Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005563.1 Hibiscus syriacus cultivar Beakdansim tig00012903_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: 93473
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:420 original size:21 final size:21
Alignment explanation
Indices: 355--420 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
345 GTGAATCGGG
*
355 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
375 CCTCTTCAAC-GTGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
396 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
417 CTCT
1 CTCT
421 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.18, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:440 original size:42 final size:42
Alignment explanation
Indices: 393--476 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
383 ACGTGACAGT
* * *
393 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
435 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
477 TGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:2536 original size:33 final size:33
Alignment explanation
Indices: 2479--2577 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2469 ACGAGATAAT
*
2479 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2513 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2546 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2578 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2571 original size:19 final size:19
Alignment explanation
Indices: 2454--2619 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
2444 TCTTTTGGTT
*
2454 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2473 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2493 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2511 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2527 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2545 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2560 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2580 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2599 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2618 GA
1 GA
2620 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2648 original size:19 final size:19
Alignment explanation
Indices: 2615--2681 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2605 AAAATCGCAA
**
2615 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2634 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2653 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2673 TGCGATTTT
1 TGCGATTTT
2682 CATTCTCGAA
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:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3289 original size:21 final size:21
Alignment explanation
Indices: 3260--3334 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
3250 ATAGTAAGTA
*
3260 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
3281 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
3302 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
3322 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3335 ACTTATTCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:3290 original size:41 final size:41
Alignment explanation
Indices: 3198--3292 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
3188 CGCTATGTAA
* * * * ** *
3198 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
3239 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
3281 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3293 TTTCCCAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:3338 original size:19 final size:20
Alignment explanation
Indices: 3279--3351 Score: 94
Period size: 19 Copynumber: 3.6 Consensus size: 20
3269 GATTTTCCCA
* **
3279 ATTCGCGTTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
3300 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
3320 ATTCGCGTTGCGA-TTACTT
1 ATTCGCGTTGCGATTTACTT
*
3339 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
3352 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.38
20 17 0.35
21 13 0.27
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:3839 original size:27 final size:23
Alignment explanation
Indices: 3797--3862 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
3787 TTTTCATATT
3797 ATTAATT-TT-AA-AAATATTACA
1 ATTAATTATTAAACAAATATTA-A
*
3818 ATTTATATTATTAAACAGAATATTAT
1 A-TTA-ATTATTAAACA-AATATTAA
3844 ATTAATTATTAAACAAATA
1 ATTAATTATTAAACAAATA
3863 ACTATTGGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 1 0.03
22 3 0.08
23 7 0.18
24 13 0.34
25 5 0.13
26 2 0.05
27 7 0.18
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTAATTATTAAACAAATATTAA
Found at i:5709 original size:3 final size:3
Alignment explanation
Indices: 5701--5736 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
5691 GCATAAGCAT
5701 AAG AAG AAG AAG AAG AAG AAG AGAG AATG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG A-AG AA-G AAG AAG A
5737 TGCTTGAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:7001 original size:18 final size:17
Alignment explanation
Indices: 6972--7014 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
6962 AGAAATAGAT
6972 TTTAAGAATATAAAAAATA
1 TTTAA-AATATAAAAAA-A
* *
6991 TTTAAAATATATAAGAA
1 TTTAAAATATAAAAAAA
7008 TTTAAAA
1 TTTAAAA
7015 ATTTTAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
TTTAAAATATAAAAAAA
Found at i:8948 original size:3 final size:3
Alignment explanation
Indices: 8940--8984 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
8930 GGAAATAGTC
8940 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8985 GCTCAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10358 original size:20 final size:20
Alignment explanation
Indices: 10333--10411 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
10323 ATTTCTGTTA
*
10333 CGCAACTCGATTTTTAAATT
1 CGCAACACGATTTTTAAATT
* ***
10353 CGCAACACGAGTTTTGTTTT
1 CGCAACACGATTTTTAAATT
* **
10373 CGCAACTCGATTTTCGAATT
1 CGCAACACGATTTTTAAATT
*
10393 CGCAACACGA-ATTTAAATT
1 CGCAACACGATTTTTAAATT
10412 TTGCAACTCA
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (20 bp):
CGCAACACGATTTTTAAATT
Found at i:10377 original size:40 final size:40
Alignment explanation
Indices: 10311--10406 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
10301 ATTTGACATT
* *
10311 TTCGTAACACGAATTTCTGTTACGCAACTCGATTTTTAAA
1 TTCGCAACACGAATTTCTGTTACGCAACTCGATTTTCAAA
* * *
10351 TTCGCAACACGAGTTT-TGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCTG-TTACGCAACTCGATTTTCAAA
10391 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
10407 AAATTTTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 2 0.04
40 47 0.96
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (40 bp):
TTCGCAACACGAATTTCTGTTACGCAACTCGATTTTCAAA
Found at i:10418 original size:40 final size:40
Alignment explanation
Indices: 10213--10440 Score: 121
Period size: 40 Copynumber: 5.7 Consensus size: 40
10203 CAACGAATTT
* ***
10213 GCAACTC-AATTTCGAATTCGCAACACGAAAGCCAA-TTTC
1 GCAACTCGATTTTCGAATTCGCAACACG-AATTTAATTTTC
* * * *
10252 GCAACAC-AGTTTCTGAATTCGCAACACAGAA-GTAGA-ATTC
1 GCAACTCGATTTTC-GAATTCGCAACAC-GAATTTA-ATTTTC
* * * * *
10292 GCAACTCAAATTT-GACATTTTCGTAACACGAATTT-CTGTTAC
1 GCAACTCGATTTTCGA-A--TTCGCAACACGAATTTAAT-TTTC
** * **
10334 GCAACTCGATTTTTAAATTCGCAACACGAGTTTTGTTTTC
1 GCAACTCGATTTTCGAATTCGCAACACGAATTTAATTTTC
10374 GCAACTCGATTTTCGAATTCGCAACACGAATTTAAATTTT-
1 GCAACTCGATTTTCGAATTCGCAACACGAATTT-AATTTTC
* * **
10414 GCAACTCAAATTTCGTTTTCGCAACAC
1 GCAACTCGATTTTCGAATTCGCAACAC
10441 AAATGTTTTG
Statistics
Matches: 148, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
39 14 0.09
40 96 0.65
41 13 0.09
42 24 0.16
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (40 bp):
GCAACTCGATTTTCGAATTCGCAACACGAATTTAATTTTC
Found at i:10437 original size:20 final size:20
Alignment explanation
Indices: 10351--10444 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
10341 GATTTTTAAA
* * *
10351 TTCGCAACACGAGTTTTGTT
1 TTCGCAACACAAATTTCGTT
* * * **
10371 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACAAATTTCGTT
* **
10391 TTCGCAACACGAATTTAAATT
1 TTCGCAACACAAATTT-CGTT
*
10412 TT-GCAACTCAAATTTCGTT
1 TTCGCAACACAAATTTCGTT
10431 TTCGCAACACAAAT
1 TTCGCAACACAAAT
10445 GTTTTGGGTA
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
19 4 0.07
20 50 0.89
21 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAATTTCGTT
Found at i:12608 original size:93 final size:92
Alignment explanation
Indices: 12449--12625 Score: 300
Period size: 93 Copynumber: 1.9 Consensus size: 92
12439 GGATACGACG
* *
12449 GTTGGATTGGGATGAGATACTATCATATATGACGATCGATGATGTAAGTAAATACAAATACTTAT
1 GTTGGATTGGGATGAGATACTACCATATATGACGATCGATGATGTAAGTAAACACAAATACTTAT
*
12514 TTAAATTGGTGGTTATTGGGATCTGACA
66 TTAAAATGGTGGTT-TTGGGATCTGACA
* *
12542 GTTGGATTGGGATGGGATACTACCATATGTGACGATCGATGATGTAAGTAAACACAAATACTTAT
1 GTTGGATTGGGATGAGATACTACCATATATGACGATCGATGATGTAAGTAAACACAAATACTTAT
12607 TTAAAATGGTGGTTTTGGG
66 TTAAAATGGTGGTTTTGGG
12626 TGTACACACA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 5 0.06
93 74 0.94
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.33
Consensus pattern (92 bp):
GTTGGATTGGGATGAGATACTACCATATATGACGATCGATGATGTAAGTAAACACAAATACTTAT
TTAAAATGGTGGTTTTGGGATCTGACA
Found at i:12869 original size:42 final size:42
Alignment explanation
Indices: 12822--13029 Score: 280
Period size: 42 Copynumber: 5.0 Consensus size: 42
12812 CCCAACTTTT
* *
12822 TCATCGAGTCGATTCTCCACTTCGACACCAAGATCCATCACC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
* *
12864 TCATCGAGCTGATTCTCCACTTCGACACCGAGATCCATCACT
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
* *
12906 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATTACC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
* *
12948 TCATCGAGCCGATTCTACACCTT-GACATCGAGATCCATCACC
1 TCATCGAGCCGATTCTCCA-CTTCGACACCGAGATCCATCACC
* * *
12990 TC-T--AGCCGACTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
13029 T
1 T
13030 ATTCCATCAC
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.01
39 31 0.21
41 1 0.01
42 112 0.75
43 3 0.02
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.24
Consensus pattern (42 bp):
TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
Found at i:13155 original size:21 final size:21
Alignment explanation
Indices: 13129--13176 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
13119 ACCTCCACGG
*
13129 GATGAGTTAGACGCTTAACGT
1 GATGAGATAGACGCTTAACGT
** *
13150 GATGAGATAGGTGCTTTACGT
1 GATGAGATAGACGCTTAACGT
13171 GATGAG
1 GATGAG
13177 GTCGGTGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.29
Consensus pattern (21 bp):
GATGAGATAGACGCTTAACGT
Found at i:13183 original size:21 final size:21
Alignment explanation
Indices: 13141--13319 Score: 150
Period size: 21 Copynumber: 8.5 Consensus size: 21
13131 TGAGTTAGAC
*
13141 GCTTAACGTGATGAGATAGGT
1 GCTTTACGTGATGAGATAGGT
* *
13162 GCTTTACGTGATGAGGTCGGT
1 GCTTTACGTGATGAGATAGGT
*
13183 GCTTTACGTGATGACA-ATGGT
1 GCTTTACGTGATGAGATA-GGT
* *
13204 GCTTTACGTTATGAGGTAGGT
1 GCTTTACGTGATGAGATAGGT
* * *
13225 GCTTCACGTGATGACA-ATGGC
1 GCTTTACGTGATGAGATA-GGT
* * * *
13246 GATTTATGTGATGAGGTATGT
1 GCTTTACGTGATGAGATAGGT
* *
13267 GCTTTACGTGATAACA-ATGGT
1 GCTTTACGTGATGAGATA-GGT
*
13288 GCTTTACGTGATGAGGTAGGT
1 GCTTTACGTGATGAGATAGGT
13309 G-TTCTACGTGA
1 GCTT-TACGTGA
13320 GATTGTTTCA
Statistics
Matches: 121, Mismatches: 30, Indels: 14
0.73 0.18 0.08
Matches are distributed among these distances:
20 4 0.03
21 114 0.94
22 3 0.02
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (21 bp):
GCTTTACGTGATGAGATAGGT
Found at i:13192 original size:42 final size:42
Alignment explanation
Indices: 13141--13319 Score: 236
Period size: 42 Copynumber: 4.3 Consensus size: 42
13131 TGAGTTAGAC
* * *
13141 GCTTAACGTGATGA-GATAGGTGCTTTACGTGATGAGGTCGGT
1 GCTTTACGTGATGACAAT-GGTGCTTTACGTGATGAGGTAGGT
*
13183 GCTTTACGTGATGACAATGGTGCTTTACGTTATGAGGTAGGT
1 GCTTTACGTGATGACAATGGTGCTTTACGTGATGAGGTAGGT
* * * * *
13225 GCTTCACGTGATGACAATGGCGATTTATGTGATGAGGTATGT
1 GCTTTACGTGATGACAATGGTGCTTTACGTGATGAGGTAGGT
*
13267 GCTTTACGTGATAACAATGGTGCTTTACGTGATGAGGTAGGT
1 GCTTTACGTGATGACAATGGTGCTTTACGTGATGAGGTAGGT
13309 G-TTCTACGTGA
1 GCTT-TACGTGA
13320 GATTGTTTCA
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
41 2 0.02
42 115 0.97
43 2 0.02
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (42 bp):
GCTTTACGTGATGACAATGGTGCTTTACGTGATGAGGTAGGT
Found at i:13737 original size:21 final size:21
Alignment explanation
Indices: 13644--13768 Score: 80
Period size: 21 Copynumber: 6.0 Consensus size: 21
13634 GAAGAAGCCT
* *
13644 GATCTACCTACCATTGTTCAG
1 GATCTACCTCCCATCGTTCAG
* * * *
13665 GGTCCACCTCACATTC-TTTAG
1 GATCTACCTCCCA-TCGTTCAG
*
13686 GAT-TCACCTCTCATCGTTCAAG
1 GATCT-ACCTCCCATCGTTC-AG
*
13708 AGA-C-CCCTCCCATCGTTCAG
1 -GATCTACCTCCCATCGTTCAG
*
13728 GATCTACCTCCCATCGTTCAA
1 GATCTACCTCCCATCGTTCAG
*
13749 GATCCACC-CCGCATCGTTCA
1 GATCTACCTCC-CATCGTTCA
13769 AAATCCACAT
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.03
20 7 0.09
21 66 0.82
22 3 0.04
23 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.14, T:0.28
Consensus pattern (21 bp):
GATCTACCTCCCATCGTTCAG
Found at i:13769 original size:21 final size:21
Alignment explanation
Indices: 13690--13776 Score: 97
Period size: 21 Copynumber: 4.1 Consensus size: 21
13680 CTTTAGGATT
* *
13690 CACCTCTCATCGTTCAAGAGAC
1 CACCTCCCATCGTTCAAGA-TC
*
13712 C-CCTCCCATCGTTCAGGATC
1 CACCTCCCATCGTTCAAGATC
*
13732 TACCTCCCATCGTTCAAGATC
1 CACCTCCCATCGTTCAAGATC
*
13753 CACC-CCGCATCGTTCAAAATC
1 CACCTCC-CATCGTTCAAGATC
13774 CAC
1 CAC
13777 ATTCCATACT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
20 3 0.05
21 52 0.93
22 1 0.02
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.23
Consensus pattern (21 bp):
CACCTCCCATCGTTCAAGATC
Found at i:17073 original size:20 final size:20
Alignment explanation
Indices: 16982--17079 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 20
16972 AATGCTTTAA
*
16982 GAAAATCAAATTCGCAACTC
1 GAAAATGAAATTCGCAACTC
* *
17002 AAAAATCG-AATTCGCAATTC
1 GAAAAT-GAAATTCGCAACTC
* * * *
17022 GAAATTTAAATTTGCAACAC
1 GAAAATGAAATTCGCAACTC
*
17042 G---A--AAA-TCACAACTC
1 GAAAATGAAATTCGCAACTC
17056 GAAAATGAAATTCGCAACTC
1 GAAAATGAAATTCGCAACTC
17076 GAAA
1 GAAA
17080 TCGAGTTGCG
Statistics
Matches: 56, Mismatches: 14, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
14 7 0.12
15 3 0.05
17 1 0.02
19 3 0.05
20 42 0.75
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.21
Consensus pattern (20 bp):
GAAAATGAAATTCGCAACTC
Found at i:17154 original size:20 final size:20
Alignment explanation
Indices: 17079--17156 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
17069 GCAACTCGAA
* *
17079 ATCGAGTTGCGAA-TTCAAA
1 ATCGAGTTGCGAATTTGAAT
* *
17098 ATTCGAGTTGCGAATTCGATT
1 A-TCGAGTTGCGAATTTGAAT
* *
17119 TTCGAGTTACGAATTTGAAT
1 ATCGAGTTGCGAATTTGAAT
17139 ATCGAGTTGCGAATTTGA
1 ATCGAGTTGCGAATTTGA
17157 GTTACAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGAGTTGCGAATTTGAAT
Found at i:18131 original size:12 final size:12
Alignment explanation
Indices: 18116--18149 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18106 AGGTGAAGGC
*
18116 GATTGTGATTGA
1 GATTTTGATTGA
*
18128 GATTTTGATTGC
1 GATTTTGATTGA
18140 GATTTTGATT
1 GATTTTGATT
18150 TCCCTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (12 bp):
GATTTTGATTGA
Found at i:20489 original size:24 final size:24
Alignment explanation
Indices: 20461--20514 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
20451 ATGAAACATC
*
20461 ATCAAAATCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
20485 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
20509 ATCAAA
1 ATCAAA
20515 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:20528 original size:24 final size:24
Alignment explanation
Indices: 20477--20528 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20467 ATCCGGGTAT
* *
20477 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
20501 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
20525 TGAC
1 TGAC
20529 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:31210 original size:23 final size:23
Alignment explanation
Indices: 31178--31249 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
31168 TTATTACAAA
*
31178 TATTA-AATATAATATCTTATAT
1 TATTATAATATAATATATTATAT
* *
31200 TATTATAATATAAT-TGGTTATTT
1 TATTATAATATAATAT-ATTATAT
*
31223 TATTATAATATAAAAATATTATAT
1 TATTATAATAT-AATATATTATAT
31247 TAT
1 TAT
31250 ATTATTAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 6 0.15
23 24 0.59
24 10 0.24
25 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
TATTATAATATAATATATTATAT
Found at i:31247 original size:21 final size:22
Alignment explanation
Indices: 31218--31265 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
31208 TATAATTGGT
*
31218 TATTTTATTATAATA-TAAAAA
1 TATTATATTATAATATTAAAAA
* *
31239 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAAAAA
31261 TATTA
1 TATTA
31266 ATAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:31256 original size:29 final size:30
Alignment explanation
Indices: 31217--31298 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
31207 ATATAATTGG
*
31217 TTATTTTATTATAATA-TAA-AAATATTATA
1 TTATATTATTATAATATTAATAAATA-TATA
* *
31246 TTATATTATTAGAAATATTAATAAATATATT
1 TTATATTATTA-TAATATTAATAAATATATA
*
31277 TTA-ATTATTTTAATAATTAATA
1 TTATATTATTATAAT-ATTAATA
31299 TTTTGATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 13 0.30
30 17 0.39
31 9 0.20
32 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TTATATTATTATAATATTAATAAATATATA
Found at i:31299 original size:24 final size:23
Alignment explanation
Indices: 31263--31307 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31253 ATTAGAAATA
31263 TTAATAAATATATTTTAATTATT
1 TTAATAAATATATTTTAATTATT
* *
31286 TTAATAATTAATATTTTGATTA
1 TTAATAAAT-ATATTTTAATTA
31308 AATGATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTAATAAATATATTTTAATTATT
Found at i:31572 original size:14 final size:14
Alignment explanation
Indices: 31539--31574 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31529 AACAAACACG
31539 AAAAAATATTTTCC
1 AAAAAATATTTTCC
**
31553 GGAAAATATTTTCC
1 AAAAAATATTTTCC
31567 AAAAAATA
1 AAAAAATA
31575 AATTATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (14 bp):
AAAAAATATTTTCC
Found at i:44130 original size:3 final size:3
Alignment explanation
Indices: 44124--44159 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
44114 CGACGACAAC
44124 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44160 GTATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46262 original size:29 final size:29
Alignment explanation
Indices: 46230--46291 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
46220 TTCTATAAAA
46230 AAATATTTTTTATATTTTTGGGTCGGATC
1 AAATATTTTTTATATTTTTGGGTCGGATC
46259 AAATATTTTTTATATTTTTGGGTCGGATC
1 AAATATTTTTTATATTTTTGGGTCGGATC
46288 AAAT
1 AAAT
46292 CGGTTTGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.50
Consensus pattern (29 bp):
AAATATTTTTTATATTTTTGGGTCGGATC
Found at i:46995 original size:21 final size:21
Alignment explanation
Indices: 46971--47034 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
46961 GCAAATTCAT
46971 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
46992 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
47012 TTTCCATTTCGCGTTACGATA
1 GTTGCATTTCGCGTTGCGATA
47033 GT
1 GT
47035 CTACAGTTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:47073 original size:41 final size:41
Alignment explanation
Indices: 47005--47113 Score: 139
Period size: 41 Copynumber: 2.6 Consensus size: 41
46995 GAAAATCGCG
* * *
47005 TTGCGATTTTCC-ATTTCGCGTTACGATAGTCTACAGTTGTCA
1 TTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGCTGTCA
* * *
47047 TTGTGATTTTCCAAATTTGTTGCGATAGTCTACAGCTGTCG
1 TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGCTGTCA
47088 TTGCGATTTTCCAAATTCGTTGCGAT
1 TTGCGATTTTCCAAATTCGTTGCGAT
47114 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 44 0.76
42 11 0.19
43 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.41
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGCTGTCA
Found at i:47109 original size:19 final size:19
Alignment explanation
Indices: 47085--47132 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
47075 TCTACAGCTG
47085 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
47104 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
47123 TCGTTGCGAT
1 TCGTTGCGAT
47133 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:47924 original size:41 final size:41
Alignment explanation
Indices: 47867--47959 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
47857 CTTTTTTTTA
* * *
47867 ACTATCGCAACGAATTTGGAAAATCGCAACTACAACTGTAG
1 ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
*
47908 ACTATCGCAACAAATTTGAAAAATTGCAACGACAACTGTAG
1 ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
47949 ACTATCGCAAC
1 ACTATCGCAAC
47960 GCGAAATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
Found at i:47960 original size:22 final size:22
Alignment explanation
Indices: 47889--47960 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
47879 AATTTGGAAA
*
47889 ATCGCAACTACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
47911 ATCGCAAC-A-AA-T-TTGAAAA
1 ATCGCAACGACAACTGTAG-ACT
*
47930 ATTGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
47952 ATCGCAACG
1 ATCGCAACG
47961 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
20 3 0.08
21 3 0.08
22 18 0.49
23 2 0.05
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:47977 original size:20 final size:20
Alignment explanation
Indices: 47952--48004 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
47942 ACTGTAGACT
47952 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
47972 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
47992 ATCGCAATGCGAA
1 ATCGCAACGCGAA
48005 TTTGCGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:48011 original size:28 final size:28
Alignment explanation
Indices: 47980--48034 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
47970 AAATCGCAAC
47980 GCGA-AATGGAAAATCGCAATGCGAATTT
1 GCGATAATGG-AAATCGCAATGCGAATTT
* *
48008 GCGATACTGGAGATCGCAATGCGAATT
1 GCGATAATGGAAATCGCAATGCGAATT
48035 AGAGATCGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (28 bp):
GCGATAATGGAAATCGCAATGCGAATTT
Found at i:50083 original size:76 final size:76
Alignment explanation
Indices: 49880--50085 Score: 292
Period size: 75 Copynumber: 2.7 Consensus size: 76
49870 CCGTTGTACA
* * * *
49880 AGGGGGGAATCGGTACCCCCTTTGGGGGG-ATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGA
** *
49943 GCAAAACTGTTT
65 GCAAAACCATTC
*
49955 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAG
*
50019 CCAAACCATTC
66 CAAAACCATTC
*
50030 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
50086 TTTTTGGCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 5 0.04
75 81 0.69
76 31 0.26
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAG
CAAAACCATTC
Found at i:52736 original size:21 final size:21
Alignment explanation
Indices: 52666--52750 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
52656 ACATAACCCC
* *
52666 AGGGGGGTATCGATTCCC-CTG
1 AGGGGGGAATCGATTCCCTC-A
*
52687 TGGGGGGAATCGATTCCCCTTCA
1 AGGGGGGAATCGATT-CCC-TCA
* *
52710 AAGGGGGAATCGGTTCCCTCA
1 AGGGGGGAATCGATTCCCTCA
*
52731 AGGGGGGGATCGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
52751 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
21 33 0.63
22 6 0.12
23 12 0.23
24 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
AGGGGGGAATCGATTCCCTCA
Found at i:56597 original size:22 final size:21
Alignment explanation
Indices: 56555--56594 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56545 GAGTTTGTTT
*
56555 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
56576 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
56595 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:58616 original size:74 final size:74
Alignment explanation
Indices: 58517--58720 Score: 277
Period size: 74 Copynumber: 2.7 Consensus size: 74
58507 GTTGTACAAG
* *
58517 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
** *
58581 AAACTGTTTA
65 AAACCATTCA
* * * *
58591 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCAA
58656 AACCATTCA
66 AACCATTCA
*
58665 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
58721 TTTGGCTTTG
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
74 89 0.78
75 25 0.22
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (74 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCAA
AACCATTCA
Found at i:79785 original size:25 final size:25
Alignment explanation
Indices: 79755--79803 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
79745 TTCCACTCGA
79755 AAAATTAATGTTTTCGACTCGACTC
1 AAAATTAATGTTTTCGACTCGACTC
* * *
79780 AAAATTGATTTTTTCGACTTGACT
1 AAAATTAATGTTTTCGACTCGACT
79804 TGATTCAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (25 bp):
AAAATTAATGTTTTCGACTCGACTC
Found at i:88710 original size:25 final size:25
Alignment explanation
Indices: 88682--88752 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
88672 ATAAACATCA
*
88682 AATACATTAAATAATATTATTTATT
1 AATAAATTAAATAATATTATTTATT
* *
88707 AATAAAAT-AATAATAATATTT-TT
1 AATAAATTAAATAATATTATTTATT
88730 AA-AATATTAGAATAAT-TTATTTA
1 AATAA-ATTA-AATAATATTATTTA
88753 ATATTATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 6 0.16
24 17 0.46
25 12 0.32
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
AATAAATTAAATAATATTATTTATT
Found at i:89125 original size:59 final size:60
Alignment explanation
Indices: 89046--89162 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 60
89036 ATTAATTTTA
* * * * * *
89046 TTAATAATTTATTATATTATTAAAATAAAAGTATAATATTATATTATTAA-AAATATAAT
1 TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATAAT
* * *
89105 TTAATAATTAATAATTTTATTAAAATGATACTAAAATAATATATTAATAATAAATATA
1 TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATA
89163 TAAAATAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 41 0.85
60 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (60 bp):
TTAATAATTAATAATATTATTAAAATAAAACTAAAATAATATATTAATAATAAATATAAT
Found at i:89378 original size:12 final size:13
Alignment explanation
Indices: 89351--89393 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
89341 TACTATATTA
* *
89351 TATAATATATATT
1 TATATTATATAAT
89364 TATATTATA-AAT
1 TATATTATATAAT
89376 TATATTATATAA-
1 TATATTATATAAT
89388 TATATT
1 TATATT
89394 CAGCTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTATATAAT
Found at i:90531 original size:20 final size:19
Alignment explanation
Indices: 90506--90549 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
90496 ATTCCTTTTA
*
90506 TTATTATTATTCTTTGGATT
1 TTATTATTATTATTT-GATT
*
90526 TTATTATTATTATTTTATT
1 TTATTATTATTATTTGATT
90545 TTATT
1 TTATT
90550 TTCCCTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (19 bp):
TTATTATTATTATTTGATT
Found at i:90647 original size:2 final size:2
Alignment explanation
Indices: 90640--90730 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
90630 TATGTCGTGT
90640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90724 TA TA TA T
1 TA TA TA T
90731 TACCTTTTTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90769 original size:12 final size:13
Alignment explanation
Indices: 90749--90857 Score: 57
Period size: 13 Copynumber: 8.2 Consensus size: 13
90739 TAATTTTAAT
90749 TTTATTTTCTTTA
1 TTTATTTTCTTTA
90762 TTTA-TTTCTTTA
1 TTTATTTTCTTTA
*
90774 TTTA---CCATTTA
1 TTTATTTTC-TTTA
* * *
90785 CTGATTTTATTTA
1 TTTATTTTCTTTA
90798 TTTATTTTCTTTA
1 TTTATTTTCTTTA
*
90811 CTTTATCTTTGTTTTA
1 -TTTAT-TTT-CTTTA
*
90827 TCTTA-TTTATTTA
1 T-TTATTTTCTTTA
90840 TGTATATTTTCTTATA
1 T-T-TATTTTCTT-TA
90856 TT
1 TT
90858 GCTTATTTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
10 1 0.01
11 6 0.08
12 12 0.16
13 24 0.33
14 10 0.14
15 10 0.14
16 10 0.14
ACGTcount: A:0.19, C:0.09, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTATTTTCTTTA
Done.