Indices: 756431--756479 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
756421 GATGTAGGAG
756431 TCTTTTTCTTTTCTTTTTTGTTTT
1 TCTTTTTCTTTTCTTTTTTGTTTT
756455 TCTTCTTTCTTTTTCTCTTTTTGTT
1 TCTT-TTTC-TTTTCT-TTTTTGTT
756480 GCTATTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 6 0.27
27 8 0.36
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (24 bp):
TCTTTTTCTTTTCTTTTTTGTTTT
Found at i:757341 original size:13 final size:12
Alignment explanation
Indices: 757322--757409 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 12
757312 ATATAGGCGT
757322 GATATGGTGATG
1 GATATGGTGATG
757334 GAATATGGTGAT-
1 G-ATATGGTGATG
*
757346 GATATAGGCG-T-
1 GATAT-GGTGATG
757357 GATAATGGTGATG
1 GAT-ATGGTGATG
757370 GACTATGGTGAT-
1 GA-TATGGTGATG
*
757382 GATATAGGCG-T-
1 GATAT-GGTGATG
757393 GATAATGGTGATG
1 GAT-ATGGTGATG
757406 GATA
1 GATA
757410 GATTGTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.34
12 17 0.27
13 23 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:757377 original size:36 final size:36
Alignment explanation
Indices: 757304--757407 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
757294 ATTTATAAGT
*
757304 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
757339 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
757375 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
757408 TAGATTGTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:761778 original size:33 final size:33
Alignment explanation
Indices: 761699--761802 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
761689 ATACAATCTG
* *
761699 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
761735 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
761768 TCCATTACCATTTCAACACCATTAA-ATCATCCT
1 TCCATCACCATATC-ACGCCAATAACATCATCCT
761801 TC
1 TC
761803 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 23 0.38
34 8 0.13
35 17 0.28
36 12 0.20
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:768604 original size:35 final size:36
Alignment explanation
Indices: 768557--768638 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
768547 ATTTATAAGT
* *
768557 TGGTGATAATATAGGCATGAT-ATGGTGTTGGAATA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAATA
* *
768592 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAATA
768628 TGGTGATGATA
1 TGGTGATGATA
768639 GGCATTAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 19 0.45
36 23 0.55
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGAATA
Found at i:773303 original size:29 final size:29
Alignment explanation
Indices: 773261--773322 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
773251 AATTATATCT
773261 TTGTAAGGATAGACTTTGTTTTAATGAAA
1 TTGTAAGGATAGACTTTGTTTTAATGAAA
773290 TTGTAAGGATAGACTTTGTTTTAATGAAA
1 TTGTAAGGATAGACTTTGTTTTAATGAAA
773319 TTGT
1 TTGT
773323 GAGAGTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (29 bp):
TTGTAAGGATAGACTTTGTTTTAATGAAA
Found at i:779102 original size:23 final size:23
Alignment explanation
Indices: 779066--779123 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
779056 AAAATCAGCA
779066 AAGAAAATAAAGCACTC-AAAAG
1 AAGAAAATAAAGCACTCGAAAAG
*
779088 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAT-AAAGCACTCGAAAAG
*
779112 AAGAAAAAAAAG
1 AAGAAAATAAAG
779124 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 13 0.42
24 11 0.35
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.09
Consensus pattern (23 bp):
AAGAAAATAAAGCACTCGAAAAG
Found at i:784510 original size:23 final size:23
Alignment explanation
Indices: 784465--784510 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
784455 TTATACCTAT
*
784465 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
784488 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
784511 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:789013 original size:23 final size:23
Alignment explanation
Indices: 788968--789013 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
788958 TTATACCTAT
*
788968 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
788991 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
789014 TTATACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:797815 original size:15 final size:15
Alignment explanation
Indices: 797795--797824 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
797785 TCAAAAGTCC
797795 AGCTCAAGTGAGCTA
1 AGCTCAAGTGAGCTA
797810 AGCTCAAGTGAGCTA
1 AGCTCAAGTGAGCTA
797825 TGAGCTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (15 bp):
AGCTCAAGTGAGCTA
Found at i:802117 original size:53 final size:52
Alignment explanation
Indices: 802012--802118 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 52
802002 ACGAAAAAAG
802012 AATATAAAATGAATCAACATTTTGAGGAGGTGTAAGGATTCATTCAAAGGCTTT
1 AATATAAAATGAATCAACATTTTGAGGAGGTGTAA-GA-TCATTCAAAGGCTTT
802066 AATATTAAAATGAATCAGAACATTTGTGAGGAGGTGT-A-A-CATTCAAAGGCTTT
1 AATA-TAAAATGAATC--AACATTT-TGAGGAGGTGTAAGATCATTCAAAGGCTTT
802119 TAAATTCATC
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
53 14 0.29
54 4 0.08
55 12 0.24
57 8 0.16
58 11 0.22
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (52 bp):
AATATAAAATGAATCAACATTTTGAGGAGGTGTAAGATCATTCAAAGGCTTT
Found at i:804138 original size:160 final size:162
Alignment explanation
Indices: 803970--804291 Score: 598
Period size: 162 Copynumber: 2.0 Consensus size: 162
803960 AGAAATTGAT
803970 GTGAGAAACGTTGGAGTCGAAAATGAGAAAGTTGAAAAGATTGAATTTGGGAGCAAA-GGGGATG
1 GTGAGAAACGTTGGAGTCGAAAATGAGAAAGTTGAAAAGATTGAATTTGGGAGCAAAGGGGGATG
804034 TACGTGTGGAAGAG-AAATGAAAGGATTACAAGTGAGGTTGTGGTTAAAAGATATGATGGAGTTG
66 TACGTGTGGAAGAGAAAATGAAAGGATTACAAGTGAGGTTGTGGTTAAAAGATATGATGGAGTTG
804098 AACATGAACAAATC-AAGAAGA-ACTTGTGAGAA
131 AACATGAACAAATCAAAGAA-ACA-TTGTGAGAA
804130 GTGAGAAACGTTGGAGTCGAAAATGAGAAAGTTGAAAAGATTGAATTTGGGAGCAAAGGGGGATG
1 GTGAGAAACGTTGGAGTCGAAAATGAGAAAGTTGAAAAGATTGAATTTGGGAGCAAAGGGGGATG
804195 TACGTGTGGAAGAGAAAATGAAAGGATTACAAGTGAGGTTGTGGTTAAAAGATATGATGGAGTTG
66 TACGTGTGGAAGAGAAAATGAAAGGATTACAAGTGAGGTTGTGGTTAAAAGATATGATGGAGTTG
804260 AACATGAACAAATCAAAGAAACATTGTGAGAA
131 AACATGAACAAATCAAAGAAACATTGTGAGAA
804292 AACCAAGACA
Statistics
Matches: 158, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 57 0.36
161 21 0.13
162 74 0.47
163 6 0.04
ACGTcount: A:0.41, C:0.06, G:0.32, T:0.22
Consensus pattern (162 bp):
GTGAGAAACGTTGGAGTCGAAAATGAGAAAGTTGAAAAGATTGAATTTGGGAGCAAAGGGGGATG
TACGTGTGGAAGAGAAAATGAAAGGATTACAAGTGAGGTTGTGGTTAAAAGATATGATGGAGTTG
AACATGAACAAATCAAAGAAACATTGTGAGAA
Found at i:817595 original size:45 final size:43
Alignment explanation
Indices: 817530--817651 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 43
817520 AATAAAATCT
*
817530 CTTACCATT-TCCCATAAGCTCGTAAGCTTATTTACC-AAATA
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTACCTAAATA
* *
817571 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTA-TTTACCTAAATA
* * *
817618 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
817652 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
41 7 0.10
42 2 0.03
43 3 0.04
44 20 0.29
45 20 0.29
46 7 0.10
47 10 0.14
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (43 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTACCTAAATA
Found at i:817800 original size:40 final size:40
Alignment explanation
Indices: 817756--817916 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
817746 ACCGTAGTGC
817756 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
817796 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
817836 TACACATAA-GTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
817875 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
817915 TA
1 TA
817917 TAAACCTGCA
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 38 0.32
40 79 0.68
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:817893 original size:79 final size:80
Alignment explanation
Indices: 817756--817916 Score: 297
Period size: 79 Copynumber: 2.0 Consensus size: 80
817746 ACCGTAGTGC
817756 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCATGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCATGCCCACCATA
817821 TACACCGAAGTGTAT
66 TACACCGAAGTGTAT
*
817836 TACACATAA-GTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCATGCCCACCATA
*
817900 TACATCGAAGTGTAT
66 TACACCGAAGTGTAT
817915 TA
1 TA
817917 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 70 0.89
80 9 0.11
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (80 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCATGCCCACCATA
TACACCGAAGTGTAT
Found at i:831676 original size:47 final size:45
Alignment explanation
Indices: 831606--831731 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
831596 TATAAAATCT
*
831606 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
831651 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
831698 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
831732 ACATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:831880 original size:40 final size:40
Alignment explanation
Indices: 831836--831996 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
831826 ACCGTAGTGC
831836 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
831876 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
831916 TACACATAA-GTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
831955 TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
831995 TA
1 TA
831997 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
39 39 0.33
40 80 0.67
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:831968 original size:79 final size:80
Alignment explanation
Indices: 831836--831996 Score: 306
Period size: 79 Copynumber: 2.0 Consensus size: 80
831826 ACCGTAGTGC
831836 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
*
831901 TACACCGAAGTGTAT
66 CACACCGAAGTGTAT
831916 TACACATAA-GTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
831980 CACACCGAAGTGTAT
66 CACACCGAAGTGTAT
831995 TA
1 TA
831997 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 71 0.89
80 9 0.11
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (80 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
CACACCGAAGTGTAT
Found at i:840065 original size:16 final size:16
Alignment explanation
Indices: 840032--840080 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
840022 TAAGGTAATG
840032 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
840050 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
840066 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
840081 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:840299 original size:12 final size:12
Alignment explanation
Indices: 840282--840329 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
840272 TGTAGGAGTC
840282 TTTTTCTTTTCT
1 TTTTTCTTTTCT
840294 TTTTTCTTTT-T
1 TTTTTCTTTTCT
840305 TTTTTCTTCTTTCT
1 TTTTTC-T-TTTCT
840319 TTTTCTCTTTT
1 TTTT-TCTTTT
840330 TGTTGCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.22
12 11 0.34
13 6 0.19
14 6 0.19
15 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:840303 original size:18 final size:18
Alignment explanation
Indices: 840280--840324 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
840270 GATGTAGGAG
*
840280 TCTTTTTCTTTTCTTTTT
1 TCTTTTTCTTTTCTTCTT
*
840298 TCTTTTTTTTTTCTTCTT
1 TCTTTTTCTTTTCTTCTT
840316 TCTTTTTCT
1 TCTTTTTCT
840325 CTTTTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TCTTTTTCTTTTCTTCTT
Found at i:844719 original size:16 final size:16
Alignment explanation
Indices: 844681--844721 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
844671 CTTTATTATC
*
844681 TTATTTCATCTTCCGT
1 TTATTTTATCTTCCGT
**
844697 TTATTTTATCTTTTGT
1 TTATTTTATCTTCCGT
844713 TTATTTTAT
1 TTATTTTAT
844722 TCTAATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (16 bp):
TTATTTTATCTTCCGT
Found at i:845083 original size:8 final size:8
Alignment explanation
Indices: 845070--845106 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
845060 TATTTTTTTC
845070 CAAAAAAA
1 CAAAAAAA
845078 CAAAAAAA
1 CAAAAAAA
845086 CAAAAAAA
1 CAAAAAAA
*
845094 -AAACAAA
1 CAAAAAAA
845101 -AAAAAA
1 CAAAAAA
845107 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 11 0.41
8 16 0.59
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:845113 original size:11 final size:10
Alignment explanation
Indices: 845071--845106 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
845061 ATTTTTTTCC
845071 AAAAAAACAA
1 AAAAAAACAA
*
845081 AAAAACA-AA
1 AAAAAAACAA
845090 AAAAAAACAA
1 AAAAAAACAA
845100 AAAAAAA
1 AAAAAAA
845107 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:845113 original size:12 final size:11
Alignment explanation
Indices: 845079--845106 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
845069 CCAAAAAAAC
845079 AAAAAAACAAA
1 AAAAAAACAAA
845090 AAAAAAACAAA
1 AAAAAAACAAA
845101 AAAAAA
1 AAAAAA
845107 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:851350 original size:11 final size:13
Alignment explanation
Indices: 851318--851347 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
851308 TGGCCAAAGA
851318 TGAAAAGGTATGT
1 TGAAAAGGTATGT
851331 TGAAAAGGTATG-
1 TGAAAAGGTATGT
851343 TGAAA
1 TGAAA
851348 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:854815 original size:22 final size:22
Alignment explanation
Indices: 854788--854841 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
854778 GGAAGAAGAC
854788 CCATGTGCATTCATGTAGG-TT
1 CCATGTGCATTCATGTAGGCTT
* *
854809 GTCATGTTCATTCATGTAGGCTT
1 -CCATGTGCATTCATGTAGGCTT
854832 CCATGTGCAT
1 CCATGTGCAT
854842 GATTCAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (22 bp):
CCATGTGCATTCATGTAGGCTT
Found at i:855051 original size:22 final size:19
Alignment explanation
Indices: 855008--855060 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
854998 TTGGCAAGAG
*
855008 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
855027 CATGTATTTTCATTAAACAAAT
1 CATGTATTTTCATT--A-AAAT
855049 CATGTATTTTCA
1 CATGTATTTTCA
855061 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
21 1 0.03
22 16 0.53
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:857548 original size:23 final size:21
Alignment explanation
Indices: 857522--857569 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
857512 TTATATATGG
857522 TTATAATAAT-AATCTTTAATTCA
1 TTATAAT-ATGAAT-TTTAATT-A
857545 TTATAATATGAATTTTAATTA
1 TTATAATATGAATTTTAATTA
857566 TTAT
1 TTAT
857570 TGTAGCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.21
22 9 0.38
23 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATAATATGAATTTTAATTA
Found at i:860535 original size:33 final size:33
Alignment explanation
Indices: 860491--860559 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
860481 CATCACCATA
*
860491 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
860524 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
860557 TTC
1 TTC
860560 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:866204 original size:33 final size:33
Alignment explanation
Indices: 866125--866228 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
866115 ATACAATCTG
* *
866125 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
866161 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
866194 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
866227 TC
1 TC
866229 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:867181 original size:24 final size:25
Alignment explanation
Indices: 867135--867183 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
867125 ATTTTGTTAA
867135 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGA-CCTTACATCAAGT
867161 GGCATCAGAAGA-CTTACATCAAG
1 GGCATCAGAAGACCTTACATCAAG
867184 CGGTAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.48
26 12 0.52
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (25 bp):
GGCATCAGAAGACCTTACATCAAGT
Found at i:867334 original size:27 final size:28
Alignment explanation
Indices: 867292--867354 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
867282 AGAAAATCAG
*
867292 AAAAGAAATTGAAGCACTCCAAAAGAAA
1 AAAAGAAATTGAAGCACTCAAAAAGAAA
* * *
867320 AAAAGAAATT-CAGCATTCAAAAAGAAG
1 AAAAGAAATTGAAGCACTCAAAAAGAAA
867347 AAAAGAAA
1 AAAAGAAA
867355 AGAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11
Consensus pattern (28 bp):
AAAAGAAATTGAAGCACTCAAAAAGAAA
Found at i:871596 original size:24 final size:26
Alignment explanation
Indices: 871553--871602 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
871543 AATTTGTTAA
871553 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
871579 GGCATCAG-A-AGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
871603 TGGCTGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.62
25 1 0.04
26 8 0.33
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (26 bp):
GGCATCAGAAGAGCCTTACATCAAGT
Found at i:875121 original size:5 final size:6
Alignment explanation
Indices: 875084--875119 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
875074 CAAAAAAATG
875084 AGAAAGA AG-AAA AGAAAA AGAAAA AGAAAA AGAAAA
1 AGAAA-A AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
875120 GACTCCTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 3 0.11
6 23 0.82
7 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:877566 original size:412 final size:412
Alignment explanation
Indices: 876802--877630 Score: 1633
Period size: 412 Copynumber: 2.0 Consensus size: 412
876792 CCCATCTTTC
876802 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTCATGTGAATGATAAAGTAT
1 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTCATGTGAATGATAAAGTAT
*
876867 GCCTTGTAGCCATTGATGGTGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTTG
66 GCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTTG
876932 GGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGTT
131 GGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGTT
876997 AGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGTG
196 AGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGTG
877062 ATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGCA
261 ATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGCA
877127 TTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTCC
326 TTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTCC
877192 AATGTGCCCAAATCAAGTCCAT
391 AATGTGCCCAAATCAAGTCCAT
877214 GAATGGATTACGGACAGCAAAGGAGGAATCCA-TTCATACTCGTTTTCATGTGAATGATAAAGTA
1 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCG-TTTCATGTGAATGATAAAGTA
877278 TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
65 TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
877343 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
130 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
877408 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
195 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
877473 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
260 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
877538 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
325 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
877603 CAATGTGCCCAAATCAAGTCCAT
390 CAATGTGCCCAAATCAAGTCCAT
877626 GAATG
1 GAATG
877631 CCAAGTTATC
Statistics
Matches: 415, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
411 10 0.02
412 405 0.98
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (412 bp):
GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTCATGTGAATGATAAAGTAT
GCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTTG
GGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGTT
AGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGTG
ATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGCA
TTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTCC
AATGTGCCCAAATCAAGTCCAT
Found at i:880973 original size:65 final size:65
Alignment explanation
Indices: 880843--880966 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 65
880833 TGACCAGCCC
*
880843 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCTCTCCCTATTCGACCAAG
1 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGACCAAG
* * *
880908 CCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCTCTCCCTATTCG
1 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCG
880967 GGCAAGCATC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (65 bp):
CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGACCAAG
Found at i:881822 original size:9 final size:9
Alignment explanation
Indices: 881798--881830 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
881788 ACTCAAGAGC
881798 AAGAAAA-A
1 AAGAAAAGA
881806 AA-AAAAGA
1 AAGAAAAGA
881814 AAGAAAAGA
1 AAGAAAAGA
881823 AAGAAAAG
1 AAGAAAAG
881831 TTGGAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.17
8 5 0.22
9 14 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:887402 original size:27 final size:28
Alignment explanation
Indices: 887372--887424 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
887362 CCACGTCTAC
*
887372 TTAGATTTATAT-TATGTTTACATATGT
1 TTAGATTCATATATATGTTTACATATGT
* *
887399 TTAGATTCATTTATATGTTTGCATAT
1 TTAGATTCATATATATGTTTACATAT
887425 CATTTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (28 bp):
TTAGATTCATATATATGTTTACATATGT
Found at i:888032 original size:58 final size:58
Alignment explanation
Indices: 887925--888034 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
887915 GGACCATACC
* ** * *
887925 ACACGTTGGGATAGTTTGGTGGAGCATTTTGAAGACATATACAGGTCACAAACAGATG
1 ACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATG
* **
887983 ACACGTTGGGACAACTTGGTGGAGCATTTGGGAGACATATATTGCTCACAAA
1 ACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAA
888035 TAGCTCACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (58 bp):
ACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATG
Done.