Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014663.1 Corchorus capsularis cultivar CVL-1 contig14684, 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: 94326
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5389 original size:136 final size:136
Alignment explanation
Indices: 5145--5416 Score: 445
Period size: 136 Copynumber: 2.0 Consensus size: 136
5135 CCGGAGATGA
* * * * * * * *
5145 GTGATAATCTTATAAATTCGAGTACGTGGGAGTTATCATGTTAAATCACACATATAATCATATAT
1 GTGATAATCTTATAAACTCGAGTACGTGGGAATTAACACGCTAAATCAAAAATATAATCATATAC
* *
5210 TCATTCTGAAACTCTATCATAATCAATTTTTAGAAGTTCATATCTACTCAAAAAATAAATAAAAA
66 TCATTCTGAAACCCTATCATAATCAATTTTTAGAAGTCCATATCTACTCAAAAAATAAATAAAAA
5275 ATTTAT
131 ATTTAT
5281 GTGATAATCTTATAAACTCGAGTACGTGGGAATTAACACGCTAAATCAAAAATATAATCATATAC
1 GTGATAATCTTATAAACTCGAGTACGTGGGAATTAACACGCTAAATCAAAAATATAATCATATAC
*
5346 TCATTCTGAAACCCTATCATAATTAATTTTTAGAAGTCCATATCTACTCAAAAAATAAATAAAAA
66 TCATTCTGAAACCCTATCATAATCAATTTTTAGAAGTCCATATCTACTCAAAAAATAAATAAAAA
5411 ATTTAT
131 ATTTAT
5417 TTGGGGCTAA
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (136 bp):
GTGATAATCTTATAAACTCGAGTACGTGGGAATTAACACGCTAAATCAAAAATATAATCATATAC
TCATTCTGAAACCCTATCATAATCAATTTTTAGAAGTCCATATCTACTCAAAAAATAAATAAAAA
ATTTAT
Found at i:8543 original size:211 final size:211
Alignment explanation
Indices: 8173--8569 Score: 704
Period size: 211 Copynumber: 1.9 Consensus size: 211
8163 TTTTTTTTTT
* * *
8173 CCAGAAACTTCAAATTGAAGCTTTTTCTAGAAATCCTTTTCAGAAGCACTTATGTCAATAGATAA
1 CCAGAAACTTCAAATTGAAACTTTTTCCAGAAATCATTTTCAGAAGCACTTATGTCAATAGATAA
8238 GTTAGGCCAAACAGAAGCGAGAGCCGAGCTTGAGGGAGAAAATGGGACCATATTTTTGTGAGAGA
66 GTTAGGCCAAACAGAAGCGAGAGCCGAGCTTGAGGGAGAAAATGGGACCATATTTTTGTGAGAGA
*
8303 GTACGGTGGAAGCAATGGAGACATGGCCAATAATGGGAAGTGATTTAGGTGGGCTTTCGGGGGGG
131 GTACGGTGGAAGCAATGGAGACATGGCCAATAAAGGGAAGTGATTTAGGTGGGCTTTCGGGGGGG
8368 GTTTTTTTAATAAAAG
196 GTTTTTTTAATAAAAG
* * *
8384 CCAGAAACTTTAAATTGAAACTTTTTCCATAAATCATTTTTAGAAGCACTTATGTCAATAGATAA
1 CCAGAAACTTCAAATTGAAACTTTTTCCAGAAATCATTTTCAGAAGCACTTATGTCAATAGATAA
*
8449 GTTAGGTCAAACAGAAGCGAGAGCCGAGCTTGAGGGAGAAAATGGGACCATATTTTTGTGAGAGA
66 GTTAGGCCAAACAGAAGCGAGAGCCGAGCTTGAGGGAGAAAATGGGACCATATTTTTGTGAGAGA
* *
8514 GTACGGTGGAAGCGATGGAGACGTGGCCAATAAAGGGAAGTGATTTAGGTGGGCTT
131 GTACGGTGGAAGCAATGGAGACATGGCCAATAAAGGGAAGTGATTTAGGTGGGCTT
8570 GGTCTAGGTT
Statistics
Matches: 176, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
211 176 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (211 bp):
CCAGAAACTTCAAATTGAAACTTTTTCCAGAAATCATTTTCAGAAGCACTTATGTCAATAGATAA
GTTAGGCCAAACAGAAGCGAGAGCCGAGCTTGAGGGAGAAAATGGGACCATATTTTTGTGAGAGA
GTACGGTGGAAGCAATGGAGACATGGCCAATAAAGGGAAGTGATTTAGGTGGGCTTTCGGGGGGG
GTTTTTTTAATAAAAG
Found at i:9482 original size:34 final size:35
Alignment explanation
Indices: 9437--9505 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
9427 TTTTTTTTTC
**
9437 TTTTTTCTTTTTTTCCTTAATGCCAATTTCTTTGA
1 TTTTTTCTTTTTTTCCAGAATGCCAATTTCTTTGA
**
9472 TTTTTT-TTTTTTTTGAGAATGCCAATTTCTTTGA
1 TTTTTTCTTTTTTTCCAGAATGCCAATTTCTTTGA
9506 CTAACTGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (35 bp):
TTTTTTCTTTTTTTCCAGAATGCCAATTTCTTTGA
Found at i:12678 original size:25 final size:27
Alignment explanation
Indices: 12626--12678 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12616 TTACTAAACT
**
12626 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
12653 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
12678 A
1 A
12679 TCTAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:13778 original size:31 final size:31
Alignment explanation
Indices: 13715--13780 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
13705 AACTATATGT
* *
13715 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
13746 TTTCCAATTGTA-CCTT-TTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTATTTTT--AAAACATA
13777 TTTC
1 TTTC
13781 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.16
30 4 0.13
31 22 0.71
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:15231 original size:19 final size:19
Alignment explanation
Indices: 15209--15245 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15199 TCTATTATTT
15209 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
15228 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
15246 AATATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:15485 original size:22 final size:22
Alignment explanation
Indices: 15409--15491 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
15399 CTTGTCTCTA
15409 TGTGGTTATC-AAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
* * *
15431 -ATGGTTATTATAATTTC--A-
1 TGTGGTTATCAAAATTTCATAG
* *
15449 TG-GGTTACCAGAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
15470 TGTGGTTATCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
15492 GATCAGGTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 12 0.26
19 1 0.02
20 1 0.02
21 9 0.20
22 23 0.50
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:15507 original size:24 final size:23
Alignment explanation
Indices: 15460--15549 Score: 71
Period size: 22 Copynumber: 4.0 Consensus size: 23
15450 GGGTTACCAG
*
15460 AATTTCATAGTG-T-GGTTATCAA
1 AATTTCATAG-GATAGGTTATTAA
15482 AATTTCATAGGATCAGGTTATTAA
1 AATTTCATAGGAT-AGGTTATTAA
* * * *
15506 AATCTCTTAGG-TTGGTTATTGA
1 AATTTCATAGGATAGGTTATTAA
*
15528 AATTTTATAGGAT-GGTTCATTA
1 AATTTCATAGGATAGGTT-ATTA
15550 TCACAATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 31 0.57
23 5 0.09
24 17 0.31
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (23 bp):
AATTTCATAGGATAGGTTATTAA
Found at i:15770 original size:22 final size:22
Alignment explanation
Indices: 15582--15971 Score: 158
Period size: 22 Copynumber: 17.7 Consensus size: 22
15572 TCAAAGAGGC
* * * *
15582 TATCAAAATGTCATAGTGTGGT
1 TATCAAAATTTCATAGAGAGAT
* *
15604 TAACAAAATTTCATTAG-GAGGT
1 TATCAAAATTTCA-TAGAGAGAT
* * * *
15626 TA-CTAATATTTCATGGGGAGGT
1 TATC-AAAATTTCATAGAGAGAT
* * * *
15648 TATCAAAATTTTATAGTGTGGT
1 TATCAAAATTTCATAGAGAGAT
*
15670 TATCAAAATTTCATATGA-AGGTAA
1 TATCAAAATTTCATA-GAGA-G-AT
* ** *
15694 AAGTCTGAATTTCATA-AGA-AA
1 TA-TCAAAATTTCATAGAGAGAT
* * *
15715 TACCAAAATTTGATAGA-AGGT
1 TATCAAAATTTCATAGAGAGAT
* *
15736 TATC-AAATCTCATAGAGTGAT
1 TATCAAAATTTCATAGAGAGAT
*
15757 TATCTAAATTTCATAGAGATCGGAT
1 TATCAAAATTTCATAGAGA---GAT
*
15782 TATCAAAATTT-ATAGAAAGAT
1 TATCAAAATTTCATAGAGAGAT
* *
15803 TATCAAAATTTCATAGTGTTG-T
1 TATCAAAATTTCATAGAG-AGAT
* * *
15825 T-TCAAAATTTCAAAGCGAGGT
1 TATCAAAATTTCATAGAGAGAT
* *
15846 TATCAAAATTACATA-ATGTGAT
1 TATCAAAATTTCATAGA-GAGAT
* * * *
15868 TATTAGAATTTCATAGAGGGGT
1 TATCAAAATTTCATAGAGAGAT
* * * *
15890 CAACAAAATTTTATAAAGAGAT
1 TATCAAAATTTCATAGAGAGAT
* *
15912 TATCAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAGAGAGAT
* * *
15934 TATCAAATTTTCA-AAATATGAT
1 TATCAAAATTTCATAGAGA-GAT
15956 TA-CAAAAATTTCATAG
1 TATC-AAAATTTCATAG
15972 TGGTACTTAT
Statistics
Matches: 276, Mismatches: 67, Indels: 49
0.70 0.17 0.12
Matches are distributed among these distances:
20 21 0.08
21 51 0.18
22 162 0.59
23 10 0.04
24 8 0.03
25 24 0.09
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGAGAT
Found at i:15831 original size:109 final size:109
Alignment explanation
Indices: 15718--15926 Score: 252
Period size: 109 Copynumber: 1.9 Consensus size: 109
15708 TAAGAAATAC
* *
15718 CAAAATTTGATAG-AAGGTTATC-AAATCT-CATAGA-GTGATTATCTA-AATTTCATAGAGATC
1 CAAAATTTCAAAGCAAGGTTATCAAAAT-TACATA-ATGTGATTAT-TAGAATTTCATAGAG---
* *
15778 GGATTATCAAAA-TTTATAGAA-AGATTATCAAAATTTCATAGTGTTGTTT
60 GGATCAACAAAATTTTATA-AAGAGATTATCAAAATTTCATAGTGTTGTTT
* *
15827 CAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGATTATTAGAATTTCATAGAGGGGTCA
1 CAAAATTTCAAAGCAAGGTTATCAAAATTACATAATGTGATTATTAGAATTTCATAGAGGGATCA
15892 ACAAAATTTTATAAAGAGATTATCAAAATTTCATA
66 ACAAAATTTTATAAAGAGATTATCAAAATTTCATA
15927 AAGAGGTTAT
Statistics
Matches: 87, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
108 11 0.13
109 36 0.41
110 12 0.14
111 28 0.32
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (109 bp):
CAAAATTTCAAAGCAAGGTTATCAAAATTACATAATGTGATTATTAGAATTTCATAGAGGGATCA
ACAAAATTTTATAAAGAGATTATCAAAATTTCATAGTGTTGTTT
Found at i:16072 original size:20 final size:20
Alignment explanation
Indices: 16047--16084 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16037 TTTTATTATA
*
16047 GAGGATATCAAAATTTCAGG
1 GAGGATACCAAAATTTCAGG
16067 GAGGATACCAAAATTTCA
1 GAGGATACCAAAATTTCA
16085 TATGAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (20 bp):
GAGGATACCAAAATTTCAGG
Found at i:16128 original size:248 final size:247
Alignment explanation
Indices: 15913--16473 Score: 662
Period size: 248 Copynumber: 2.2 Consensus size: 247
15903 TAAAGAGATT
* * * * *
15913 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAAT-ATGATTA-CAAAAATTTCATAGTGGT
1 ATCAAAATATCATAAAGAGATTAACAAAATTTCAAAATGA-GATTATC-AAAATTTAATAGTGGT
*
15976 ACTTATGGGGAGTTTATCAAAATTTCATAGTATGATTACCAAATTAGGAAGGTTATTAAACTTTT
64 ACTTATGGGGAGGTTATCAAAATTTCATAGTATGATTACCAAATTAGGAAGGTTATTAAACTTTT
16041 ATTATAGAGGATATCAAAATTTCAGGGAGGATACCAAAATTTCATATGAAAGTTATCAAAATTTC
129 ATTATAGAGGA-ATCAAAATTTCAGGGAGGATACCAAAATTTCATATGAAAGTTATCAAAATTTC
* *
16106 ATAGTTTAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTACGTAG
193 ATAGTTTAGTTTTCAAAATTTCATAAGAGGGTCAACAAAATTTCATAGTACGTAG
** * * *
16161 ATCAAAATATCATAGGGAGATTAAGAAAATTTCATAATGAGATTATCAAAATTTAATAGTGGTAT
1 ATCAAAATATCATAAAGAGATTAACAAAATTTCAAAATGAGATTATCAAAATTTAATAGTGGTAC
* *
16226 TTATGGGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAGCTTTTAT
66 TTATGGGGAGGTTATCAAAATTTCATAGTATGATTACCAAATTAGGAAGGTTATTAAACTTTTAT
* * * *
16291 TATGGAGTAATCAAAATTTCAGGGAGGATATCAAAA-TTCAGGGAGGATATCAAAATTCGGGGAG
131 TATAGAGGAATCAAAATTTCAGGGAGGATACCAAAATTTC-------ATAT--GAA-------AG
* * * * * *
16355 AATATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGGTTATCAAGATTTCGTAGTAT
180 -TTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGGTCAACAAAATTTCATAGTAC
16420 GTAG
244 GTAG
** *
16424 ATC-AAATATCATAGGGAGATTAACAAAATTTCATAATGAGATTATCAAAA
1 ATCAAAATATCATAAAGAGATTAACAAAATTTCAAAATGAGATTATCAAAA
16474 AAATCATAAG
Statistics
Matches: 272, Mismatches: 22, Indels: 24
0.86 0.07 0.08
Matches are distributed among these distances:
246 3 0.01
247 26 0.10
248 120 0.44
249 2 0.01
253 4 0.01
255 2 0.01
262 48 0.18
263 67 0.25
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (247 bp):
ATCAAAATATCATAAAGAGATTAACAAAATTTCAAAATGAGATTATCAAAATTTAATAGTGGTAC
TTATGGGGAGGTTATCAAAATTTCATAGTATGATTACCAAATTAGGAAGGTTATTAAACTTTTAT
TATAGAGGAATCAAAATTTCAGGGAGGATACCAAAATTTCATATGAAAGTTATCAAAATTTCATA
GTTTAGTTTTCAAAATTTCATAAGAGGGTCAACAAAATTTCATAGTACGTAG
Found at i:16166 original size:44 final size:43
Alignment explanation
Indices: 16075--16174 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
16065 GGGAGGATAC
* **
16075 CAAAATTTCATATGAAAGTTATCAAAATTTCATAGTTTAGTTTT
1 CAAAATTTCATAAGAAAGTTATCAAAATTTCATAG-TTAGTGAT
**
16119 CAAAATTTCATAAGAGGGTTATCAAAATTTCATAG-TACGTAGAT
1 CAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTA-GT-GAT
*
16163 CAAAATATCATA
1 CAAAATTTCATA
16175 GGGAGATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 2 0.04
44 44 0.92
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (43 bp):
CAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTAGTGAT
Found at i:16211 original size:22 final size:22
Alignment explanation
Indices: 16075--16214 Score: 92
Period size: 22 Copynumber: 6.4 Consensus size: 22
16065 GGGAGGATAC
*
16075 CAAAATTTCAT-ATGAAAGTTAT
1 CAAAATTTCATAATGAGA-TTAT
* * *
16097 CAAAATTTCATAGTTTAG-TTTT
1 CAAAATTTCATA-ATGAGATTAT
*
16119 CAAAATTTCATAA-GAGGGTTAT
1 CAAAATTTCATAATGA-GATTAT
* *
16141 CAAAATTTCATAGT-ACG-TAGAT
1 CAAAATTTCATAATGA-GAT-TAT
* ** *
16163 CAAAATATCATAGGGAGATTAA
1 CAAAATTTCATAATGAGATTAT
*
16185 GAAAATTTCATAATGAGATTAT
1 CAAAATTTCATAATGAGATTAT
16207 CAAAATTT
1 CAAAATTT
16215 AATAGTGGTA
Statistics
Matches: 90, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 83 0.92
23 2 0.02
24 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAATGAGATTAT
Found at i:16330 original size:19 final size:19
Alignment explanation
Indices: 16300--16366 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
16290 TTATGGAGTA
16300 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
16320 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
* *
16339 ATCAAAATTCGGGGAGAAT
1 ATCAAAATTCAGGGAGGAT
16358 ATCAAAATT
1 ATCAAAATT
16367 TCATAGTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 38 0.84
20 7 0.16
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:16406 original size:22 final size:22
Alignment explanation
Indices: 16381--16630 Score: 64
Period size: 22 Copynumber: 11.6 Consensus size: 22
16371 AGTTTAGTTT
16381 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * * *
16403 TCAAGATTTCGT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
*
16425 TC-AAATATCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
* *
16446 ACAAAATTTCATAATGA-GATTA
1 TCAAAATTTCATAA-GAGGGTTA
**
16468 TCAAAAAAATCATAAG-GAGGTTA
1 TC-AAAATTTCATAAGAG-GGTTA
*
16491 TCAAAATTT-GT---A-G-TTA
1 TCAAAATTTCATAAGAGGGTTA
* * **
16507 TCAAGATTTCATGAGAAAG-TA
1 TCAAAATTTCATAAGAGGGTTA
* * *
16528 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA-AGAGGGTTA
* * **
16551 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
*
16574 TCAAAATTTCAT-AGCGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
* * *
16596 TCACAATTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAGAG-GGTTA
16618 TCAAAATTTCATA
1 TCAAAATTTCATA
16631 GTGTGATTAC
Statistics
Matches: 164, Mismatches: 40, Indels: 47
0.65 0.16 0.19
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
20 1 0.01
21 29 0.18
22 70 0.43
23 49 0.30
24 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:16552 original size:23 final size:23
Alignment explanation
Indices: 16526--16807 Score: 138
Period size: 22 Copynumber: 12.7 Consensus size: 23
16516 CATGAGAAAG
*
16526 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGAGGTT
* * *
16549 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGGAGGTT
*
16572 TATCAAAATTTCATAGCGAGG-T
1 TATCAAAATTTCATAGGGAGGTT
* * * *
16594 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAGGGAGGTT
* * *
16616 TATCAAAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAGGGAGGTT
**
16638 TA-CTAACAA-TTCATATAGAGGTT
1 TATC-AA-AATTTCATAGGGAGGTT
* * * *
16661 T-TTAAATTTTCATAGCGTGG-T
1 TATCAAAATTTCATAGGGAGGTT
* * *
16682 TATCAATATATCATATGGAGG-T
1 TATCAAAATTTCATAGGGAGGTT
* * ***
16704 TATCAACATCTCATAGTTTTGG-T
1 TATCAAAATTTCATAG-GGAGGTT
* *
16727 TATCAAAATTTCATTGGGAAG-T
1 TATCAAAATTTCATAGGGAGGTT
** * *
16749 TATCAAAATTTCATATTGTGGTC
1 TATCAAAATTTCATAGGGAGGTT
* *
16772 T-TCAAAATTCCTTAGGGAGG-T
1 TATCAAAATTTCATAGGGAGGTT
*
16793 TAACAAAATTTCATA
1 TATCAAAATTTCATA
16808 AGAAGGTTAA
Statistics
Matches: 195, Mismatches: 54, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
21 6 0.03
22 129 0.66
23 60 0.31
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (23 bp):
TATCAAAATTTCATAGGGAGGTT
Found at i:16800 original size:44 final size:45
Alignment explanation
Indices: 16526--16807 Score: 163
Period size: 44 Copynumber: 6.3 Consensus size: 45
16516 CATGAGAAAG
* * * * * * *
16526 TATCAAAATTTTATAG-GGAGGTTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGTTGTGG-TTATCAAAATTTCATTGGGAG-GT
* * * * * * *
16572 TATCAAAATTTCATAG-CGAGGTTATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTTGTGGTTATCAAAATTTCATTGGGAGGT
* *
16616 TATCAAAATTTCATAG-TGTGATTA-CTAACAA-TTCATAT-AGAGGT
1 TATCAAAATTTCATAGTTGTGGTTATC-AA-AATTTCAT-TGGGAGGT
* * * * * *
16660 TTTTAAATTTTCATAG-CGTGGTTATCAATATATCATAT-GGAGGT
1 TATCAAAATTTCATAGTTGTGGTTATCAAAATTTCAT-TGGGAGGT
* * * *
16704 TATCAACATCTCATAGTTTTGGTTATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAGTTGTGGTTATCAAAATTTCATTGGGAGGT
*
16749 TATCAAAATTTCATA-TTGTGGTCT-TCAAAA-TTCCTTAGGGAGGT
1 TATCAAAATTTCATAGTTGTGGT-TATCAAAATTTCATT-GGGAGGT
*
16793 TAACAAAATTTCATA
1 TATCAAAATTTCATA
16808 AGAAGGTTAA
Statistics
Matches: 187, Mismatches: 40, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
43 7 0.04
44 107 0.57
45 54 0.29
46 19 0.10
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (45 bp):
TATCAAAATTTCATAGTTGTGGTTATCAAAATTTCATTGGGAGGT
Found at i:16814 original size:22 final size:22
Alignment explanation
Indices: 16724--16896 Score: 88
Period size: 22 Copynumber: 7.9 Consensus size: 22
16714 TCATAGTTTT
**
16724 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
* *
16747 -GTTATCAAAATTTCATATTG-T
1 GGTTATCAAAATTTCATA-AGAA
* * * *
16768 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
16790 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** *
16812 GGTTAAAAAAAATTT-ATAAAAA
1 GGTT-ATCAAAATTTCATAAGAA
* * *
16834 GGTTCTCGAAA-TTC-TATAGTAT
1 GGTTATCAAAATTTCATA-AG-AA
* * *
16856 CGTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
16878 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
16897 TGGGATCATA
Statistics
Matches: 110, Mismatches: 29, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
20 4 0.04
21 7 0.06
22 83 0.75
23 14 0.13
24 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:21479 original size:39 final size:39
Alignment explanation
Indices: 21425--21501 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
21415 TATAGTATTT
* *
21425 TAGGGATTGCAAGAACTTTGGAA-GAGATGAGAGGGAAAA
1 TAGGGATTCCAAGAACTTT-GAATGAGATGAAAGGGAAAA
21464 TAGGGATTCCAAGAACTTTGAATGAGATGAAAGGGAAA
1 TAGGGATTCCAAGAACTTTGAATGAGATGAAAGGGAAA
21502 GTAGAAGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 3 0.09
39 32 0.91
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (39 bp):
TAGGGATTCCAAGAACTTTGAATGAGATGAAAGGGAAAA
Found at i:22205 original size:121 final size:121
Alignment explanation
Indices: 21991--22211 Score: 345
Period size: 121 Copynumber: 1.8 Consensus size: 121
21981 AGAAGGTCTT
* *
21991 TTGGTGGACATCATTGACCCTATGGGCTCTCAGTCCATGCTCCCTCTTAAACCTAAGGGACTCCA
1 TTGGTGGACATCATTGACCCTAAGGGCTCTCAGTCCATGCTCCCTCTTAAACCGAAGGGACTCCA
* *
22056 TGGCGAGGGGTACACCCGCAGTCAGTAATTGGGCGACTTCGTGGCAAACGACGCAC
66 TGGCGAGGGGCACACCCGCAGTCAGTAATGGGGCGACTTCGTGGCAAACGACGCAC
* * **
22112 TTGGTGGGCATCATTGACCCTAAGGGCTCTCAGTCCCTTGCTCCCTCTTAAA-CGGCGGGACTCC
1 TTGGTGGACATCATTGACCCTAAGGGCTCTCAGT-CCATGCTCCCTCTTAAACCGAAGGGACTCC
*
22176 ATGGCGAGGGGCACACTCGCAGTCAGTAATGGGGCG
65 ATGGCGAGGGGCACACCCGCAGTCAGTAATGGGGCG
22212 TGCCAAGATT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 74 0.82
122 16 0.18
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (121 bp):
TTGGTGGACATCATTGACCCTAAGGGCTCTCAGTCCATGCTCCCTCTTAAACCGAAGGGACTCCA
TGGCGAGGGGCACACCCGCAGTCAGTAATGGGGCGACTTCGTGGCAAACGACGCAC
Found at i:35443 original size:647 final size:648
Alignment explanation
Indices: 34172--35471 Score: 2112
Period size: 647 Copynumber: 2.0 Consensus size: 648
34162 AAACAAAAGC
34172 AAGAGAAAAGTTGGGGGATTCAAAGTCTCTGAATTTATTTTTTTTGACGAAAACAAAGGAAAATC
1 AAGAGAAAAGTTGGGGGATTCAAAGTCTCTG-ATTTATTTTTTTTGACGAAAACAAAGGAAAATC
* * **
34237 AAGGTCTTTGTTTAGGCTAAGATTTAATGGTGTATTTCTGGTAGCTTCAAGGCTTATGGTGGAGT
65 AAAGTCTCTGTTTAGGCTAAGATTTAATGGTGTATTTCCAGTAGCTTCAAGGCTTATGGTGGAGT
*
34302 AGGTTTAGGGTTTGAGTTAGAGAAGAGGAGTTGGGTTTGGCCTCTAAGATCAATAGATCTAGGAC
130 AGGTTTAGGGTTTGAGTTAGAGAAGAGGAGTTGGGTTTGGCCACTAAGATCAATAGATCTAGGAC
* *
34367 TTGTGGGTAGGATTTTGGCAATCTTAGGTTGAGATTTAAAGTTAGGATCTAAGTTTTGACGAGAT
195 TTGTGGGTAGGATTTTGGCAATCTTAGGTTGAGATTTAAAGTAAGGATCTAAGTTTTAACGAGAT
* * *
34432 TTAGAGTTTCGGTGATGCGACTGACAGCGCGGTGAGCGGAGTGGTTTTGGACGGAGGTCAGCTGT
260 TTAGAGTTTCGGTGATGCGACTGACAGCGCGATGAGCGGAGTGATTTTGGACGGAGGTCAGCTAT
*
34497 TTCATTTTTGTGTTGTTTTTGGGACTTCATTCTTTTTTTGGAAAATATGGCTGCTTGATTTTTTT
325 TTCATTTTTGTGTTGTTTTTGGGACTTCATTCTTTTTTTGGAAAATATGGCCGCTTGATTTTTTT
*
34562 TCTTTTTTATTTTGACATCTAGGTTTTGGTTGTTAGGTTTAGAGAGATGGGAGAAAACTTGAATT
390 TCTTTTTTATTTTGAAATCTAGGTTTTGGTTGTTAGGTTTAGAGAGATGGGAGAAAACTTGAATT
* *
34627 TAAAGAGAATAAGCTTCGGAGAAAATTAGGGCCATTTTATAATTTTCAACAAGTGGATCCACTGC
455 TAAAGAGAAGAAGCTTCGGAGAAAATTAGGGCCATTTTATAATTTTCAACAAGTGGACCCACTGC
** *
34692 CATGTGGACTTCATGATATTCCACATCAGCAAAATAGACAATCCTTAGTCACGTGACTAGTGGAC
520 CACATGGACTTCATGATATTCCACATCAGCAAAATAGACAATCCTTAGTCACGTGACTAATGGAC
*
34757 CGTCCAAAAGGTGCTAACTTGGCCCGTTTTCAAAAGTTTTAGGATTTATATGTCCCAAAAAAAAT
585 CGTCCAAAAAGTGCTAACTTGGCCCGTTTTCAAAAGTTTTAGGATTTATATGT-CCAAAAAAAA-
34822 A
648 A
* *
34823 AAGAGAAAAGTTGGGGGATTCAAAGTCTCTG-TTT-TTTTTTTT-AGGAAAACAAAGGAAATTCA
1 AAGAGAAAAGTTGGGGGATTCAAAGTCTCTGATTTATTTTTTTTGACGAAAACAAAGGAAAATCA
* *
34885 AAGTCTCTGTTTAGGCTAAGATTTAATGGTGTATTTCCAGTGGTTTCAAGGCTTATGGTGGAGTA
66 AAGTCTCTGTTTAGGCTAAGATTTAATGGTGTATTTCCAGTAGCTTCAAGGCTTATGGTGGAGTA
*
34950 GGTTTAGGGTTTGAGTTAGGGAGGAGGAGGAGTTGGGTTTGGCCACTAAGATCAATAGATCTAGG
131 GGTTTAGGGTTTGAGTTA--GA-GAAGAGGAGTTGGGTTTGGCCACTAAGATCAATAGATCTAGG
* * * *
35015 ACTTGTGGGTTGGATTTTGGCGATCTTAGGTTGAGATTTAAAGTAAGGAT-TGAGGTTTTAATGA
193 ACTTGTGGGTAGGATTTTGGCAATCTTAGGTTGAGATTTAAAGTAAGGATCT-AAGTTTTAACGA
* *
35079 GATTTAGAGTTTCGGTGATGCGACTGACGGCGCGATGAGCGGAGT-ATTTTGGGCGGAGGTC-GC
257 GATTTAGAGTTTCGGTGATGCGACTGACAGCGCGATGAGCGGAGTGATTTTGGACGGAGGTCAG-
*
35142 CTATTTCATTTTT-TGTTGTTTTTGTGACTTCATTCTTTTTTTGGAAAATATGGCCGCTTGATTT
321 CTATTTCATTTTTGTGTTGTTTTTGGGACTTCATTCTTTTTTTGGAAAATATGGCCGCTTGATTT
*
35206 TTTTTC-TTTTTATTTTTAAATCTAGGTTTTGGTTGTTAGGTTTAGAGAGATGGGAGAAAACTTG
386 TTTTTCTTTTTTATTTTGAAATCTAGGTTTTGGTTGTTAGGTTTAGAGAGATGGGAGAAAACTTG
* * * *
35270 AATTTAGAGAGAAGAAGTTTCGGAGAAAATTAGGGTCATTTTATAATTTTCAATAAGTGGACCCA
451 AATTTAAAGAGAAGAAGCTTCGGAGAAAATTAGGGCCATTTTATAATTTTCAACAAGTGGACCCA
35335 CTGCCACATGGACTTCATGATATTCCACATCAGCAAAATAGACAATCCTTAGTCACGTGACTAAT
516 CTGCCACATGGACTTCATGATATTCCACATCAGCAAAATAGACAATCCTTAGTCACGTGACTAAT
* * * * *
35400 GGACTGTCCAAAAAGTGCTAACTTGGCCCGTTTTCGAAAGTTTTGGGGTTTATTTGTCCAAAAAA
581 GGACCGTCCAAAAAGTGCTAACTTGGCCCGTTTTCAAAAGTTTTAGGATTTATATGTCCAAAAAA
35465 AAA
646 AAA
35468 AAGA
1 AAGA
35472 AAATTGCCCG
Statistics
Matches: 604, Mismatches: 40, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
645 5 0.01
646 10 0.02
647 323 0.53
648 64 0.11
649 32 0.05
650 139 0.23
651 31 0.05
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (648 bp):
AAGAGAAAAGTTGGGGGATTCAAAGTCTCTGATTTATTTTTTTTGACGAAAACAAAGGAAAATCA
AAGTCTCTGTTTAGGCTAAGATTTAATGGTGTATTTCCAGTAGCTTCAAGGCTTATGGTGGAGTA
GGTTTAGGGTTTGAGTTAGAGAAGAGGAGTTGGGTTTGGCCACTAAGATCAATAGATCTAGGACT
TGTGGGTAGGATTTTGGCAATCTTAGGTTGAGATTTAAAGTAAGGATCTAAGTTTTAACGAGATT
TAGAGTTTCGGTGATGCGACTGACAGCGCGATGAGCGGAGTGATTTTGGACGGAGGTCAGCTATT
TCATTTTTGTGTTGTTTTTGGGACTTCATTCTTTTTTTGGAAAATATGGCCGCTTGATTTTTTTT
CTTTTTTATTTTGAAATCTAGGTTTTGGTTGTTAGGTTTAGAGAGATGGGAGAAAACTTGAATTT
AAAGAGAAGAAGCTTCGGAGAAAATTAGGGCCATTTTATAATTTTCAACAAGTGGACCCACTGCC
ACATGGACTTCATGATATTCCACATCAGCAAAATAGACAATCCTTAGTCACGTGACTAATGGACC
GTCCAAAAAGTGCTAACTTGGCCCGTTTTCAAAAGTTTTAGGATTTATATGTCCAAAAAAAAA
Found at i:37373 original size:16 final size:16
Alignment explanation
Indices: 37352--37397 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
37342 ATATATATAT
*
37352 ATATATAATAGTATTA
1 ATATATAATAGTAATA
37368 ATATATAATAG-AATA
1 ATATATAATAGTAATA
*
37383 ATAGATATATAGTAA
1 ATATATA-ATAGTAA
37398 ATAAAAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 9 0.35
16 15 0.58
17 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
ATATATAATAGTAATA
Found at i:38890 original size:33 final size:33
Alignment explanation
Indices: 38852--38919 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
38842 GTTAATCCTT
38852 ATGTGCTTTTGCATTTCAAAAGTGTTTTTGGAC
1 ATGTGCTTTTGCATTTCAAAAGTGTTTTTGGAC
*
38885 ATGTGCTTTTGCGTTTCAAAAGTGTTTTTGGAC
1 ATGTGCTTTTGCATTTCAAAAGTGTTTTTGGAC
38918 AT
1 AT
38920 TAAATGACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.46
Consensus pattern (33 bp):
ATGTGCTTTTGCATTTCAAAAGTGTTTTTGGAC
Found at i:42196 original size:21 final size:21
Alignment explanation
Indices: 42172--42213 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42162 CTATCGCTGG
42172 TCTGTACAGTATCTAATCTCA
1 TCTGTACAGTATCTAATCTCA
* *
42193 TCTGTACAGTGTTTAATCTCA
1 TCTGTACAGTATCTAATCTCA
42214 CCATTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (21 bp):
TCTGTACAGTATCTAATCTCA
Found at i:45927 original size:16 final size:16
Alignment explanation
Indices: 45902--45937 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
45892 ACCACCACAG
*
45902 GAGAACGAAAAGAAAA
1 GAGAAAGAAAAGAAAA
45918 GAGAAAGAAAAGAAAA
1 GAGAAAGAAAAGAAAA
45934 GAGA
1 GAGA
45938 TCGGAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAAGAAAA
Found at i:47539 original size:12 final size:12
Alignment explanation
Indices: 47522--47548 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
47512 AACGCTTCTT
47522 CTAACTTTTAAC
1 CTAACTTTTAAC
47534 CTAACTTTTAAC
1 CTAACTTTTAAC
47546 CTA
1 CTA
47549 GTGTGACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (12 bp):
CTAACTTTTAAC
Found at i:48041 original size:29 final size:29
Alignment explanation
Indices: 47985--48041 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
47975 GAAAAAAATA
** *
47985 AAAGACGAGATTATTTTATTTTTTTATAG
1 AAAGACGAGATTATTTTATGGTTCTATAG
48014 AAAGACGAGATTATTTTATGGTTCTATA
1 AAAGACGAGATTATTTTATGGTTCTATA
48042 ATTGTTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (29 bp):
AAAGACGAGATTATTTTATGGTTCTATAG
Found at i:52541 original size:88 final size:87
Alignment explanation
Indices: 52401--52567 Score: 280
Period size: 88 Copynumber: 1.9 Consensus size: 87
52391 TTTATATACC
** *
52401 ATATATATAGTTGTAGAATAGAAATGTCCTTTGTCTATCTTTAAAGTCTAAAGTTAACCAGAAAA
1 ATATATATAGTTGTAGAATAGAAATGTCCTTTGTCTATCACTAAAGTATAAAGTTAA-CAGAAAA
*
52466 AGATTAGCCTTCTTTTATACTAT
65 AGACTAGCCTTCTTTTATACTAT
*
52489 ATATATATAGTTGTAGAATAGAAATGTCCTTTGTCTATCACTAAAGTATAAAGTTAATAGAAAAA
1 ATATATATAGTTGTAGAATAGAAATGTCCTTTGTCTATCACTAAAGTATAAAGTTAACAGAAAAA
52554 GACTAGCCTTCTTT
66 GACTAGCCTTCTTT
52568 CCCTTGAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 20 0.27
88 54 0.73
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (87 bp):
ATATATATAGTTGTAGAATAGAAATGTCCTTTGTCTATCACTAAAGTATAAAGTTAACAGAAAAA
GACTAGCCTTCTTTTATACTAT
Found at i:68048 original size:29 final size:29
Alignment explanation
Indices: 67990--68054 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
67980 ACAAAACGAT
***
67990 CAAATAAGCCCCTGAACTCTAATTGCAGC
1 CAAATAAGCCCCTGAACTCTAATAAAAGC
68019 CAAATAAGCCCCTGAACTCTTAA-AAAAGC
1 CAAATAAGCCCCTGAACTC-TAATAAAAGC
68048 CAAATAA
1 CAAATAA
68055 ACCCTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTAATAAAAGC
Found at i:69206 original size:7 final size:7
Alignment explanation
Indices: 69194--69218 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
69184 GAGAAATCAT
69194 AGACTTG
1 AGACTTG
69201 AGACTTG
1 AGACTTG
69208 AGACTTG
1 AGACTTG
69215 AGAC
1 AGAC
69219 CCAACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (7 bp):
AGACTTG
Found at i:77923 original size:12 final size:12
Alignment explanation
Indices: 77906--77931 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
77896 CTAAAAAACT
77906 ACACATGTAAAA
1 ACACATGTAAAA
77918 ACACATGTAAAA
1 ACACATGTAAAA
77930 AC
1 AC
77932 TCAAACTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (12 bp):
ACACATGTAAAA
Found at i:80389 original size:53 final size:53
Alignment explanation
Indices: 80309--80451 Score: 277
Period size: 53 Copynumber: 2.7 Consensus size: 53
80299 TATCATTTCA
*
80309 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAATTCG
1 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
80362 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
1 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
80415 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAA
1 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAA
80452 AAGCCGCACG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 89 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (53 bp):
CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
Found at i:81925 original size:82 final size:82
Alignment explanation
Indices: 81769--81922 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 82
81759 AATTATACGA
* *
81769 GGAATTCTTCATAGTTAGATTACAATTTCCAATCAGTCCACTAAATGAGAAAATATACAGGGCAC
1 GGAATTCTTCATAATTAGATTACAATTTCCAATCAGTCCACTAAATGAGAAAACATACAGGGCAC
81834 CCCAAAACTTATGTAAG
66 CCCAAAACTTATGTAAG
* * * * * *
81851 GGAA-TCTTCATAATTTGATTGCAATTTCCAATTAGTCTATTAAAATGACGAAATACATACA-TG
1 GGAATTCTTCATAATTAGATTACAATTTCCAATCAGTCCACT-AAATGA-GAAA-ACATACAGGG
81914 CACCCCAAA
63 CACCCCAAA
81923 CTTTAATGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
81 31 0.51
82 10 0.16
83 14 0.23
84 6 0.10
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (82 bp):
GGAATTCTTCATAATTAGATTACAATTTCCAATCAGTCCACTAAATGAGAAAACATACAGGGCAC
CCCAAAACTTATGTAAG
Found at i:90229 original size:147 final size:147
Alignment explanation
Indices: 89962--90240 Score: 531
Period size: 147 Copynumber: 1.9 Consensus size: 147
89952 TCAGGTAGAT
89962 GAAGCAAACTATTATTCGACCCCTTGAACCGCATGAATACAATATTAATCATCTTCTCAAAAATA
1 GAAGCAAACTATTATTCGACCCCTTGAACCGCATGAATACAATATTAATCATCTTCTCAAAAATA
*
90027 GAATGGCATATCTGTAGCATCTTTGAAATATTATCCATATCTAAGGATATTCTTGTAATTGAATT
66 GAAGGGCATATCTGTAGCATCTTTGAAATATTATCCATATCTAAGGATATTCTTGTAATTGAATT
90092 AGAAAGCTCTTGGTTTG
131 AGAAAGCTCTTGGTTTG
* *
90109 GAAGCAACCTATTATTCGACTCCTTGAACCGCATGAATACAATATTAATCATCTTCTCAAAAATA
1 GAAGCAAACTATTATTCGACCCCTTGAACCGCATGAATACAATATTAATCATCTTCTCAAAAATA
90174 GAAGGGCATATCTGTAGCATCTTTGAAATATTATCCATATCTAAGGATATTCTTGTAATTGAATT
66 GAAGGGCATATCTGTAGCATCTTTGAAATATTATCCATATCTAAGGATATTCTTGTAATTGAATT
90239 AG
131 AG
90241 TCCCCTAATC
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 129 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (147 bp):
GAAGCAAACTATTATTCGACCCCTTGAACCGCATGAATACAATATTAATCATCTTCTCAAAAATA
GAAGGGCATATCTGTAGCATCTTTGAAATATTATCCATATCTAAGGATATTCTTGTAATTGAATT
AGAAAGCTCTTGGTTTG
Found at i:90853 original size:3 final size:3
Alignment explanation
Indices: 90837--90891 Score: 92
Period size: 3 Copynumber: 17.7 Consensus size: 3
90827 TTTTTTTTAC
90837 ATA ATGA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
90884 ATA ATA AT
1 ATA ATA AT
90892 TAATTAATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:90904 original size:11 final size:11
Alignment explanation
Indices: 90849--90907 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 11
90839 AATGAATAAA
90849 TAATAA-TAA-
1 TAATAATTAAT
90858 TAATAA-TAA-
1 TAATAATTAAT
90867 TAATAA-TAA-
1 TAATAATTAAT
90876 TAATAA-TAA-
1 TAATAATTAAT
90885 TAATAATTAAT
1 TAATAATTAAT
*
90896 TAATTATTAAT
1 TAATAATTAAT
90907 T
1 T
90908 TTTTGACAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
9 33 0.70
10 3 0.06
11 11 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATAATTAAT
Found at i:92027 original size:146 final size:149
Alignment explanation
Indices: 91867--92158 Score: 563
Period size: 146 Copynumber: 2.0 Consensus size: 149
91857 AGTTATTTTC
91867 TAAAAAAACTGTAATATTTAAACAATGTCATATAAGAAATATATTTTAAAAATTCTAATATATCT
1 TAAAAAAACTGTAATATTTAAACAATGTCATATAAGAAATATATTTTAAAAATTCTAATATATCT
91932 AA-TTTTTTTAATTAAATTAGTAAAATGAT-AAAA-AAAATAGGTATAAGGATATTATAATTAAA
66 AAGTTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATAATTAAA
91994 TAAAAAATAGTTTTTTAAA
131 TAAAAAATAGTTTTTTAAA
92013 TAAAAAAACTGTAATATTTAAACAATGTCATATAAGAAATATATTTTAAAAATTCTAATATATCT
1 TAAAAAAACTGTAATATTTAAACAATGTCATATAAGAAATATATTTTAAAAATTCTAATATATCT
92078 AAGTTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATAATTAAA
66 AAGTTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATAATTAAA
92143 TAAAAAATAGTTTTTT
131 TAAAAAATAGTTTTTT
92159 TAGTTGAGTA
Statistics
Matches: 143, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
146 67 0.47
147 27 0.19
148 4 0.03
149 45 0.31
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.38
Consensus pattern (149 bp):
TAAAAAAACTGTAATATTTAAACAATGTCATATAAGAAATATATTTTAAAAATTCTAATATATCT
AAGTTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATAATTAAA
TAAAAAATAGTTTTTTAAA
Found at i:92201 original size:137 final size:138
Alignment explanation
Indices: 92055--92308 Score: 361
Period size: 137 Copynumber: 1.8 Consensus size: 138
92045 TAAGAAATAT
* * **
92055 ATTTTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAATTAGTAAAA-TGATAAAAATAAAAT
1 ATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAAGAGTAAAATTGATAAAAATAAAAT
**
92119 AGGTATAAGGATATT-A-TAATTAAATAAAAAATAGTTTTTTTAGTTGAGTAGAAGTGTAAAACT
65 AGGTATAAGGATATTAATTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAGAAGTGTAAAACT
92182 ATAAAAGTAC
129 ATAAAAGTAC
* *
92192 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAAGAGTAAAATTGGTAAAAATTAAATA
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAAGAGTAAAATTGATAAAAATAAAATA
* *
92257 GTTATAAGGATATTAGATTTAATTAGATAAAAATAGAGTTTTTAGTTGAGTA
66 GGTATAAGGATATTA-A-TTAATTAAATAAAAATAGAGTTTTTAGTTGAGTA
92309 AAACTATAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
136 20 0.20
137 51 0.50
139 1 0.01
140 22 0.22
141 8 0.08
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.39
Consensus pattern (138 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAAGAGTAAAATTGATAAAAATAAAATA
GGTATAAGGATATTAATTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAGAAGTGTAAAACTAT
AAAAGTAC
Done.