Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003203.1 Hibiscus syriacus cultivar Beakdansim tig00006742_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: 64054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3156 original size:2 final size:2
Alignment explanation
Indices: 3149--3187 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
3139 TGTATTGTTA
3149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
3188 GGCGTGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12848 original size:21 final size:21
Alignment explanation
Indices: 12807--12849 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12797 CCCCGGGAGG
*
12807 TAGTTCTTCACGAGCTGCTCC
1 TAGTTCTTCACGAGCTCCTCC
* *
12828 TAGTTCTTCTCGTGCTCCTCC
1 TAGTTCTTCACGAGCTCCTCC
12849 T
1 T
12850 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.35, G:0.16, T:0.40
Consensus pattern (21 bp):
TAGTTCTTCACGAGCTCCTCC
Found at i:13498 original size:31 final size:31
Alignment explanation
Indices: 13427--13506 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
13417 ATTTAACAAA
* * **
13427 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
*
13458 AAGGGGGAGTAAGTTTTTGATGTGCTATATT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
13489 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
13507 CAAAAATCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.33
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:13538 original size:13 final size:13
Alignment explanation
Indices: 13504--13532 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13494 GGAGTAAGTT
13504 TTTCAAAAATCAA
1 TTTCAAAAATCAA
13517 TTTCAAAAAT-AA
1 TTTCAAAAATCAA
13529 TTTC
1 TTTC
13533 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTCAAAAATCAA
Found at i:18922 original size:2 final size:2
Alignment explanation
Indices: 18915--18942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18905 ACCATATACA
18915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18943 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18947 original size:2 final size:2
Alignment explanation
Indices: 18942--18969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18932 TATATATATA
18942 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18970 AATGTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19601 original size:14 final size:14
Alignment explanation
Indices: 19559--19634 Score: 53
Period size: 14 Copynumber: 5.0 Consensus size: 14
19549 TCTACAATAG
*
19559 TATTAGTACTACAA
1 TATTCGTACTACAA
*
19573 TAGTATCAATACTACAA
1 TA-T-TC-GTACTACAA
19590 TATTCGTACTACAA
1 TATTCGTACTACAA
* *
19604 CAGTATCGGTACTACTA
1 TA-T-TC-GTACTACAA
*
19621 TATTGGTACTACAA
1 TATTCGTACTACAA
19635 CAATATTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
14 19 0.40
15 5 0.10
16 5 0.10
17 19 0.40
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (14 bp):
TATTCGTACTACAA
Found at i:19602 original size:31 final size:31
Alignment explanation
Indices: 19559--19665 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 31
19549 TCTACAATAG
*
19559 TATTAGTACTACAATAGTATCAATACTACAA
1 TATTAGTACTACAACAGTATCAATACTACAA
* ** *
19590 TATTCGTACTACAACAGTATCGGTACTACTA
1 TATTAGTACTACAACAGTATCAATACTACAA
* * ** * *
19621 TATTGGTACTACAACAATATTGATTCTACAT
1 TATTAGTACTACAACAGTATCAATACTACAA
*
19652 TATTGGTACTACAA
1 TATTAGTACTACAA
19666 GAACATTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (31 bp):
TATTAGTACTACAACAGTATCAATACTACAA
Found at i:19617 original size:17 final size:17
Alignment explanation
Indices: 19550--19618 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
19540 AGTATTGATT
*
19550 CTACAATAGTATTAGTA
1 CTACAATAGTATCAGTA
*
19567 CTACAATAGTATCAATA
1 CTACAATAGTATCAGTA
19584 CTACAATA-T-TC-GTA
1 CTACAATAGTATCAGTA
* *
19598 CTACAACAGTATCGGTA
1 CTACAATAGTATCAGTA
19615 CTAC
1 CTAC
19619 TATATTGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.20
15 3 0.07
16 3 0.07
17 30 0.67
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (17 bp):
CTACAATAGTATCAGTA
Found at i:19642 original size:17 final size:17
Alignment explanation
Indices: 19586--19642 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
19576 TATCAATACT
*
19586 ACAATATTCGTACTACA
1 ACAATATTGGTACTACA
* *
19603 ACAGTATCGGTACT---
1 ACAATATTGGTACTACA
*
19617 ACTATATTGGTACTACA
1 ACAATATTGGTACTACA
19634 ACAATATTG
1 ACAATATTG
19643 ATTCTACATT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 11 0.37
17 19 0.63
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (17 bp):
ACAATATTGGTACTACA
Found at i:19673 original size:20 final size:20
Alignment explanation
Indices: 19648--19705 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
19638 TATTGATTCT
*
19648 ACATTATTGGTACTACAAGA
1 ACATTATTGATACTACAAGA
*
19668 ACATTAATGATACTACAAGA
1 ACATTATTGATACTACAAGA
* *
19688 ACAATATAGATACTACAA
1 ACATTATTGATACTACAA
19706 CTGAGAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (20 bp):
ACATTATTGATACTACAAGA
Found at i:20225 original size:14 final size:14
Alignment explanation
Indices: 20206--20233 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20196 ACTACAATTG
20206 TATTGGTACTACAA
1 TATTGGTACTACAA
20220 TATTGGTACTACAA
1 TATTGGTACTACAA
20234 CAATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TATTGGTACTACAA
Found at i:20236 original size:17 final size:17
Alignment explanation
Indices: 20216--20289 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
20206 TATTGGTACT
20216 ACAATATTGGTACTACA
1 ACAATATTGGTACTACA
* * *
20233 ACAATATAT--TAATCCT
1 ACAATAT-TGGTACTACA
*
20249 ACAATATTCGTACTACA
1 ACAATATTGGTACTACA
* *
20266 ATAATTTTGGTACTACA
1 ACAATATTGGTACTACA
20283 ACAATAT
1 ACAATAT
20290 CGGTTCTATA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
15 1 0.02
16 11 0.26
17 30 0.70
18 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (17 bp):
ACAATATTGGTACTACA
Found at i:20336 original size:20 final size:20
Alignment explanation
Indices: 20313--20354 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
20303 TTTGTAATAT
* *
20313 AAGAATAATATCGATACTAC
1 AAGAACAATATAGATACTAC
20333 AAGAACAATATAGATACTAC
1 AAGAACAATATAGATACTAC
20353 AA
1 AA
20355 CAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (20 bp):
AAGAACAATATAGATACTAC
Found at i:20879 original size:21 final size:21
Alignment explanation
Indices: 20831--20873 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20821 TGAGATGAAG
* **
20831 AATGGAGAAGAAAACTAAAGA
1 AATGAAGAAGAAAAAAAAAGA
20852 AATGAAGAAGAAAAAAAAAGA
1 AATGAAGAAGAAAAAAAAAGA
20873 A
1 A
20874 GAGAAGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (21 bp):
AATGAAGAAGAAAAAAAAAGA
Found at i:22257 original size:14 final size:14
Alignment explanation
Indices: 22238--22266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22228 GAATAGGAGC
22238 ATGCATCAACTTCT
1 ATGCATCAACTTCT
22252 ATGCATCAACTTCT
1 ATGCATCAACTTCT
22266 A
1 A
22267 ATTTAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (14 bp):
ATGCATCAACTTCT
Found at i:22449 original size:31 final size:30
Alignment explanation
Indices: 22411--22469 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
22401 GACCTATGTT
22411 CCCTTAAAA-TTTAAAATAATTATAATTTAAA
1 CCCTTAAAAGTTTAAAAT-ATT-TAATTTAAA
22442 CCCTTAAAAGTTTTAAAATATTTAATTT
1 CCCTTAAAAG-TTTAAAATATTTAATTT
22470 GGCCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 15 0.58
32 3 0.12
33 8 0.31
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (30 bp):
CCCTTAAAAGTTTAAAATATTTAATTTAAA
Found at i:24799 original size:24 final size:23
Alignment explanation
Indices: 24772--24819 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
24762 TTTTTGGGTG
24772 AAATGAATTAACTATTTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
24796 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
24819 A
1 A
24820 TAGAGATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:29707 original size:186 final size:184
Alignment explanation
Indices: 29396--29766 Score: 708
Period size: 186 Copynumber: 2.0 Consensus size: 184
29386 CGGTGCTTTG
29396 AGTAACGTTGGACAGTTGCAACATGAAGAACATGCCTAGCTTATAGTAAATAAAGAAAGAAGTGG
1 AGTAACGTTGGACAGTTGCAACATGAAGAACATGCCTAGCTTATAGTAAATAAAGAAAGAAGTGG
29461 GATATACTATTTATTTTATTACCGAAGGCTTAGGCTTCTATGGGACCAGCCGAACATGCTTCGGG
66 GATATACTATTTATTTTATTACCGAAGGCTTAGGCTTCTATGGGACCAGCCGAACATGCTTCGGG
29526 ACATC-GTCTCGCAGGATACAACAACAAACGTTCCCAACAGTAAGCACAACCAC
131 ACATCGGTCTCGCAGGATACAACAACAAACGTTCCCAACAGTAAGCACAACCAC
29579 AGTAACGTTGGACAGTTGCAACATGAAGAACATGCCTTAGCTTATAGGTAAAATAAAGAAAGAAG
1 AGTAACGTTGGACAGTTGCAACATGAAGAACATGCC-TAGCTTATA-GT-AAATAAAGAAAGAAG
29644 TGGGATATACTATTTATTTTATTACCGAAGGCTTAGGCTTCTATGGGACCAGCCGAACATGCTTC
63 TGGGATATACTATTTATTTTATTACCGAAGGCTTAGGCTTCTATGGGACCAGCCGAACATGCTTC
29709 GGGACATCGGTCTCGCAGGATACAACAACAAACGTTCCCAACAGTAAGCACAACCAC
128 GGGACATCGGTCTCGCAGGATACAACAACAAACGTTCCCAACAGTAAGCACAACCAC
29766 A
1 A
29767 ATGAACAATC
Statistics
Matches: 184, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
183 36 0.20
184 9 0.05
185 2 0.01
186 88 0.48
187 49 0.27
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (184 bp):
AGTAACGTTGGACAGTTGCAACATGAAGAACATGCCTAGCTTATAGTAAATAAAGAAAGAAGTGG
GATATACTATTTATTTTATTACCGAAGGCTTAGGCTTCTATGGGACCAGCCGAACATGCTTCGGG
ACATCGGTCTCGCAGGATACAACAACAAACGTTCCCAACAGTAAGCACAACCAC
Found at i:30432 original size:20 final size:21
Alignment explanation
Indices: 30407--30499 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
30397 TTTTCCCAAT
*
30407 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
30427 TCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
30448 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30468 TCGCAAAGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
30489 TCGCAATGCGA
1 TCGCAATGCGA
30500 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:30452 original size:41 final size:41
Alignment explanation
Indices: 30407--30499 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
30397 TTTTCCCAAT
* *
30407 TCGCAATGCGAATAAGTAAATCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
30448 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
30489 TCGCAATGCGA
1 TCGCAATGCGA
30500 TACTTACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
Found at i:30512 original size:41 final size:41
Alignment explanation
Indices: 30426--30560 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
30416 GAATAAGTAA
* ** *
30426 ATCGCAACGTGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
*
30467 ATCGCAAAGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
30508 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
30549 TTCGCAACGCGA
1 ATCGCAACGCGA
30561 TACTGACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 5 0.06
41 72 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:30513 original size:20 final size:20
Alignment explanation
Indices: 30488--30581 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
30478 AATTGGGAAA
*
30488 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
30508 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
30529 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
30549 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
30569 TTCGCAACGCGAT
1 ATCGCAACGCGAT
30582 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:31137 original size:19 final size:19
Alignment explanation
Indices: 31098--31164 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31088 TTCGAGAATG
31098 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCG-AAATA
**
31118 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
31137 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
31156 AAAATCGCA
1 AAAATCGCA
31165 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:31182 original size:19 final size:19
Alignment explanation
Indices: 31160--31344 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
31150 GAAACCAAAA
*
31160 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31179 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
31198 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
31217 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
31237 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
31253 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
31270 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
31284 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
31303 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
31323 ATCTCATTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
31343 TC
1 TC
31345 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31237 original size:39 final size:38
Alignment explanation
Indices: 31160--31344 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
31150 GAAACCAAAA
*
31160 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
31198 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
31237 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
31270 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
31303 TCCGCGTTGCGATTCTCATTATCTCATTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
31343 TC
1 TC
31345 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 17 0.14
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:31321 original size:20 final size:20
Alignment explanation
Indices: 31287--31344 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
31277 GCGATTCTCT
**
31287 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
31307 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
* *
31327 CATTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
31345 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:33404 original size:42 final size:42
Alignment explanation
Indices: 33344--33466 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
33334 GCCCGACTCG
* * *
33344 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
33386 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
33428 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
33467 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:33424 original size:21 final size:21
Alignment explanation
Indices: 33400--33466 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
33390 TCATTCCTCG
33400 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
33421 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
33442 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
33463 AGAG
1 AGAG
33467 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:34841 original size:14 final size:14
Alignment explanation
Indices: 34822--34855 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
34812 ATTGTTTAAT
34822 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
34836 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
34850 TGATTT
1 TGATTT
34856 ATTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:35058 original size:19 final size:19
Alignment explanation
Indices: 35036--35186 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
35026 CGAAATTAAA
35036 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
35055 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
35070 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
35088 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
35102 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
35121 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
35136 -TCTCGTTGCGATTTACAT
1 TTCGCGTTGCGATTTTCAT
* ** *
35154 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
35173 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
35187 GGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 27 0.30
16 5 0.05
17 6 0.07
19 43 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:35082 original size:33 final size:32
Alignment explanation
Indices: 35040--35166 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
35030 ATTAAATTCG
35040 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
35073 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
35106 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
35139 CGTTGCGATTTACATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
35167 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:35129 original size:66 final size:66
Alignment explanation
Indices: 35033--35165 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
35023 ACGCGAAATT
* *
35033 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTACATTTCGCATTGC
35098 G
66 G
* *
35099 AAATTAGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTACATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTACATTTCGCATTGC
35164 G
66 G
35165 A
1 A
35166 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTACATTTCGCATTGC
G
Found at i:35185 original size:20 final size:19
Alignment explanation
Indices: 35139--35193 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
35129 GTGATTCTCT
*
35139 CGTTGCGATTTACATTTCG
1 CGTTGCGATGTACATTTCG
*
35158 CATTGCGATAGTA-ATTTCCG
1 CGTTGCGAT-GTACATTT-CG
*
35178 CGTTGCGATGGACATT
1 CGTTGCGATGTACATT
35194 AAGATGATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (19 bp):
CGTTGCGATGTACATTTCG
Found at i:37476 original size:12 final size:12
Alignment explanation
Indices: 37459--37483 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37449 TCTTCGGGGA
37459 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37471 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37483 C
1 C
37484 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37692 original size:24 final size:24
Alignment explanation
Indices: 37658--37711 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37648 CTGAAACATC
* *
37658 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
37682 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
37706 ATCAAA
1 ATCAAA
37712 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:38796 original size:20 final size:20
Alignment explanation
Indices: 38771--38828 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
38761 ATTCATTTGA
38771 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
38791 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
38811 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
38829 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:40929 original size:20 final size:19
Alignment explanation
Indices: 40894--40960 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
40884 GAAACTTAAA
40894 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
40913 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
40933 ATCGCAATGCAAAATGAAA
1 ATCGCAACGCGAAATGACT
40952 ATCGCAACG
1 ATCGCAACG
40961 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:40966 original size:14 final size:14
Alignment explanation
Indices: 40949--41006 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
40939 ATGCAAAATG
40949 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40963 AAAATCGCAACGAGAA
1 AAAATCGCAAC--GAC
40979 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
40995 AAAATCGCAACG
1 AAAATCGCAACG
41007 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40991 original size:32 final size:33
Alignment explanation
Indices: 40944--41011 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
40934 TCGCAATGCA
40944 AAATGAAAATCGCAACGACAAAATCGCAACGAG
1 AAATGAAAATCGCAACGACAAAATCGCAACGAG
*
40977 AAATG-AAATCGCAACGACAAAATCGCAACGCG
1 AAATGAAAATCGCAACGACAAAATCGCAACGAG
41009 AAA
1 AAA
41012 CACAAATCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGACAAAATCGCAACGAG
Found at i:41059 original size:14 final size:14
Alignment explanation
Indices: 41040--41097 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
41030 TTTCATTTCG
41040 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
41054 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
41070 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
41086 CGTTGCGATTTT
1 CGTTGCGATTTT
41098 CATTTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:41109 original size:33 final size:33
Alignment explanation
Indices: 41023--41113 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
41013 ACAAATCGCA
*
41023 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
41056 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
41088 TTGCGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
41114 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:41120 original size:19 final size:20
Alignment explanation
Indices: 41098--41141 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41088 TTGCGATTTT
41098 CATTT-CACATTGCGATAGC
1 CATTTCCACATTGCGATAGC
* * *
41117 CATTTCCGCGTTGCGATAGT
1 CATTTCCACATTGCGATAGC
41137 CATTT
1 CATTT
41142 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCACATTGCGATAGC
Found at i:41132 original size:20 final size:20
Alignment explanation
Indices: 41107--41152 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41097 TCATTTCACA
41107 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
41127 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
41147 TTGCGA
1 TTGCGA
41153 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:41645 original size:18 final size:18
Alignment explanation
Indices: 41619--41663 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
41609 GTCGATCAGA
*
41619 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
41637 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
41655 TGATGGCTC
1 TGATGGCTC
41664 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:43008 original size:20 final size:20
Alignment explanation
Indices: 42983--43020 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42973 AATAGTTTCT
42983 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
43003 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
43021 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:43309 original size:22 final size:22
Alignment explanation
Indices: 43284--43327 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43274 GATTTAGATA
43284 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
43306 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
43328 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:43540 original size:20 final size:20
Alignment explanation
Indices: 43515--43608 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
43505 GATTATGTAT
43515 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
43535 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
43555 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
43576 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
43596 TATCGCATTGCGA
1 TATCGCGTTGCGA
43609 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:43609 original size:20 final size:20
Alignment explanation
Indices: 43495--43609 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
43485 CGCTTTGAAA
*
43495 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
43516 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
43536 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
43556 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
43577 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
43597 ATCGCATTGCGAT
1 ATCGCATTGCGAT
43610 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:43627 original size:21 final size:21
Alignment explanation
Indices: 43598--43690 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
43588 ATAGTCAGTA
43598 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
43619 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
43639 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
43660 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
43680 TCGCATTGCGA
1 TCGCATTGCGA
43691 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:43628 original size:41 final size:41
Alignment explanation
Indices: 43537--43671 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
43527 AAAGTCAGTA
* * * ** *
43537 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
43577 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
43619 TCGCGTTGCGAT-TTACTTATTCGCATTACGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
43660 TCGCGTTGCGAT
1 TCGCGTTGCGAT
43672 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:43672 original size:41 final size:41
Alignment explanation
Indices: 43598--43686 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
43588 ATAGTCAGTA
*
43598 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
43639 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
43680 TCGCATT
1 TCGCATT
43687 GCGAATTGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (41 bp):
TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:51368 original size:24 final size:24
Alignment explanation
Indices: 51355--51464 Score: 150
Period size: 24 Copynumber: 4.6 Consensus size: 24
51345 AAACATAATT
* *
51355 CATGTCAAGTATCATATCACAATC
1 CATGTCAAGTATCAGATCAGAATC
*
51379 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
51403 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
51427 CATGTCAAGTATCAGATCAGAATT
1 CATGTCAAGTATCAGATCAGAATC
* *
51451 CAAGTCGAGTATCA
1 CATGTCAAGTATCA
51465 TATAAAATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
23 2 0.03
24 73 0.95
25 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:55959 original size:24 final size:24
Alignment explanation
Indices: 55946--56064 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
55936 AAACATAATT
*
55946 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
55970 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
55994 TAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
56018 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
56042 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
56065 TCAAGTCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:56080 original size:48 final size:47
Alignment explanation
Indices: 55946--56082 Score: 175
Period size: 48 Copynumber: 2.9 Consensus size: 47
55936 AAACATAATT
* * *
55946 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCCAAGTCAA-TATCATATCAGAATC
* * *
55994 TAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCCAAGTCA-ATATCATATCAGAATC
* *
56042 CATGTCAAGTATCAGATCAGAATTCAAGTCGAAAATCATAT
1 CATGTCAAGTATCAGATCAGAATCCAAGTC-AATATCATAT
56083 AACATATTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 75 0.97
49 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (47 bp):
CATGTCAAGTATCAGATCAGAATCCAAGTCAATATCATATCAGAATC
Found at i:57694 original size:17 final size:18
Alignment explanation
Indices: 57663--57698 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
57653 AAACTAACAT
57663 TTTTTATACACATCAATA
1 TTTTTATACACATCAATA
*
57681 TTTTTAT-CAGATCAATA
1 TTTTTATACACATCAATA
57698 T
1 T
57699 GTCTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTTATACACATCAATA
Found at i:58602 original size:18 final size:18
Alignment explanation
Indices: 58542--58604 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
58532 CGCCGGTTAA
58542 CGGGTCGGGTCAA-GGGT
1 CGGGTCGGGTCAATGGGT
*
58559 CGGGTCGGGTCAATGAGT
1 CGGGTCGGGTCAATGGGT
* *
58577 CAGATCGGGTCAATGGGT
1 CGGGTCGGGTCAATGGGT
58595 CGGGTCGGGT
1 CGGGTCGGGT
58605 TGTAACCGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 13 0.33
18 26 0.67
ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTCAATGGGT
Found at i:63434 original size:157 final size:161
Alignment explanation
Indices: 63146--63456 Score: 524
Period size: 157 Copynumber: 2.0 Consensus size: 161
63136 CAGGCTCTAA
63146 TTAACCAAATTAATTATGTTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAA
1 TTAACCAAATTAATTATGTTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAA
* * **
63211 GTCTAAGGGTTAGGGCTTTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATTGAATAATC
66 GTCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATCAAATAATC
63276 GATG-AAACCC-TCGGCATAAAGGCGATGGC
131 GATGAAAACCCTTCGGCATAAAGGCGATGGC
*
63305 TTAACCTAATTAATTATG-TTAAAT-ACATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAA
1 TTAACCAAATTAATTATGTTTAAATGA-ATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAA
63368 AGTCTAA-GGTTAAGGCTCTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATCAAATAAT
65 AGTCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATCAAATAAT
*
63432 CGATGAAAACCCTTGGGCATAAAGG
130 CGATGAAAACCCTTCGGCATAAAGG
63457 TGAGGGCCAA
Statistics
Matches: 143, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
157 59 0.41
158 56 0.39
159 28 0.20
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (161 bp):
TTAACCAAATTAATTATGTTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAA
GTCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATCAAATAATC
GATGAAAACCCTTCGGCATAAAGGCGATGGC
Done.