Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006739.1 Hibiscus syriacus cultivar Beakdansim tig00016914_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: 163835
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:869 original size:43 final size:43
Alignment explanation
Indices: 778--879 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
768 TAATTAGCGA
*
778 CGTTTTTCTTAAAAACACCGCTATAGATCTTGATATTTTGCAG
1 CGTTTTTCTTAAAAACACCACTATAGATCTTGATATTTTGCAG
* * * **
821 TGTTTTTCTTAAAAACTCCACTATAGATTTTGA-ACTTTTGTGG
1 CGTTTTTCTTAAAAACACCACTATAGATCTTGATA-TTTTGCAG
**
864 CGTTTTTAATAAAAAC
1 CGTTTTTCTTAAAAAC
880 CGATGCTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (43 bp):
CGTTTTTCTTAAAAACACCACTATAGATCTTGATATTTTGCAG
Found at i:1427 original size:3 final size:3
Alignment explanation
Indices: 1406--1446 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1396 ATGTAGTATA
*
1406 AAT AA- AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1447 CGGTCTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1684 original size:41 final size:41
Alignment explanation
Indices: 1639--1719 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
1629 TGATTCACTC
*
1639 CACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTT
1 CACTGCTCTTCAGGGAAGATTGAATCAAGGTAGATTTGTTT
*
1680 CACTGCTCTTCAGGGAAGATTGAATCAAGGTATATTTGTT
1 CACTGCTCTTCAGGGAAGATTGAATCAAGGTAGATTTGTT
1720 CCATAATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
CACTGCTCTTCAGGGAAGATTGAATCAAGGTAGATTTGTTT
Found at i:2231 original size:132 final size:129
Alignment explanation
Indices: 1927--2293 Score: 387
Period size: 130 Copynumber: 2.8 Consensus size: 129
1917 TGAAGGTTTC
* * * * ** * * *
1927 TGCTCCACTGCTCTTCAGTGTAGATCAGATCTGGAAATTTTGATTCACTCCACTACTCTTC-TGA
1 TGCTCCAATGCTCTTCAGGGTAGATCAGATATGAAAACATTGATTCATTCCACTGCTCTTCAGGA
* * * * * * * *
1991 GTAGATTGAATCGAGGTAGATTTGCTAT-ACTGCTCCTCATGGAATATCAAATCTGAAAAAGGGG
66 -AAGATTGAATCAAGGTAGATTTG-T-TCACTTCTCTTCAAGGAAAATCAAATATAAAAAAGGGG
2055 TA
128 TA
* * * * * * *
2057 TGCTCCAATGCTCTTCATGGTAGATCAGATCTGGAAACATTGATTCATTCTAGTGCTCTTTAGGG
1 TGCTCCAATGCTCTTCAGGGTAGATCAGATATGAAAACATTGATTCATTCCACTGCTCTTCAGGA
*
2122 AAGATTGAATCAAGGTAGATTTGTTGCACTTCTCTTCAAGGAAAATGAAATATAAAACAAGGGGA
66 AAGATTGAATCAAGGTAGATTTGTT-CACTTCTCTTCAAGGAAAATCAAATATAAAA-AAGGGG-
*
2187 TC
128 TA
* *
2189 TGCTCTAATGCTCTTCAGGGTAGATCATATATGAAAACATTGATTCATTCCACTGCTCTTCAGGA
1 TGCTCCAATGCTCTTCAGGGTAGATCAGATATGAAAACATTGATTCATTCCACTGCTCTTCAGGA
* *
2254 AAGATTGAATCAAGGTAGATTTGCTTCTCTTATCTTCAAG
66 AAGATTGAATCAAGGTAGATTTG-TTCACTTCTCTTCAAG
2294 AAGATCGAAT
Statistics
Matches: 198, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
128 1 0.01
129 1 0.01
130 95 0.48
131 7 0.04
132 92 0.46
133 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (129 bp):
TGCTCCAATGCTCTTCAGGGTAGATCAGATATGAAAACATTGATTCATTCCACTGCTCTTCAGGA
AAGATTGAATCAAGGTAGATTTGTTCACTTCTCTTCAAGGAAAATCAAATATAAAAAAGGGGTA
Found at i:12580 original size:12 final size:13
Alignment explanation
Indices: 12555--12592 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12545 AGATCTCATT
*
12555 AAAAATACATACA
1 AAAAATACAAACA
12568 AAAAATA-AAACA
1 AAAAATACAAACA
*
12580 AAAATTACAAACA
1 AAAAATACAAACA
12593 TATATCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATACAAACA
Found at i:14594 original size:17 final size:17
Alignment explanation
Indices: 14569--14608 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
14559 GTAAGTTGTT
*
14569 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
14586 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
14603 CATTTA
1 CATTTA
14609 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:14635 original size:17 final size:17
Alignment explanation
Indices: 14615--14673 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
14605 TTTAGGGAAG
14615 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
14632 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
14648 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
14665 TAGTTCATT
1 TAGTTCATT
14674 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:16781 original size:758 final size:758
Alignment explanation
Indices: 15326--16841 Score: 2748
Period size: 758 Copynumber: 2.0 Consensus size: 758
15316 TGGACATGTA
* *
15326 GGATGTCCTCATTCATCCTATGACTTCATTTATCCTCTTTTCTTCCATTTGCAAGCAAAGCAAGG
1 GGATGTCCACATTCATCCTATGACTTCATTTATCCTCTTTTCTTCAATTTGCAAGCAAAGCAAGG
*
15391 CAGCCCAAGAGTCACCCTCCTTTTTGGACGAATTTAAAGCTGAAATTATCTCAAATTAAAGCTTA
66 CAACCCAAGAGTCACCCTCCTTTTTGGACGAATTTAAAGCTGAAATTATCTCAAATTAAAGCTTA
*
15456 ATTCATCCATTTTCAATCTACATGGCCAGCCATCAAAGGATAAGAAGAATGACAAGCCATTTAAT
131 ATTCATCCATTTTCAATATACATGGCCAGCCATCAAAGGATAAGAAGAATGACAAGCCATTTAAT
*
15521 TGAATTCAATTGCATTTAGGTGATTGTTTTCTTTTAATTGTAAAAACTCTTCATATGGTGCCTAT
196 TGAATTCAATTGCATTTAGGTGAATGTTTTCTTTTAATTGTAAAAACTCTTCATATGGTGCCTAT
15586 CAACACTATAAATAGGCACCTCAATTGCATTTGTACATAGAAATTTTTGCATAATAAACTCTTTG
261 CAACACTATAAATAGGCACCTCAATTGCATTTGTACATAGAAATTTTTGCATAATAAACTCTTTG
*
15651 AAAGGTTGCTTTCATTTTAGTTCTTGGATTAGAACTCTATCGGTTTCTTGTCAGTTTTGAAGCCT
326 AAAGGTTGCTTTCATTTTAGTTCTTGGATTAGAACTCTATCGGTTTCTTGTCAGTCTTGAAGCCT
15716 TCATCCATTTCATCTTGTTATAGCGTTAGTTCCTAGCTCTACTATAGCTAGTGGGTCACGTTCCA
391 TCATCCATTTCATCTTGTTATAGCGTTAGTTCCTAGCTCTACTATAGCTAGTGGGTCACGTTCCA
*
15781 CCCTCTATCACTTCGATTCCATCTTTATTATATTGTTGGTTTCTAACTCATATATAGTTTTAGGG
456 CCCTCTATCACTTCGATTCCATCTTTATTATATTGTTGGTTCCTAACTCATATATAGTTTTAGGG
*
15846 TCACAATCCATCCTTTGAATTACTATCATTCTCCACGCCAACCACAAACATCCTTCACCATTTTT
521 TCACAATCCATCCTTTGAATTACTATCATTCTCCACGCCAACCACAAACATCCGTCACCATTTTT
15911 GTTACATCCATTCAACCAGTATCACCACCACACTTCTTTCATTTACAATCCACTTCAACTTTACT
586 GTTACATCCATTCAACCAGTATCACCACCACACTTCTTTCATTTACAATCCACTTCAACTTTACT
15976 CTATTATTTCCATTACTTCCATACACATATTTATATATACATATTTCCCTTCTTATAACGTTGTT
651 CTATTATTTCCATTACTTCCATACACATATTTATATATACATATTTCCCTTCTTATAACGTTGTT
16041 TGTACATTTTCAGACTTCAATCAAAGCACTGCGAAGTTCTTAC
716 TGTACATTTTCAGACTTCAATCAAAGCACTGCGAAGTTCTTAC
*
16084 GGATGTCCACATTCATCCTATGACTTCATTTATCCTTTTTTCTTCAATTTGCAAGCAAAGCAAGG
1 GGATGTCCACATTCATCCTATGACTTCATTTATCCTCTTTTCTTCAATTTGCAAGCAAAGCAAGG
**
16149 CAACCCAAGAGTCACCCTCCTTTTTGGACGAATTTATGGCTGAAATTATCTCAAATTAAAGCTTA
66 CAACCCAAGAGTCACCCTCCTTTTTGGACGAATTTAAAGCTGAAATTATCTCAAATTAAAGCTTA
* *
16214 ATTTATCCATTTTCAATATACATGGCCAGCCATCAAAGGATAAGAAGAATGACAAGTCATTTAAT
131 ATTCATCCATTTTCAATATACATGGCCAGCCATCAAAGGATAAGAAGAATGACAAGCCATTTAAT
16279 TGAATTCAATTGCATTTAGGTGAATGTTTTCTTTTAATTGTAAAAACTCTTCATATGGTGCCTAT
196 TGAATTCAATTGCATTTAGGTGAATGTTTTCTTTTAATTGTAAAAACTCTTCATATGGTGCCTAT
* *
16344 CAACACTATAAATAGGCACCTCCATTGCATTTGTGCATAGAAATTTTTGCATAATAAACTCTTTG
261 CAACACTATAAATAGGCACCTCAATTGCATTTGTACATAGAAATTTTTGCATAATAAACTCTTTG
* * *
16409 AAAGGTTGCTTTCATTTTAGTTCTTGGATTAGAACTCTCTCGGTTTCTTGTTAGTCTTGAATCCT
326 AAAGGTTGCTTTCATTTTAGTTCTTGGATTAGAACTCTATCGGTTTCTTGTCAGTCTTGAAGCCT
*
16474 TCATCCATTTCATCTTGTTATAGCGTTGGTTCCTAGCTCTACTATAGCTAGTGGGTCACGTTCCA
391 TCATCCATTTCATCTTGTTATAGCGTTAGTTCCTAGCTCTACTATAGCTAGTGGGTCACGTTCCA
*
16539 CCCTCTATTACTTCGATTCCATCTTTATTATATTGTTGGTTCCTAACTCATATATAGTTTTAGGG
456 CCCTCTATCACTTCGATTCCATCTTTATTATATTGTTGGTTCCTAACTCATATATAGTTTTAGGG
* * *
16604 TCACAATCCATCCTTTGAATTGCTATCATTCTCCACGCCAACCATAAACATCCGTGACCATTTTC
521 TCACAATCCATCCTTTGAATTACTATCATTCTCCACGCCAACCACAAACATCCGTCACCATTTT-
* *
16669 T-TTACAAT-CATTCAACCATTATCACCACCACACTTCTTTCATTTACAATCCTCTTCAACTTTA
585 TGTTAC-ATCCATTCAACCAGTATCACCACCACACTTCTTTCATTTACAATCCACTTCAACTTTA
*
16732 CTCTATTATTTCCATTACTTTCATACACATATTTATATATACATATTTCCCTTCTTATAACGTTG
649 CTCTATTATTTCCATTACTTCCATACACATATTTATATATACATATTTCCCTTCTTATAACGTTG
**
16797 TTTGTACATTTTCAGTTTTCAATCAAAGCACTGCGAAGTTCTTAC
714 TTTGTACATTTTCAGACTTCAATCAAAGCACTGCGAAGTTCTTAC
16842 TAGAATCACG
Statistics
Matches: 728, Mismatches: 28, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
758 725 1.00
759 3 0.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (758 bp):
GGATGTCCACATTCATCCTATGACTTCATTTATCCTCTTTTCTTCAATTTGCAAGCAAAGCAAGG
CAACCCAAGAGTCACCCTCCTTTTTGGACGAATTTAAAGCTGAAATTATCTCAAATTAAAGCTTA
ATTCATCCATTTTCAATATACATGGCCAGCCATCAAAGGATAAGAAGAATGACAAGCCATTTAAT
TGAATTCAATTGCATTTAGGTGAATGTTTTCTTTTAATTGTAAAAACTCTTCATATGGTGCCTAT
CAACACTATAAATAGGCACCTCAATTGCATTTGTACATAGAAATTTTTGCATAATAAACTCTTTG
AAAGGTTGCTTTCATTTTAGTTCTTGGATTAGAACTCTATCGGTTTCTTGTCAGTCTTGAAGCCT
TCATCCATTTCATCTTGTTATAGCGTTAGTTCCTAGCTCTACTATAGCTAGTGGGTCACGTTCCA
CCCTCTATCACTTCGATTCCATCTTTATTATATTGTTGGTTCCTAACTCATATATAGTTTTAGGG
TCACAATCCATCCTTTGAATTACTATCATTCTCCACGCCAACCACAAACATCCGTCACCATTTTT
GTTACATCCATTCAACCAGTATCACCACCACACTTCTTTCATTTACAATCCACTTCAACTTTACT
CTATTATTTCCATTACTTCCATACACATATTTATATATACATATTTCCCTTCTTATAACGTTGTT
TGTACATTTTCAGACTTCAATCAAAGCACTGCGAAGTTCTTAC
Found at i:17098 original size:3 final size:3
Alignment explanation
Indices: 17090--17124 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17080 ATAAAATAAG
*
17090 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17125 GGTCTCTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:21882 original size:4 final size:4
Alignment explanation
Indices: 21873--21897 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21863 TTATAAAATA
21873 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
21898 ACAACCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:23125 original size:110 final size:109
Alignment explanation
Indices: 22942--23177 Score: 271
Period size: 110 Copynumber: 2.2 Consensus size: 109
22932 GTTTAACGCA
* ** * *
22942 TTTTTGCATGTTGGTCACCTGTGAGGACCAAAATTATTATTTACTCTTTTTCATGCATGTTATAT
1 TTTTTGCATTTTGGTCACCTGCAAGGACCAAAATTATTATTTACCCTTTTTCATACATGTTATAT
* * * *
23007 ATTGTTTGGGATATTTTCTATTTAGTCCCCCATAGTTT-AGCGTG
66 ACTGTTTGGAACATTTTCTATTTAGTCCCCCATA-TTTAAGAGTG
* * * *
23051 TTTTTTGCATTTTGGTCACCTGCAAGGATC-AAATCTATTATTTACCCTGTTTTCCTATATTTTA
1 -TTTTTGCATTTTGGTCACCTGCAAGGACCAAAAT-TATTATTTACCCT-TTTTCATACATGTTA
* *
23115 TATACT-TTTGGAACATTTTCTGTTTAGTTCCCCATATTTAAGAGTG
63 TATACTGTTTGGAACATTTTCTATTTAGTCCCCCATATTTAAGAGTG
*
23161 ATTTTGCATTTTGGTCA
1 TTTTTGCATTTTGGTCA
23178 TATGTACTAA
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
109 23 0.21
110 68 0.64
111 16 0.15
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (109 bp):
TTTTTGCATTTTGGTCACCTGCAAGGACCAAAATTATTATTTACCCTTTTTCATACATGTTATAT
ACTGTTTGGAACATTTTCTATTTAGTCCCCCATATTTAAGAGTG
Found at i:25747 original size:45 final size:45
Alignment explanation
Indices: 25680--25781 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 45
25670 CATGTTAAGT
* * * *
25680 ATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGC
1 ATTTCATTTATGGCATACTTTCAAGCCAATAATGCACCATTATGA
* * ** *
25725 ATTTCATTTATGGCATATTTTCAAGTCAATAATGCACTGTTATTA
1 ATTTCATTTATGGCATACTTTCAAGCCAATAATGCACCATTATGA
25770 ATTTCATTTATG
1 ATTTCATTTATG
25782 TATTCGTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATACTTTCAAGCCAATAATGCACCATTATGA
Found at i:26409 original size:95 final size:95
Alignment explanation
Indices: 26231--26426 Score: 257
Period size: 95 Copynumber: 2.1 Consensus size: 95
26221 CTACCATGGT
* * * * * *
26231 ATCGATACTTCTATACTATGGTACTGATACACCCTTTCAGTATCGATACCATTTCTACATTTTGT
1 ATCGATACTTCTATACTATAGTACCGATACACCCTTTCAGTATCAATACCATTTCGACATTCTGA
* ** *
26296 AATTCATGGTATCGATACCTTTCTCTTAGA
66 AATACATAATATCAATACCTTTCTCTTAGA
* *
26326 ATCGATACTTCTATACTATAGTACCGATACTCCCTTTCAGTATCAATACTATTTCGACATTCTGA
1 ATCGATACTTCTATACTATAGTACCGATACACCCTTTCAGTATCAATACCATTTCGACATTCTGA
* * *
26391 AATACCTAATATCAATACCTTTCTCTTGGT
66 AATACATAATATCAATACCTTTCTCTTAGA
26421 ATCGAT
1 ATCGAT
26427 GCCCACAGAA
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (95 bp):
ATCGATACTTCTATACTATAGTACCGATACACCCTTTCAGTATCAATACCATTTCGACATTCTGA
AATACATAATATCAATACCTTTCTCTTAGA
Found at i:31844 original size:45 final size:45
Alignment explanation
Indices: 31738--32009 Score: 391
Period size: 45 Copynumber: 6.0 Consensus size: 45
31728 TCTTTTTTTT
* * *
31738 ATTTATGGCATCCGTTCATGCTTATAATGCACCATTATGCATTTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA-TTTC
* *
31784 ATTTATGACATCCTTTAATGCTGATAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
* * *
31829 ATTTATGGCATCCTTTCATTCTGATAATGCAACGTTAAGCATTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
*
31874 ATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCATTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
* * * * *
31919 ATTTGTAGCATCATTTCATGCCGATAATGCACCGTTATACATTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
* *
31964 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGTATTTC
1 ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
32009 A
1 A
32010 ATAATATATT
Statistics
Matches: 201, Mismatches: 25, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
45 165 0.82
46 36 0.18
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (45 bp):
ATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCATTTC
Found at i:32561 original size:22 final size:22
Alignment explanation
Indices: 32510--32564 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
32500 TTTGTAATTC
* * *
32510 ATGGTATCGATACTTTTCTCCT
1 ATGGTATCGATACTTCTATACT
32532 A--GTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
32552 ATGGTATCGATAC
1 ATGGTATCGATAC
32565 CTTTCAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:32576 original size:16 final size:17
Alignment explanation
Indices: 32555--32586 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32545 CTATACTATG
32555 GTATCGATACC-TTTCA
1 GTATCGATACCATTTCA
32571 GTATCGATACCATTTC
1 GTATCGATACCATTTC
32587 GACATTCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (17 bp):
GTATCGATACCATTTCA
Found at i:32629 original size:92 final size:92
Alignment explanation
Indices: 32416--32634 Score: 226
Period size: 92 Copynumber: 2.3 Consensus size: 92
32406 TCCAGGCTCA
* * * *
32416 ATAGTATCGATACCCCTGCTATTGTATAGATAGTTCAATACTATGGTATCGATAAGCCCTTTCAG
1 ATAGTATCGATACCTCT-CTCTTGTATCGATACTTCAATACTATGGTATCGATAA-CCCTTTCAG
* * * * *
32481 TATCAAACCATTTCTATATTTTGTAATTC
64 TATCAAACCATTTCGACATTCTGGAATCC
* * * * *
32510 ATGGTATCGATACTTTTCTCCTAGTATCGATACTTCTATACTATGGTATCGAT-A-CCTTTCAGT
1 ATAGTATCGATACCTCTCT-CTTGTATCGATACTTCAATACTATGGTATCGATAACCCTTTCAGT
*
32573 ATCGATACCATTTCGACATTCTGGAATCC
65 ATC-AAACCATTTCGACATTCTGGAATCC
* *
32602 CTAGTATCGATACCTCTCTCTTGGTATCAATAC
1 ATAGTATCGATACCTCTCTCTT-GTATCGATAC
32635 CCACAGCAGT
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
91 14 0.14
92 43 0.43
93 3 0.03
94 41 0.41
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (92 bp):
ATAGTATCGATACCTCTCTCTTGTATCGATACTTCAATACTATGGTATCGATAACCCTTTCAGTA
TCAAACCATTTCGACATTCTGGAATCC
Found at i:38832 original size:45 final size:45
Alignment explanation
Indices: 38718--39034 Score: 307
Period size: 45 Copynumber: 7.2 Consensus size: 45
38708 TATTCTTTAT
* *
38718 TTTCATTTATGGAATCCGTTCATGC-GTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTG-ATAATGCACCATTATGCA
* * *
38763 TTTTAATTTATGGCATCCTTTCATGCTGATAATACACTATTATGCA
1 -TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCA
* * *
38809 ATTCATTTATGGCTTCCTTTCATGCTTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCA
* ** *
38854 TTTCATTTATGGCATCCTTTCATGCCGAT-ATGTGCTATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCA
* * * * *
38898 TTTCA-CT-T---AT--TTTCTTGCAGATAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCA
**
38936 TTTCATTTATGGCATCCTTTCATG-TCGATAATGTGCC-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGCT-GATAATGCACCATTATGCA
* * * *
38980 TTTCATTTATGGCATCCGTTT-ATACCGATAATGCACCTTTATACA
1 TTTCATTTATGGCATCC-TTTCATGCTGATAATGCACCATTATGCA
39025 TTTCATTTAT
1 TTTCATTTAT
39035 ATATTCGTTT
Statistics
Matches: 221, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
37 10 0.05
38 15 0.07
39 3 0.01
40 1 0.00
42 1 0.00
43 3 0.01
44 51 0.23
45 98 0.44
46 38 0.17
47 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCATTATGCA
Found at i:38977 original size:82 final size:82
Alignment explanation
Indices: 38836--38989 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 82
38826 TTTCATGCTT
*
38836 ATAATGCACCATTATGCATTTCATTTATGGCATCCTTTCATGCCGATATGTGCTATTATGCATTT
1 ATAATGCACCATTATACATTTCATTTATGGCATCCTTTCATGCCGATATGTGCTATTATGCATTT
38901 CACTTATTTTCTTGCAG
66 CACTTATTTTCTTGCAG
* * *
38918 ATAATGCACCGTTATACATTTCATTTATGGCATCCTTTCATGTCGATAATGTGC-CTTATGCATT
1 ATAATGCACCATTATACATTTCATTTATGGCATCCTTTCATGCCGAT-ATGTGCTATTATGCATT
*
38982 TCATTTAT
65 TCACTTAT
38990 GGCATCCGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
82 60 0.91
83 6 0.09
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (82 bp):
ATAATGCACCATTATACATTTCATTTATGGCATCCTTTCATGCCGATATGTGCTATTATGCATTT
CACTTATTTTCTTGCAG
Found at i:38984 original size:44 final size:45
Alignment explanation
Indices: 38917--39034 Score: 159
Period size: 44 Copynumber: 2.6 Consensus size: 45
38907 TTTTCTTGCA
* **
38917 GATAATGCACCGTTATACATTTCATTTATGGCATCC-TTTCATGTC
1 GATAATGCACCTTTATACATTTCATTTATGGCATCCGTTT-ATACC
** *
38962 GATAATGTGCC-TTATGCATTTCATTTATGGCATCCGTTTATACC
1 GATAATGCACCTTTATACATTTCATTTATGGCATCCGTTTATACC
39006 GATAATGCACCTTTATACATTTCATTTAT
1 GATAATGCACCTTTATACATTTCATTTAT
39035 ATATTCGTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 35 0.56
45 28 0.44
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (45 bp):
GATAATGCACCTTTATACATTTCATTTATGGCATCCGTTTATACC
Found at i:44454 original size:2 final size:2
Alignment explanation
Indices: 44449--44481 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44439 TAAAATGGAC
44449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44482 AGATTCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47718 original size:17 final size:17
Alignment explanation
Indices: 47696--47729 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
47686 ACTTTGACCA
47696 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
*
47713 AAAAGTCATATTTTATG
1 AAAAGTCAAATTTTATG
47730 TTTTTTGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:52582 original size:16 final size:17
Alignment explanation
Indices: 52546--52589 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
52536 AGTCAACTCA
*
52546 TTGACTTTGACTGACCG
1 TTGACTTTGACTCACCG
*
52563 TTGACTTTGAC-CAGCG
1 TTGACTTTGACTCACCG
52579 TTGACTTTGAC
1 TTGACTTTGAC
52590 AAAAAAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (17 bp):
TTGACTTTGACTCACCG
Found at i:56609 original size:29 final size:31
Alignment explanation
Indices: 56545--56691 Score: 163
Period size: 31 Copynumber: 4.8 Consensus size: 31
56535 AGGCTATGCA
* * * *
56545 GCCCTGATATCATTCTTGGGTAGGCACTGTG
1 GCCCTGAGATCTTTCTTGGGTAGGCCCCGTG
*
56576 ACCCTG-GAT-TTTCTTGGGTAGGCCCCGTG
1 GCCCTGAGATCTTTCTTGGGTAGGCCCCGTG
* * * * * *
56605 GCCCTGAGATCATTATTAGCTAGGCCCTGCG
1 GCCCTGAGATCTTTCTTGGGTAGGCCCCGTG
*
56636 GCTCTGAGATCTTTCTTGGGTAGGCCCCGTG
1 GCCCTGAGATCTTTCTTGGGTAGGCCCCGTG
*
56667 GCCCTGAGAACTTTCTTGGGTAGGC
1 GCCCTGAGATCTTTCTTGGGTAGGC
56692 TCTTATGCCC
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
29 22 0.24
30 5 0.05
31 66 0.71
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (31 bp):
GCCCTGAGATCTTTCTTGGGTAGGCCCCGTG
Found at i:60639 original size:31 final size:30
Alignment explanation
Indices: 60604--60679 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
60594 CTAATGTTAC
*
60604 TCTTGGGTAGGCTCTATGGCCTTCAGATCTT
1 TCTTGGGTAGGCTCTATGGCC-TCAGAACTT
* * *
60635 TCTTGGGTAGGCCCTGTGGCCTGAGAACTT
1 TCTTGGGTAGGCTCTATGGCCTCAGAACTT
60665 TCTTGGGTAGGCTCT
1 TCTTGGGTAGGCTCT
60680 CCGGCCCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 21 0.52
31 19 0.47
ACGTcount: A:0.12, C:0.22, G:0.30, T:0.36
Consensus pattern (30 bp):
TCTTGGGTAGGCTCTATGGCCTCAGAACTT
Found at i:62620 original size:101 final size:101
Alignment explanation
Indices: 62445--62648 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
62435 CTTGTCTCCA
*
62445 TCGTCACCGATGCGTGGGGGAGGTTAGGAAGTTTAAGTTTCTGACGTTTCAGAATCGAGCTCTAC
1 TCGTCACCGATGCGTGGGGGAGGTTAGGAAGTTTAAGTTTATGACGTTTCAGAATCGAGCTCTAC
62510 GCCATCCAAAATTGTGAACCGAGCTTGGTAATTGTC
66 GCCATCCAAAATTGTGAACCGAGCTTGGTAATTGTC
*
62546 TCGTCACCGATGCGTGGGGGAGGTTAGGAAGTTTAAGTTTATGACGTTTCCGAATCGAGCTCTAC
1 TCGTCACCGATGCGTGGGGGAGGTTAGGAAGTTTAAGTTTATGACGTTTCAGAATCGAGCTCTAC
*
62611 GCCGTCCAAAATTGTGAACCGAGCTTGGTAATTGTC
66 GCCATCCAAAATTGTGAACCGAGCTTGGTAATTGTC
62647 TC
1 TC
62649 AAAATGTATT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (101 bp):
TCGTCACCGATGCGTGGGGGAGGTTAGGAAGTTTAAGTTTATGACGTTTCAGAATCGAGCTCTAC
GCCATCCAAAATTGTGAACCGAGCTTGGTAATTGTC
Found at i:62814 original size:16 final size:15
Alignment explanation
Indices: 62789--62823 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
62779 GACCCGACCC
*
62789 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
62804 GACCGCGTTGACCGTT
1 GACC-CGTTGACCGTT
62820 GACC
1 GACC
62824 AAACCTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:63617 original size:39 final size:39
Alignment explanation
Indices: 63574--63649 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
63564 AAGTACTTAA
*
63574 GAAGTCATGTGTAAATCGATGAATTAGTAGTTTCATCTT
1 GAAGTCATGCGTAAATCGATGAATTAGTAGTTTCATCTT
63613 GAAGTCATGCGTAAATCGATGAATTAGTAGTTTCATC
1 GAAGTCATGCGTAAATCGATGAATTAGTAGTTTCATC
63650 GTTAATTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (39 bp):
GAAGTCATGCGTAAATCGATGAATTAGTAGTTTCATCTT
Found at i:65285 original size:44 final size:44
Alignment explanation
Indices: 65222--65310 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
65212 CGTCCCTGAG
* * *
65222 ATCATTCTTGGGTAGGCCCTACGGCCCTGGGATTTTTCTAGGGT
1 ATCATTCTTAGGTAGGCCCTACGGCCCTGAGATCTTTCTAGGGT
*
65266 ATCATTCTTAGGTAGGCCCTACGGCCCTGAGATCTTTCTTGGGT
1 ATCATTCTTAGGTAGGCCCTACGGCCCTGAGATCTTTCTAGGGT
65310 A
1 A
65311 GGCCTGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.34
Consensus pattern (44 bp):
ATCATTCTTAGGTAGGCCCTACGGCCCTGAGATCTTTCTAGGGT
Found at i:74222 original size:30 final size:30
Alignment explanation
Indices: 74143--74224 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
74133 TATGAGATGA
* * *
74143 AAGTGAATGATACATGTTACGAAACGAATT
1 AAGTGAATGATACATGCTATGAAACAAATT
* *
74173 AAATGAATGATACATGCTATGAAATAAATT
1 AAGTGAATGATACATGCTATGAAACAAATT
74203 AAGTGAATGGA-ACATGCTATGA
1 AAGTGAAT-GATACATGCTATGA
74225 TATGATATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 43 0.96
31 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (30 bp):
AAGTGAATGATACATGCTATGAAACAAATT
Found at i:78383 original size:30 final size:31
Alignment explanation
Indices: 78349--78407 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
78339 AAAAAAATTG
* * *
78349 GGGACC-ATTTTGTAATTTTTGAAAAGTTAA
1 GGGACCAATTTAGCAATTTTAGAAAAGTTAA
78379 GGGACCAATTTAGCAATTTTAGAAAAGTT
1 GGGACCAATTTAGCAATTTTAGAAAAGTT
78408 GTGAATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (31 bp):
GGGACCAATTTAGCAATTTTAGAAAAGTTAA
Found at i:79489 original size:7 final size:7
Alignment explanation
Indices: 79481--79533 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
79471 TTGGGCTATT
*
79481 GTTTATT
1 GTTTATG
*
79488 GTCTATG
1 GTTTATG
79495 GTTTATG
1 GTTTATG
*
79502 GTTTATT
1 GTTTATG
*
79509 GTATATG
1 GTTTATG
79516 GTTTATG
1 GTTTATG
79523 GTTTATTG
1 GTTTA-TG
79531 GTT
1 GTT
79534 AATAAATGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.15, C:0.02, G:0.25, T:0.58
Consensus pattern (7 bp):
GTTTATG
Found at i:79507 original size:21 final size:21
Alignment explanation
Indices: 79481--79530 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
79471 TTGGGCTATT
*
79481 GTTTATTGTCTATGGTTTATG
1 GTTTATTGTATATGGTTTATG
79502 GTTTATTGTATATGGTTTATG
1 GTTTATTGTATATGGTTTATG
79523 GTTTATTG
1 GTTTATTG
79531 GTTAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.58
Consensus pattern (21 bp):
GTTTATTGTATATGGTTTATG
Found at i:82179 original size:13 final size:13
Alignment explanation
Indices: 82161--82198 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
82151 AAAGCTTGAA
82161 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
82174 AAAGAAGAAGAAAG
1 AAAGAAGAA-AAAG
82188 -AAGAAGAAAAA
1 AAAGAAGAAAAA
82199 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 17 0.71
14 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:88522 original size:8 final size:8
Alignment explanation
Indices: 88511--88544 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
88501 TTCTTTTCTT
88511 TTTTTTTA
1 TTTTTTTA
88519 TTTTTTCTAA
1 TTTTTT-T-A
88529 TTTTTTTA
1 TTTTTTTA
88537 TTTTTTTA
1 TTTTTTTA
88545 CTAACCCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:88522 original size:9 final size:9
Alignment explanation
Indices: 88510--88543 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
88500 TTTCTTTTCT
88510 TTTTTTTTA
1 TTTTTTTTA
*
88519 TTTTTTCTA
1 TTTTTTTTA
*
88528 ATTTTTTTA
1 TTTTTTTTA
88537 TTTTTTT
1 TTTTTTT
88544 ACTAACCCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:88532 original size:20 final size:20
Alignment explanation
Indices: 88511--88548 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
88501 TTCTTTTCTT
88511 TTTTTTTA-TTTTTT-CTAA
1 TTTTTTTATTTTTTTACTAA
88529 TTTTTTTATTTTTTTACTAA
1 TTTTTTTATTTTTTTACTAA
88549 CCCGGGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTATTTTTTTACTAA
Found at i:92762 original size:15 final size:15
Alignment explanation
Indices: 92742--92775 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
92732 AAATATGTGT
92742 ATGAAAGTAATGGAA
1 ATGAAAGTAATGGAA
92757 ATGAAAGTAATGGAA
1 ATGAAAGTAATGGAA
92772 ATGA
1 ATGA
92776 TAGAATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (15 bp):
ATGAAAGTAATGGAA
Found at i:96556 original size:10 final size:10
Alignment explanation
Indices: 96543--96579 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
96533 TTCTTTTCTC
96543 TTTTTTTTTA
1 TTTTTTTTTA
* *
96553 TTTTTTCTGA
1 TTTTTTTTTA
96563 TTTTTTTTTA
1 TTTTTTTTTA
96573 TTTTTTT
1 TTTTTTT
96580 ACTAACCCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:96787 original size:15 final size:15
Alignment explanation
Indices: 96767--96800 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
96757 AAATATGTGT
*
96767 ATGAAAGTAATGGAA
1 ATGAAAGTAATGCAA
96782 ATGAAAGTAATGCAA
1 ATGAAAGTAATGCAA
96797 ATGA
1 ATGA
96801 TAGAATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (15 bp):
ATGAAAGTAATGCAA
Found at i:100617 original size:19 final size:18
Alignment explanation
Indices: 100593--100634 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
100583 AAAAATTTTC
100593 TTTTCT-TTTTTTTCAATTT
1 TTTTCTATTTTTTT--ATTT
100612 TTTTCTGATTTTTTTATTT
1 TTTTCT-ATTTTTTTATTT
100631 TTTT
1 TTTT
100635 ACTAACCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 14 0.67
21 7 0.33
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTCTATTTTTTTATTT
Found at i:100846 original size:15 final size:15
Alignment explanation
Indices: 100822--100855 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
100812 AAATATGTGT
100822 ATGAAAGTAATGGAA
1 ATGAAAGTAATGGAA
*
100837 ATGAATGTAATGGAA
1 ATGAAAGTAATGGAA
100852 ATGA
1 ATGA
100856 TAGAATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (15 bp):
ATGAAAGTAATGGAA
Found at i:105568 original size:25 final size:26
Alignment explanation
Indices: 105514--105569 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
105504 AAAAAAATAT
* *
105514 TAAAATTAATATTTTAATCCTACTAA
1 TAAAACTAATATTTTAATCCTACAAA
*
105540 TAAAACTATTATTTTAA-CCTA-AAA
1 TAAAACTAATATTTTAATCCTACAAA
105564 GTAAAA
1 -TAAAA
105570 ACCTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.08
25 9 0.35
26 15 0.58
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAAACTAATATTTTAATCCTACAAA
Found at i:106219 original size:57 final size:56
Alignment explanation
Indices: 106094--106226 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 56
106084 GGTTTATATT
* * *
106094 TAATTTGAATGTCTTAGTTGATGTTTGTTTCTAACTAGAGTAATTCGTGTTTGTATC
1 TAATTTGAATGT-TTAATTGATGTTTGTTTCTAACTAGACTAATTCGTGCTTGTATC
* *
106151 TAATCCT-AATGTTATAATTGATGTTTGTTTCTAATTAGACTAA-TCGGTGCTTGTATC
1 TAAT-TTGAATGTT-TAATTGATGTTTGTTTCTAACTAGACTAATTC-GTGCTTGTATC
106208 TAATTTGAATGTTCTAATT
1 TAATTTGAATGTT-TAATT
106227 AGACTATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 4 0.06
57 60 0.92
58 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (56 bp):
TAATTTGAATGTTTAATTGATGTTTGTTTCTAACTAGACTAATTCGTGCTTGTATC
Found at i:106404 original size:190 final size:190
Alignment explanation
Indices: 106097--106491 Score: 555
Period size: 190 Copynumber: 2.1 Consensus size: 190
106087 TTATATTTAA
* * *
106097 TTTGAATGTCT-TAGTTGATGTTTGTTTCTAACTAGAGTAATTCGTGTTTGTATCTAATCCTAAT
1 TTTGAATGT-TGTAATTGATATTTGTTTCTAACTAGAGTAATTCGTGTTTGTATATAATCCTAAT
* * *
106161 GTTATAATTGATGTTTGTTTCTAATTAGACTAATCGGTGCTTGTATCTAATTTGAATGTTCTAAT
65 GTTATAATTGAAGTTTGTTTCTAATTAGACTAATCGGTGCTTATATCTAATTTGAACGTTCTAAT
* * *
106226 TAGACTATTTTGATTTTTACAAGTAATTGGACTATTTGGTGGTTGTTTGGTTTGTTTCTAC
130 TAAACTATTTTGATTTTTACAAGTAATTGGACTAATTGGTGGTTGTTTGCTTTGTTTCTAC
* * *
106287 TTTGAATGTTGTAATTGATATTTGTTTTTAATTAGAGTAATT-GTTGTTTGTATATAATTCTAAT
1 TTTGAATGTTGTAATTGATATTTGTTTCTAACTAGAGTAATTCG-TGTTTGTATATAATCCTAAT
* * *
106351 TTTATAATTGAAGTTTGTTTCTAATTAGACTAAAT-GGTGTTTATATCTAATTTGAACGTTCTAG
65 GTTATAATTGAAGTTTGTTTCTAATTAGACT-AATCGGTGCTTATATCTAATTTGAACGTTCTAA
* * *
106415 TTAAACTATTTTTATTTTTACAAGTAATTGGACTAATTGGTTGTTGTTTGCTTTGTTTTTAC
129 TTAAACTATTTTGATTTTTACAAGTAATTGGACTAATTGGTGGTTGTTTGCTTTGTTTCTAC
* *
106477 TTAGAAT-TTGAAATT
1 TTTGAATGTTGTAATT
106492 TGTACGTTGT
Statistics
Matches: 182, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
189 9 0.05
190 170 0.93
191 3 0.02
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (190 bp):
TTTGAATGTTGTAATTGATATTTGTTTCTAACTAGAGTAATTCGTGTTTGTATATAATCCTAATG
TTATAATTGAAGTTTGTTTCTAATTAGACTAATCGGTGCTTATATCTAATTTGAACGTTCTAATT
AAACTATTTTGATTTTTACAAGTAATTGGACTAATTGGTGGTTGTTTGCTTTGTTTCTAC
Found at i:107527 original size:123 final size:124
Alignment explanation
Indices: 107327--107610 Score: 394
Period size: 123 Copynumber: 2.3 Consensus size: 124
107317 TTAATAACAT
* * * *
107327 ATTCAAAACTAACATCGG-AAACCTTACATACAAAATATATCCCATCATCTAACATATTTGTTAG
1 ATTCAAAACCAACA-CGGAAAACCTTACATACAAAATATATCCCATCATCTAACACATTCGTTAA
* * *
107391 CAACTGTAAATTTATAATTGCACAATTAATAACATATTCAGTAACCCATTGACACATATC
65 CAACTCTAAATTTATAATTGAACAATTAATAACATATTCAATAACCCATTGACACATATC
* * * * *
107451 ATTCAAAGCCAACACGGAAAACCTTACATACAAAA-ATCTCTCATTATTTAACACATTCGTTAAC
1 ATTCAAAACCAACACGGAAAACCTTACATACAAAATATATCCCATCATCTAACACATTCGTTAAC
*
107515 AACTCTAAATTTATAATTGAACAATTAATAACATATTCAATAACCCATTGACCCATATC
66 AACTCTAAATTTATAATTGAACAATTAATAACATATTCAATAACCCATTGACACATATC
* * *
107574 ATTCAAAACCAACATGGAAAACGTAACATA-AAAATAT
1 ATTCAAAACCAACACGGAAAACCTTACATACAAAATAT
107611 CAGCCATAAC
Statistics
Matches: 141, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
122 4 0.03
123 108 0.77
124 29 0.21
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (124 bp):
ATTCAAAACCAACACGGAAAACCTTACATACAAAATATATCCCATCATCTAACACATTCGTTAAC
AACTCTAAATTTATAATTGAACAATTAATAACATATTCAATAACCCATTGACACATATC
Found at i:115560 original size:6 final size:6
Alignment explanation
Indices: 115545--115595 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
115535 TTTTGCTTTG
*
115545 TTTG-T TTTGTT TTTGTT TTTG-T TTTGCTT TTTG-A TTTGTTT TTTGTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTG-TT TTTGTT TTTG-TT TTTGTT
115592 TTTG
1 TTTG
115596 AAAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 13 0.33
6 17 0.44
7 9 0.23
ACGTcount: A:0.02, C:0.02, G:0.18, T:0.78
Consensus pattern (6 bp):
TTTGTT
Found at i:115565 original size:17 final size:18
Alignment explanation
Indices: 115545--115596 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
115535 TTTTGCTTTG
115545 TTTGTTTTGTTTTTG-TT
1 TTTGTTTTGTTTTTGATT
115562 TTTGTTTTGCTTTTTGATT
1 TTTGTTTTG-TTTTTGATT
115581 TGTT-TTTTGTTTTTGA
1 T-TTGTTTTGTTTTTGA
115597 AAAAACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.28
18 13 0.41
19 8 0.25
20 2 0.06
ACGTcount: A:0.04, C:0.02, G:0.17, T:0.77
Consensus pattern (18 bp):
TTTGTTTTGTTTTTGATT
Found at i:131371 original size:25 final size:26
Alignment explanation
Indices: 131339--131390 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
131329 ACACTGCAAA
131339 AGTTAAAGTAC-TG-AAATAATAAAG
1 AGTTAAAGTACTTGCAAATAATAAAG
131363 AGTTGAAAGTACTTTGCAAATAATAAAG
1 AGTT-AAAGTAC-TTGCAAATAATAAAG
131391 GGTACTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 7 0.29
27 2 0.08
28 11 0.46
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (26 bp):
AGTTAAAGTACTTGCAAATAATAAAG
Found at i:131608 original size:14 final size:15
Alignment explanation
Indices: 131575--131613 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
131565 TTAAAGGACC
131575 AAAATAAAAATGAAG
1 AAAATAAAAATGAAG
*
131590 AAAATAAAAATGCAG
1 AAAATAAAAATGAAG
*
131605 AAATTAAAA
1 AAAATAAAA
131614 GGAGCAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (15 bp):
AAAATAAAAATGAAG
Found at i:131615 original size:44 final size:44
Alignment explanation
Indices: 131523--131616 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
131513 ACAAAGCACG
* * * * *
131523 AAAGGACCAAATAAAAACTGCAGAAAAGTAAAGTGCTGGAATTT
1 AAAGGACCAAATAAAAACTGAAGAAAAGTAAAATGCAGAAATTA
131567 AAAGGACCAAAATAAAAA-TGAAGAAAA-TAAAAATGCAGAAATTA
1 AAAGGACC-AAATAAAAACTGAAGAAAAGT-AAAATGCAGAAATTA
131611 AAAGGA
1 AAAGGA
131617 GCAGAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 33 0.77
45 9 0.21
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (44 bp):
AAAGGACCAAATAAAAACTGAAGAAAAGTAAAATGCAGAAATTA
Found at i:131810 original size:15 final size:15
Alignment explanation
Indices: 131792--131823 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
131782 TAGTGGTTAA
131792 AAGTTAGAAATTAGT
1 AAGTTAGAAATTAGT
*
131807 AAGTTAGAAGTTAGT
1 AAGTTAGAAATTAGT
131822 AA
1 AA
131824 AAGTTAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (15 bp):
AAGTTAGAAATTAGT
Found at i:131852 original size:15 final size:16
Alignment explanation
Indices: 131816--131855 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
131806 TAAGTTAGAA
131816 GTTAGTAAAAGTTAGTT
1 GTTAG-AAAAGTTAGTT
*
131833 GTTAGAAAAGTTTG-T
1 GTTAGAAAAGTTAGTT
131848 GTTAGAAA
1 GTTAGAAA
131856 TTAATCGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
GTTAGAAAAGTTAGTT
Found at i:133932 original size:25 final size:25
Alignment explanation
Indices: 133904--133953 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
133894 AATTTTTTTC
** *
133904 CTTTCATCTTTTCATTATTTCATTT
1 CTTTCATAATTTCATTACTTCATTT
*
133929 CTTTCTTAATTTCATTACTTCATTT
1 CTTTCATAATTTCATTACTTCATTT
133954 AAAAAATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (25 bp):
CTTTCATAATTTCATTACTTCATTT
Found at i:135178 original size:36 final size:37
Alignment explanation
Indices: 135074--135181 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 37
135064 TAATATAACA
* *
135074 TTAATAATAATAGAAGTAGTATAATAACAATAATACAC
1 TTAATAATAATAGTAGTAGTATAAT-ATAATAATACAC
* * *
135112 GT--TAATAATAGTA-TAGTAATAATATTTAATATTGC-C
1 TTAATAATAATAGTAGTAGT-ATAATA--TAATAATACAC
135148 TTAATAATAATAGTAGTAGTATAATATAATAATA
1 TTAATAATAATAGTAGTAGTATAATATAATAATA
135182 ATAATATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
35 5 0.09
36 23 0.41
37 6 0.11
38 18 0.32
39 4 0.07
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (37 bp):
TTAATAATAATAGTAGTAGTATAATATAATAATACAC
Found at i:135185 original size:14 final size:14
Alignment explanation
Indices: 135149--135198 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
135139 AATATTGCCT
*
135149 TAATAATAATAGTAG
1 TAATAATAATA-TAA
*
135164 TAGT-ATAATATAA
1 TAATAATAATATAA
*
135177 TAATAATAATATAT
1 TAATAATAATATAA
135191 TAATAATA
1 TAATAATA
135199 GTGGGATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 22 0.73
15 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:135524 original size:36 final size:36
Alignment explanation
Indices: 135484--135564 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
135474 GAAATGAACA
*
135484 AGTTCTTCTCATTATGAACTTTTTCTCCTCGAGACG
1 AGTTCTTCTCATTATGAACGTTTTCTCCTCGAGACG
*
135520 AGTTCTTCTCATTATGAACGTTTTCTCCTCGAGATG
1 AGTTCTTCTCATTATGAACGTTTTCTCCTCGAGACG
135556 AGTTCTTCT
1 AGTTCTTCT
135565 TGTTATAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (36 bp):
AGTTCTTCTCATTATGAACGTTTTCTCCTCGAGACG
Found at i:135867 original size:105 final size:105
Alignment explanation
Indices: 135520--135930 Score: 447
Period size: 105 Copynumber: 3.9 Consensus size: 105
135510 CCTCGAGACG
* * ** *
135520 AGTTCTTCTCATTATGAACGTTTTCTCC-TCGAGATGAGTTCTTCTTGTTATAAACTCTTCTGCA
1 AGTTCTTCTCATTATGAAC--TTTCTCCTTTGAGACGAGTTCTTCTCATTATGAACTCTTCTG-A
* * * * * *
135584 GAA-GTTGATCCACCTTTTTTTTTTGCGATGTG-TTTGAAAGGAACA
63 AAATGTCGGTCCACC---TCTTTCTGCGATG-GATTTGAAAGGAATA
* ** * *
135629 AGTTCTTCTCATTATGAACCTTCTAATTT-AGAGCGAGTTCTTCTCATTATGAACTCTTTTGGAA
1 AGTTCTTCTCATTATGAACTTTCTCCTTTGAGA-CGAGTTCTTCTCATTATGAACTCTTCTGAAA
* *
135693 ATGTCGGTCCACCTCCTTCTGTGAT-GATTTGAAAGGAATA
65 ATGTCGGTCCACCTCTTTCTGCGATGGATTTGAAAGGAATA
* * *
135733 AGTTCTTCTCATTATGAACTTTCTTCTTTGAGATGAGTTCTTCTCATTATGAACTCTTTTGAAAA
1 AGTTCTTCTCATTATGAACTTTCTCCTTTGAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAA
* *
135798 TATCGGTCCACCTCTTTCTGCGTTGGATTTGAAAGGAATA
66 TGTCGGTCCACCTCTTTCTGCGATGGATTTGAAAGGAATA
* * * *
135838 AGTTCTTCTCATTATGAACTTTCTCCTTTGGGGCGAGTTCTTATCATTATGAACTCTTCTGGAAA
1 AGTTCTTCTCATTATGAACTTTCTCCTTTGAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAA
*
135903 TGTCGGTCCACCTAATTT-TGCGATGGAT
66 TGTCGGTCCACCT-CTTTCTGCGATGGAT
135931 CAAAGTCAGT
Statistics
Matches: 258, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
103 1 0.00
104 88 0.34
105 105 0.41
106 3 0.01
107 9 0.03
108 33 0.13
109 19 0.07
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (105 bp):
AGTTCTTCTCATTATGAACTTTCTCCTTTGAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAA
TGTCGGTCCACCTCTTTCTGCGATGGATTTGAAAGGAATA
Found at i:144305 original size:23 final size:23
Alignment explanation
Indices: 144279--144330 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
144269 TTGAGTGGCA
* **
144279 TATGAAATTTGTCCTTAAGGACC
1 TATGAAATATGTCCCGAAGGACC
144302 TATG-AATATGTCCCGAAGGACC
1 TATGAAATATGTCCCGAAGGACC
144324 TATGAAA
1 TATGAAA
144331 CCATCGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (23 bp):
TATGAAATATGTCCCGAAGGACC
Found at i:149334 original size:71 final size:71
Alignment explanation
Indices: 149214--149584 Score: 379
Period size: 71 Copynumber: 5.2 Consensus size: 71
149204 GGAAATTCAT
* * * *
149214 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGGCGAACCATCAACCATAGAGGAAGTTGAACGC
1 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGACGAACCTTCAACCATAGAGGAAGTCGAACAC
149279 AACCCC
66 AACCCC
* * * * * * * *
149285 GAGCCTCAGTCATGGAGGATACCCCGTTAGTAGACGAGCCTTTAGCCATAGAGGAAGTCAAACAC
1 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGACGAACCTTCAACCATAGAGGAAGTCGAACAC
*
149350 AACCCT
66 AACCCC
* * * * * *
149356 GAGCCTCAGTCATAGAGGAC-ACTCATT-GATAGACAAACCCTAAACCATAGAGGAATTCAAACA
1 GAGCCTCAGTCATAGAGGACAACTCGTTAG-TAGACGAACCTTCAACCATAGAGGAAGTCGAACA
149419 CAACCCC
65 CAACCCC
* * * * * * *
149426 AAGCCTCATTCATGGAAGACAACTCATTAGTAGACGAACCTTCAACCATAGAGAAAGTCGAATAC
1 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGACGAACCTTCAACCATAGAGGAAGTCGAACAC
149491 AACCCC
66 AACCCC
* * * * * * * *
149497 GATCCTTAGTCATAGATGACACCCCGTTACTAGACGAACCTGCAACCAT-GCAGGAAGTCGAACG
1 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGACGAACCTTCAACCATAG-AGGAAGTCGAACA
* *
149561 CAATCTC
65 CAACCCC
149568 GAGCCTCAGTCATAGAG
1 GAGCCTCAGTCATAGAG
149585 CACCCTCATT
Statistics
Matches: 241, Mismatches: 55, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
69 1 0.00
70 55 0.23
71 184 0.76
72 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (71 bp):
GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGACGAACCTTCAACCATAGAGGAAGTCGAACAC
AACCCC
Found at i:149593 original size:141 final size:137
Alignment explanation
Indices: 149214--149594 Score: 379
Period size: 141 Copynumber: 2.7 Consensus size: 137
149204 GGAAATTCAT
* *
149214 GAGCCTCAGTCATAGAGGACAACTCGTTAGTAGGCGAACCATCAACCATAGAGGAAGTTGAACGC
1 GAGCCTCAGTCATAGAGGAC-ACTCGTTA-TAGACGAACC-TCAACCATAGAGGAAGTCGAACGC
* * * * *
149279 AACCCCGAGCCTCAGTCATGGAGGATACCC-CGTTAGTAGACGAGCCTTTAGCCATAGAGGAAGT
63 AACCCCGAGCCTCAGTCATGGA-G--ACCCTCATTAGTAGACGAACCTTCAACCATAGAGAAAGT
*
149343 CAAACACAACCCT
125 CAAACACAACCCC
* * * * * *
149356 GAGCCTCAGTCATAGAGGACACTCATTGATAGACAAACCCTAAACCATAGAGGAATTCAAACACA
1 GAGCCTCAGTCATAGAGGACACTCGTT-ATAGACGAA-CCTCAACCATAGAGGAAGTCGAACGCA
* * * *
149421 ACCCCAAGCCTCATTCATGGAAGACAACTCATTAGTAGACGAACCTTCAACCATAGAGAAAGTCG
64 ACCCCGAGCCTCAGTCATGG-AGAC-CCTCATTAGTAGACGAACCTTCAACCATAGAGAAAGTCA
*
149486 AATACAACCCC
127 AACACAACCCC
* * * *
149497 GATCCTTAGTCATAGATGACACCCCGTTACTAGACGAACCTGCAACCAT-GCAGGAAGTCGAACG
1 GAGCCTCAGTCATAGAGGACA-CTCGTTA-TAGACGAACCT-CAACCATAG-AGGAAGTCGAACG
* * *
149561 CAATCTCGAGCCTCAGTCATAGAGCACCCTCATT
62 CAACCCCGAGCCTCAGTCATGGAG-ACCCTCATT
149595 TAATTTCTAA
Statistics
Matches: 194, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
139 2 0.01
140 1 0.01
141 121 0.62
142 70 0.36
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (137 bp):
GAGCCTCAGTCATAGAGGACACTCGTTATAGACGAACCTCAACCATAGAGGAAGTCGAACGCAAC
CCCGAGCCTCAGTCATGGAGACCCTCATTAGTAGACGAACCTTCAACCATAGAGAAAGTCAAACA
CAACCCC
Found at i:149764 original size:35 final size:35
Alignment explanation
Indices: 149721--149825 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
149711 GAGGTTTTTT
*
149721 AAATATGCTTTGTTATTTTAGTTATTATTATATTA
1 AAATATGCTTTGTTATTTTAATTATTATTATATTA
149756 AAATATGCTTTGTTATTTTAATTATTATTATATTA
1 AAATATGCTTTGTTATTTTAATTATTATTATATTA
* * *
149791 AAATATGCTTTCTTATCTTAATTGTTATTATATTA
1 AAATATGCTTTGTTATTTTAATTATTATTATATTA
149826 TTAGTTATAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (35 bp):
AAATATGCTTTGTTATTTTAATTATTATTATATTA
Found at i:153090 original size:8 final size:8
Alignment explanation
Indices: 153077--153106 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
153067 ATTCATATGC
153077 ATACATGG
1 ATACATGG
153085 ATACATGG
1 ATACATGG
*
153093 ATACATGT
1 ATACATGG
153101 ATACAT
1 ATACAT
153107 TCATGCACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (8 bp):
ATACATGG
Found at i:153200 original size:20 final size:20
Alignment explanation
Indices: 153174--153221 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
153164 CAGGCGCATA
*
153174 CACACATGCATACATACATG
1 CACACATGCACACATACATG
* *
153194 TACACATGCACACGTACATG
1 CACACATGCACACATACATG
153214 CACACATG
1 CACACATG
153222 TTAGCATGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (20 bp):
CACACATGCACACATACATG
Found at i:155833 original size:15 final size:15
Alignment explanation
Indices: 155813--155842 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
155803 CATGGTAACA
155813 ATATCGATACTGGGT
1 ATATCGATACTGGGT
155828 ATATCGATACTGGGT
1 ATATCGATACTGGGT
155843 CACATTTTCT
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:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ATATCGATACTGGGT
Found at i:158579 original size:54 final size:55
Alignment explanation
Indices: 158466--158583 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 55
158456 AATGGCATTA
* * *
158466 TGTGTGCAAAACTAGGAAATTCATAATAAGTTTACGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTACGAATTTCCGTATGGGCAATG
* * * * *
158521 TGTGTGCAAAA-TAATAAATTCATAATAAGTTTATGAATTTCGGTATTGGTAATG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTACGAATTTCCGTATGGGCAATG
158575 TGTGTGCAA
1 TGTGTGCAA
158584 CCCACGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 44 0.80
55 11 0.20
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTACGAATTTCCGTATGGGCAATG
Found at i:159225 original size:242 final size:237
Alignment explanation
Indices: 158712--159360 Score: 810
Period size: 242 Copynumber: 2.7 Consensus size: 237
158702 ACTATTCCAA
* *
158712 AGTAAAAGATTAATGGCCTAG-CTGCATTTGATAGAAATGTGTCAATTA-CCAGTTAGATGAAAG
1 AGTAAAAGATTAATGGCCTAGTATGCATTTGACAGAAATGTGTCAATTATCCAGTTAGATGAAAG
* *
158775 GTTAAATACCTTTGAGT-AAATATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTAT
66 GTTAAATACCTTTGAGTAAAATATTAATAGCCTAG--CTGCATTTGACAGAAAT-T-TCAATTAT
*
158839 GCCAA-TTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGACTAGTTATGCATTTGAC
127 G-CAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGACTAGCTATGCATTTGAC
* *
158903 AGAAAGGTGTCAATTATTCCAGTTAGATGAAAGATTAAATACCTTTG
191 AGAAAGATGTCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTG
* *
158950 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAG-TATGCATTTGACAGAAATGTGTCAATTAT-CCAGTTAGATGAA
* * *
159015 AGGTTAAATACCTTTGAGTAAAAGACTAAT-GTCTAGCTGCATTTGACAGAAATATTCAATTATG
64 AGGTTAAATACCTTTGAGTAAAATATTAATAGCCTAGCTGCATTTGACAGAAAT-TTCAATTATG
* * *
159079 CTAGTTAGATGAAAGGTTAAATACCTTTCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTG
128 CAAGTTAGATGAAAGGTTAAATA-C---CTTTGAGTAAAAGATTAATGGACTAGCTATGCATTTG
* *
159144 ACAGAAATATGTCAATTATGCCAGTTAGATGAAATG-TT-AATATCTTTG
189 ACAGAAAGATGTCAATTATGCCAGTTAGATGAAA-GATTAAATACCTTTG
* *
159192 AGTAAAATGA-TAATGGCCTAGTTATGGATTTGACAGAAATGTGTCATTTATACCAGTTAGATGA
1 AGTAAAA-GATTAATGGCCTAG-TATGCATTTGACAGAAATGTGTCAATTAT-CCAGTTAGATGA
* * * * *
159256 AAGGTTAAATACATTTGAGTAAAATATTAATAGCCTAGCTATGCATTTAACATGAAGTGTCAATC
63 AAGGTTAAATACCTTTGAGTAAAATATTAATAGCCTAGC--TGCATTTGACA-GAAATTTCAATT
* * * * *
159321 ATGCAAGTTAGATGAAATGCTATATGCCTTTGGGTAAAAG
125 ATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
159361 TCTAAAGGTT
Statistics
Matches: 359, Mismatches: 36, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
238 23 0.06
239 28 0.08
240 42 0.12
241 12 0.03
242 129 0.36
243 83 0.23
244 2 0.01
245 36 0.10
246 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (237 bp):
AGTAAAAGATTAATGGCCTAGTATGCATTTGACAGAAATGTGTCAATTATCCAGTTAGATGAAAG
GTTAAATACCTTTGAGTAAAATATTAATAGCCTAGCTGCATTTGACAGAAATTTCAATTATGCAA
GTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGACTAGCTATGCATTTGACAGAAA
GATGTCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTG
Found at i:159358 original size:80 final size:81
Alignment explanation
Indices: 158712--159360 Score: 838
Period size: 81 Copynumber: 8.1 Consensus size: 81
158702 ACTATTCCAA
*
158712 AGTAAAAGATTAATGGCCTAGC--TGCATTTGATAGAAATGTGTCAATTA--CCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
158773 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
158789 AGT-AAATATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
158853 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
158869 AGTAAAAGATTAATGGACTAGTTATGCATTTGACAGAAAGGTGTCAATTATTCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
*
158934 AGATTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
158950 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
159015 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
159031 AGTAAAAGACTAAT-GTCTAGC--TGCATTTGACAGAAATAT-TCAATTATGCTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
159092 AGGTTAAATACCTTTCTTTG
66 AGGTTAAATA-C---CTTTG
* *
159112 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
* *
159177 ATGTT-AATATCTTTG
66 AGGTTAAATACCTTTG
* * * *
159192 AGTAAAATGA-TAATGGCCTAGTTATGGATTTGACAGAAATGTGTCATTTATACCAGTTAGATGA
1 AGTAAAA-GATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGA
*
159256 AAGGTTAAATACATTTG
65 AAGGTTAAATACCTTTG
* * * * *
159273 AGTAAAATATTAATAGCCTAGCTATGCATTTAACATG-AA-GTGTCAATCATGCAAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTATGCATTTGACA-GAAATGTGTCAATTATGCCAGTTAGATGA
* * * *
159336 AATGCTATATGCCTTTG
65 AAGGTTAAATACCTTTG
*
159353 GGTAAAAG
1 AGTAAAAG
159361 TCTAAAGGTT
Statistics
Matches: 504, Mismatches: 51, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
76 16 0.03
77 34 0.07
78 42 0.08
80 141 0.28
81 217 0.43
82 7 0.01
84 22 0.04
85 25 0.05
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Done.