Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4441
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: 14835
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Found at i:266 original size:6 final size:6
Alignment explanation
Indices: 244--425 Score: 90
Period size: 6 Copynumber: 29.8 Consensus size: 6
234 TATCAAAACT
* * *
244 AGAATC A-AATG AGAATC AGAATC AAAAT- AGAATC AG-GTGAC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* * * * * *
291 AAAATT AGAATC AGAATC AGAATT AGGTAA-C AAAATT AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC
* * * * *
340 AGGTAA-C AGAACC AGAATT AGAACC AGAATC AAAATT AGGTAA-C AGAATC
1 A-G-AATC AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
*
390 AGAATC AGTATC AGGTAA-C AGAATC AGAATC AGAAT
1 AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
426 GTGAATGCAA
Statistics
Matches: 130, Mismatches: 29, Indels: 34
0.67 0.15 0.18
Matches are distributed among these distances:
5 17 0.13
6 94 0.72
7 12 0.09
8 7 0.05
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:266 original size:17 final size:17
Alignment explanation
Indices: 244--279 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
234 TATCAAAACT
244 AGAATC-AAATGAGAATC
1 AGAATCAAAAT-AGAATC
261 AGAATCAAAATAGAATC
1 AGAATCAAAATAGAATC
278 AG
1 AG
280 GTGACAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (17 bp):
AGAATCAAAATAGAATC
Found at i:309 original size:31 final size:31
Alignment explanation
Indices: 255--371 Score: 98
Period size: 31 Copynumber: 3.8 Consensus size: 31
245 GAATCAAATG
* * * *
255 AGAATCAGAATCAAAAT-AGAATCAGGTGAC
1 AGAATCAAAATTAGAATCAGAATCAGGTAAC
*
285 AGAATCAAAATTAGAATCAGAATCA-G-AATT
1 AGAATCAAAATTAGAATCAGAATCAGGTAA-C
*
315 AGGTAA-CAAAATTAGAATCAGTATCAGGTAAC
1 A-G-AATCAAAATTAGAATCAGAATCAGGTAAC
* * *
347 AGAACCAGAATTAGAACCAGAATCA
1 AGAATCAAAATTAGAATCAGAATCA
372 AAATTAGGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
29 1 0.01
30 18 0.26
31 45 0.64
32 4 0.06
33 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATTAGAATCAGAATCAGGTAAC
Found at i:349 original size:62 final size:62
Alignment explanation
Indices: 275--425 Score: 230
Period size: 62 Copynumber: 2.4 Consensus size: 62
265 TCAAAATAGA
* * * *
275 ATCAGGTGACAGAATCAAAATTAGAATCAGAATCAGAATTAGGTAACAAAATTAGAATCAGT
1 ATCAGGTAACAGAATCAGAATTAGAATCAGAATCAAAATTAGGTAACAAAATCAGAATCAGT
* * *
337 ATCAGGTAACAGAACCAGAATTAGAACCAGAATCAAAATTAGGTAACAGAATCAGAATCAGT
1 ATCAGGTAACAGAATCAGAATTAGAATCAGAATCAAAATTAGGTAACAAAATCAGAATCAGT
*
399 ATCAGGTAACAGAATCAGAATCAGAAT
1 ATCAGGTAACAGAATCAGAATTAGAAT
426 GTGAATGCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 79 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (62 bp):
ATCAGGTAACAGAATCAGAATTAGAATCAGAATCAAAATTAGGTAACAAAATCAGAATCAGT
Found at i:356 original size:25 final size:25
Alignment explanation
Indices: 297--362 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
287 AATCAAAATT
*
297 AGAATCAGAATCAGAATTAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* * *
322 AAAATTAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
347 AGAACCAGAATTAGAA
1 AGAATCAGAATCAGAA
363 CCAGAATCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:387 original size:31 final size:31
Alignment explanation
Indices: 293--402 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
283 ACAGAATCAA
* *
293 AATTAGAATCAGAATCAGAATTAGGTAACAA
1 AATTAGAATCAGAATCAAAATTAGGTAACAG
* * *
324 AATTAGAATCAGTATCAGGTAA-CA-G-AACCAG
1 AATTAGAATCAGAATCA--AAATTAGGTAA-CAG
*
355 AATTAGAACCAGAATCAAAATTAGGTAACAG
1 AATTAGAATCAGAATCAAAATTAGGTAACAG
* *
386 AATCAGAATCAGTATCA
1 AATTAGAATCAGAATCA
403 GGTAACAGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
31 52 0.84
32 3 0.05
33 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (31 bp):
AATTAGAATCAGAATCAAAATTAGGTAACAG
Found at i:422 original size:25 final size:25
Alignment explanation
Indices: 359--425 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
349 AACCAGAATT
* * *
359 AGAACCAGAATCAAAATTAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
384 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
409 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
426 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:996 original size:26 final size:25
Alignment explanation
Indices: 967--1097 Score: 90
Period size: 26 Copynumber: 5.1 Consensus size: 25
957 TTACCCAACA
967 AGGGTATCTCTGTAATTCTACCCTAT
1 AGGGTAT-TCTGTAATTCTACCCTAT
* *
993 AGGGTATTTCAGTAATTCTACCTTAT
1 AGGGTA-TTCTGTAATTCTACCCTAT
* * *
1019 A---TATTTCAGTATTTCTACCCCTACA
1 AGGGTA-TTCTGTAATTCTA-CCCTA-T
* *
1044 AGGGTATTTTGGTAATTCTA-CCTAC
1 AGGGTATTCT-GTAATTCTACCCTAT
*
1069 AGGGGTATTTTAGTAATTCTACCCTAT
1 A-GGGTATTCT-GTAATTCTACCCTAT
1096 AG
1 AG
1098 AGTTATTTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
23 15 0.18
24 4 0.05
25 2 0.02
26 46 0.54
27 8 0.09
28 10 0.12
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (25 bp):
AGGGTATTCTGTAATTCTACCCTAT
Found at i:1094 original size:27 final size:27
Alignment explanation
Indices: 951--1193 Score: 151
Period size: 27 Copynumber: 9.2 Consensus size: 27
941 GGGGTAAATG
* * * *
951 GTAATTTTACCCAACAAGGGTATCTCT-
1 GTAATTCTACCCTACAGGGGTAT-TTTA
* *
978 GTAATTCTACCCTATA-GGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTTA
* * *
1004 GTAATTCTACCTTATA----TATTTCA
1 GTAATTCTACCCTACAGGGGTATTTTA
* * *
1027 GTATTTCTACCCCTACAAGGGTATTTTG
1 GTAATTCTA-CCCTACAGGGGTATTTTA
1055 GTAATTCTA-CCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTA
* * * **
1081 GTAATTCTACCCTATAGAGTTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTTA
* * *
1108 GTATTTCTACCTTACAGGGGTA-TTTC
1 GTAATTCTACCCTACAGGGGTATTTTA
* * * *
1134 GATATTTTTACCTTACAGGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTTA
* * * *
1162 GTATTTCTACCCTATAAGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTTA
1189 GTAAT
1 GTAAT
1194 CTTGTAAATA
Statistics
Matches: 171, Mismatches: 36, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
23 15 0.09
24 5 0.03
25 1 0.01
26 48 0.28
27 86 0.50
28 16 0.09
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTTA
Found at i:1124 original size:54 final size:54
Alignment explanation
Indices: 950--1186 Score: 175
Period size: 54 Copynumber: 4.5 Consensus size: 54
940 AGGGGTAAAT
* ** * * *
950 GGTAATTTTACCCAACAAGGGTATCTCTGTAATTCTACCCTATAG-GGTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTATAGAGGTATTTC
* * * * *
1003 AGTAATTCTACCTTATA----TATTTCAGTATTTCTACCCCTACA-AGGGTATTTT
1 GGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTA-CCCTATAGA-GGTATTTC
* *
1054 GGTAATTCTACC-TACAGGGGTATTTTAGTAATTCTACCCTATAGAGTTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTATAGAGGTATTTC
* * * * * *
1107 GGTATTTCTACCTTACAGGGGTATTTC-GATATTTTTACCTTACAGGGGTATTTC
1 GGTAATTCTACCTTACAGGGGTATTTCAG-TAATTCTACCCTATAGAGGTATTTC
* * * * *
1161 AGTATTTCTACCCTATAAGGGTATTT
1 GGTAATTCTACCTTACAGGGGTATTT
1187 TGGTAATCTT
Statistics
Matches: 145, Mismatches: 29, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
49 13 0.09
50 9 0.06
51 18 0.12
53 36 0.25
54 69 0.48
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (54 bp):
GGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTATAGAGGTATTTC
Found at i:1186 original size:81 final size:79
Alignment explanation
Indices: 964--1191 Score: 241
Period size: 81 Copynumber: 2.9 Consensus size: 79
954 ATTTTACCCA
* * *
964 ACAAGGGTATCTCTG-TAATTCTACCCTATA-GGGTATTTCAGTAATTCTACCTTATA--TATTT
1 ACAAGGGTATTTC-GATAATTCTA-CCTACAGGGGTATTTCAGTAATTCTACCCTATAGGTATTT
*
1025 CAGTATTTCTACCCCT
64 CGGTATTTCTACCCCT
* * *
1041 ACAAGGGTATTTTGGTAATTCTACCTACAGGGGTATTTTAGTAATTCTACCCTATAGAGTTATTT
1 ACAAGGGTATTTCGATAATTCTACCTACAGGGGTATTTCAGTAATTCTACCCTATAG-G-TATTT
*
1106 CGGTATTTCTA-CCTT
64 CGGTATTTCTACCCCT
* * * *
1121 ACAGGGGTATTTCGATATTTTTACCTTACAGGGGTATTTCAGTATTTCTACCCTATAAGGGTATT
1 ACAAGGGTATTTCGATAATTCTACC-TACAGGGGTATTTCAGTAATTCTACCCTAT-A-GGTATT
*
1186 TTGGTA
63 TCGGTA
1192 ATCTTGTAAA
Statistics
Matches: 127, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
76 6 0.05
77 43 0.34
80 23 0.18
81 52 0.41
82 2 0.02
83 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (79 bp):
ACAAGGGTATTTCGATAATTCTACCTACAGGGGTATTTCAGTAATTCTACCCTATAGGTATTTCG
GTATTTCTACCCCT
Found at i:1208 original size:27 final size:26
Alignment explanation
Indices: 1178--1489 Score: 146
Period size: 27 Copynumber: 11.8 Consensus size: 26
1168 CTACCCTATA
1178 AGGGTATTTTGGTAATCTTGTAAA-TAG
1 AGGGTATTTTGGTAAT-TT-TAAACTAG
**** * *
1205 AGGGTAAAACGATAATTCTGTAAATTAG
1 AGGGTATTTTGGTAATT-T-TAAACTAG
* * *
1233 -GGGTA-CTTGGTAATTTTACAAGTCG
1 AGGGTATTTTGGTAATTTTA-AACTAG
** * *
1258 AGGGTATTTTAATAATTTTACAAGTCG
1 AGGGTATTTTGGTAATTTTA-AACTAG
** * *
1285 AGGGTATTTCAGTAATTTCACAAATCAG
1 AGGGTATTTTGGTAATTTTA-AACT-AG
1313 -GGGTATTTTGGTAATTTTACAAACTAG
1 AGGGTATTTTGGTAATTTT--AAACTAG
*
1340 -GGGTATTTTGGTAATTTTACAAACCA-
1 AGGGTATTTTGGTAATTTT--AAACTAG
*
1366 AGGGTATTTTGGTAATTTTACAA--ACC
1 AGGGTATTTTGGTAATTTTA-AACTA-G
*
1392 ATGGTATTTTGGTAATTTTATAA--AG
1 AGGGTATTTTGGTAATTTTA-AACTAG
* *
1417 -GGGTATTTTAGTAATTTTACAAACCAG
1 AGGGTATTTTGGTAATTTT--AAACTAG
* *
1444 -GGGTATTTTGATAATTTTGTAAAGTA-
1 AGGGTATTTTGGTAA-TTT-TAAACTAG
1470 AGGGTATTTTGGTAATTTTA
1 AGGGTATTTTGGTAATTTTA
1490 CAAACCAGGG
Statistics
Matches: 232, Mismatches: 34, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
24 19 0.08
25 10 0.04
26 40 0.17
27 151 0.65
28 10 0.04
29 2 0.01
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTAAACTAG
Found at i:1452 original size:104 final size:106
Alignment explanation
Indices: 1231--1499 Score: 319
Period size: 104 Copynumber: 2.5 Consensus size: 106
1221 TCTGTAAATT
* ** * ** * *
1231 AGGGGTA-CTTGGTAATTTTACAAGTCGAGGGTATTTTAATAATTTTACAAGTCGAGGGTATTTC
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAA-ACCAGGGTATTTC
* *
1295 AGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACT
65 AGTAATTTCACAAA-CAGGGGTATTTTAGTAATTTTACAAACC
* **
1338 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCATGGTATTTTG
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGTATTTCA
* *
1403 GTAATTTTA-TAA-AGGGGTATTTTAGTAATTTTACAAACC
66 GTAATTTCACAAACAGGGGTATTTTAGTAATTTTACAAACC
* ** **
1442 AGGGGTATTTTGATAATTTTGTAAAGTAAGGGTATTTTGGTAATTTTACAAACCAGGG
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGG
1500 GTTGATTTTG
Statistics
Matches: 140, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
104 77 0.55
106 2 0.01
107 24 0.17
108 37 0.26
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (106 bp):
AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGTATTTCA
GTAATTTCACAAACAGGGGTATTTTAGTAATTTTACAAACC
Found at i:1501 original size:27 final size:27
Alignment explanation
Indices: 1231--1501 Score: 277
Period size: 27 Copynumber: 10.2 Consensus size: 27
1221 TCTGTAAATT
* **
1231 AGGGGTA-CTTGGTAATTTTACAAGTC
1 AGGGGTATTTTGGTAATTTTACAAACC
** **
1257 -GAGGGTATTTTAATAATTTTACAAGTC
1 AG-GGGTATTTTGGTAATTTTACAAACC
** * *
1284 -GAGGGTATTTCAGTAATTTCACAAATC
1 AG-GGGTATTTTGGTAATTTTACAAACC
*
1311 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
1338 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
1365 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
1392 A-TGGTATTTTGGTAATTTTA-TAA--
1 AGGGGTATTTTGGTAATTTTACAAACC
*
1415 AGGGGTATTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* ** **
1442 AGGGGTATTTTGATAATTTTGTAAAGT
1 AGGGGTATTTTGGTAATTTTACAAACC
*
1469 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
1496 AGGGGT
1 AGGGGT
1502 TGATTTTGTG
Statistics
Matches: 206, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.00
24 17 0.08
25 5 0.02
26 23 0.11
27 159 0.77
28 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:1704 original size:26 final size:26
Alignment explanation
Indices: 1675--1818 Score: 107
Period size: 26 Copynumber: 5.5 Consensus size: 26
1665 ACACCTATAG
1675 GGTAGAAATACTGAAATACCCTGTAA
1 GGTAGAAATACTGAAATACCCTGTAA
* *
1701 GGTAAAAATA-TCGAATAAACCCCTGTAA
1 GGTAGAAATACT-GAA-ATA-CCCTGTAA
* * *
1729 GGTA-AAATACCGAAATACTCTAT-A
1 GGTAGAAATACTGAAATACCCTGTAA
* * *
1753 GGTAGAATTACTAAAATACCCCTGTAG
1 GGTAGAAATACTGAAATA-CCCTGTAA
* *
1780 GGTAGAATTAC-AAAATACCCTGATAA
1 GGTAGAAATACTGAAATACCCTG-TAA
*
1806 GATATGAAATACT
1 GGTA-GAAATACT
1819 ATAAGTAGAA
Statistics
Matches: 93, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
24 5 0.05
25 20 0.22
26 29 0.31
27 27 0.29
28 12 0.13
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (26 bp):
GGTAGAAATACTGAAATACCCTGTAA
Found at i:2390 original size:6 final size:6
Alignment explanation
Indices: 2381--2563 Score: 90
Period size: 6 Copynumber: 29.8 Consensus size: 6
2371 TTGCATTCAC
* *
2381 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * * *
2431 ATTTTG ATTCTG GTTCTA ATTCTG GTTCTG -TTACCTG ATACTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * * * *
2480 ATTTTG -TTACCTA ATTCTG ATTCTG ATTCTA ATTTTG ATTCTG -TCACCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
2530 ATTCT- ATTTTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
2564 AGTTTTGATA
Statistics
Matches: 130, Mismatches: 31, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
5 13 0.10
6 98 0.75
7 12 0.09
8 7 0.05
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:2412 original size:25 final size:25
Alignment explanation
Indices: 2384--2447 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
2374 CATTCACATT
*
2384 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
2409 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
* *
2434 TTGATTCTGGTTCT
1 CTGATTCTGATTCT
2448 AATTCTGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:2488 original size:62 final size:62
Alignment explanation
Indices: 2381--2531 Score: 230
Period size: 62 Copynumber: 2.4 Consensus size: 62
2371 TTGCATTCAC
* * *
2381 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTTTGATTCTG
1 ATTCTAATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTG
* * *
2443 GTTCTAATTCTGGTTCTGTTACCTGATACTGATTCTAATTTTGTTACCTAATTCTGATTCTG
1 ATTCTAATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTG
* *
2505 ATTCTAATTTTGATTCTGTCACCTGAT
1 ATTCTAATTCTGATTCTGTTACCTGAT
2532 TCTATTTTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 79 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (62 bp):
ATTCTAATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTG
Found at i:4449 original size:101 final size:101
Alignment explanation
Indices: 4243--4624 Score: 340
Period size: 101 Copynumber: 3.8 Consensus size: 101
4233 TGTGAGAACA
* * **** * * *
4243 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATAGTTTTAGGTCACATGTGTAGTACT
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAG-TTTCGATTACATGTGTAGTACT
* * *
4308 AATTGCAGGCTACTACGTGCACTAGATTGTTAGGTCG
65 AAGTGCAGGCTACTACGTGCACCAGATTGATAGGTCG
*
4345 CATGTGTAGTACTAAGTGCAGGTTACTATGCGTACCCGATAGTTTCGATTACATGTGTAGTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTCGATTACATGTGTAGTACTA
* * * * * *
4410 AGTACAGCCTACTATGTGTACCGGATTGATAGGTTG
66 AGTGCAGGCTACTACGTGCACCAGATTGATAGGTCG
* **
4446 CATGTGTAGTACTAAGTGCAGGCTACTATGCATACCC-ATTAACTTCGA-T-CATGAGTGTAGTA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGA-TAGTTTCGATTACAT--GTGTAGTA
* * * * * *
4508 CTAAGTGCAGGCTACTACATGTATCAGATGGATAAGTCA
63 CTAAGTGCAGGCTACTACGTGCACCAGATTGATAGGTCG
* * * * * * * * * * *
4547 CGTGTGTAGTGCTACGTGCAGGCTACTACGTGTACCAGATTG-ATAGGTTGCATGTGTAGTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTCGATTACATGTGTAGTACTA
*
4611 AGTGTAGGCTACTA
66 AGTGCAGGCTACTA
4625 TGCGTACCAG
Statistics
Matches: 228, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
99 3 0.01
100 28 0.12
101 158 0.69
102 39 0.17
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (101 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTCGATTACATGTGTAGTACTA
AGTGCAGGCTACTACGTGCACCAGATTGATAGGTCG
Found at i:4632 original size:50 final size:50
Alignment explanation
Indices: 4243--4635 Score: 313
Period size: 50 Copynumber: 7.8 Consensus size: 50
4233 TGTGAGAACA
* *** ** **
4243 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATAGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT--TGATAGGTTG
* * * * * *
4295 CATGTGTAGTACTAATTGCAGGCTACTACGTGCACTAGATTGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTTG
* * * * * * * *
4345 CATGTGTAGTACTAAGTGCAGGTTACTATGCGTACCCGATAGTTTCGATTA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG-ATAGGTTG
* * *
4396 CATGTGTAGTACTAAGTACAGCCTACTATGTGTACCGGATTGATAGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTTG
** * * ** *
4446 CATGTGTAGTACTAAGTGCAGGCTACTATGCATACC-CATTAACTTCGAT-
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGA-TAGGTTG
** * * * **
4495 CATGAGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGATAAGTCA
1 CAT--GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTTG
* * * *
4547 CGTGTGTAGTGCTACGTGCAGGCTACTACGTGTACCAGATTGATAGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTTG
* *
4597 CATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
4636 GAGCTTTGGT
Statistics
Matches: 268, Mismatches: 67, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
49 7 0.03
50 153 0.57
51 70 0.26
52 38 0.14
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTTG
Found at i:5459 original size:179 final size:179
Alignment explanation
Indices: 5199--5523 Score: 437
Period size: 179 Copynumber: 1.8 Consensus size: 179
5189 TTCATGATGT
*
5199 GTACCATGAGATAAATAATTTTTAGTAAAGAAAGATAGGAACTGTCGGACAGTGAAATAAGGGTA
1 GTACCATGAGATAAATAATTTTTAGTAAAGAAAGATAGGAACTGTCGGACAGCGAAATAAGGGTA
* * **
5264 TATTTAATGGATAAACTGTACTAATTGGATGAATGAAAAATTCTGAAAA-TTTTATGG-TAGGAA
66 TATTTAATGAATAAACTGTACTAATTGGATAAACAAAAAATTC-GAAAATTTTTATGGTTA-GAA
*
5327 TATATGTGAGTCTCGTTTTTTTTAAACTATCATTTATTAATTTGGAGTCCC
129 TATATGTGAGTCTAGTTTTTTTTAAACTATCATTTATTAATTTGGAGTCCC
* * * * *
5378 GTACCATGAGATAAATAATTTTTATTGAAGAGAAG-TCA-GAATTGTTGGATAGCGAAAT-AGAG
1 GTACCATGAGATAAATAATTTTTAGTAAAGA-AAGAT-AGGAACTGTCGGACAGCGAAATAAG-G
* *
5440 GTA-ACTTTAATGAATAAACTGTACTAATTGGCTAAACAAAAAATTCGAAAATTTTTTTGGTTAG
63 GTATA-TTTAATGAATAAACTGTACTAATTGGATAAACAAAAAATTCGAAAATTTTTATGGTTAG
5504 AATATATGTGAGTCTAGTTT
127 AATATATGTGAGTCTAGTTT
5524 CGAGGAAAAT
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
178 8 0.06
179 113 0.89
180 6 0.05
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (179 bp):
GTACCATGAGATAAATAATTTTTAGTAAAGAAAGATAGGAACTGTCGGACAGCGAAATAAGGGTA
TATTTAATGAATAAACTGTACTAATTGGATAAACAAAAAATTCGAAAATTTTTATGGTTAGAATA
TATGTGAGTCTAGTTTTTTTTAAACTATCATTTATTAATTTGGAGTCCC
Found at i:13673 original size:103 final size:102
Alignment explanation
Indices: 13503--13802 Score: 318
Period size: 103 Copynumber: 3.0 Consensus size: 102
13493 TGTGAGAACA
* ** * * * *
13503 CATGTGTAGTACTATGTGCAGGCTACTATGTGT-TTAAGACAGTTTTAGGTCACGTGTATAGTCC
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAA-ATAGTTTTAGATCACGTGTGTAGTAC
*
13567 TAAGTGTAGGCTACTACGTTGTACCAGATTGTTAGGTCG
65 TAAGTGTAGGCTACTACG-TGTACCAGATTGATAGGTCG
* * * * *
13606 TATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAATAGTTTTTGATTACGTGTGTAGTACT
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAGTTTTAGATCACGTGTGTAGTACT
** * * *
13671 AAGTACAGGCTACTATGTGTACCGGATTGATAGGTTG
66 AAGTGTAGGCTACTACGTGTACCAGATTGATAGGTCG
*** ** * *
13708 CATGTGTAGTACTAAGTG-AGGCTACTATGTGTACCTGTTA-ACTTCGATCACTTGTGTAGTACT
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAGTTTTAGATCACGTGTGTAGTACT
* *
13771 AAGTGTAGGCTACTACGTGTATCAGATGGATA
66 AAGTGTAGGCTACTACGTGTACCAGATTGATA
13803 AGTACGTGTA
Statistics
Matches: 162, Mismatches: 34, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
100 44 0.27
101 18 0.11
102 34 0.21
103 65 0.40
104 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (102 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAGTTTTAGATCACGTGTGTAGTACT
AAGTGTAGGCTACTACGTGTACCAGATTGATAGGTCG
Found at i:13764 original size:50 final size:49
Alignment explanation
Indices: 13608--13791 Score: 156
Period size: 52 Copynumber: 3.7 Consensus size: 49
13598 TTAGGTCGTA
* ** * * *
13608 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAATAGTTTTTGATTAC
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGTTA--ATTCGATCAC
* * * ** *
13659 GTGTGTAGTACTAAGTACAGGCTACTATGTGTACCGGATTGATAGGTTGCA-
1 -TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCG-TTAATTCGAT-CAC
*
13710 TGTGTAGTACTAAGTG-AGGCTACTATGTGTACCTGTTAACTTCGATCAC
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGTTAA-TTCGATCAC
* *
13759 TTGTGTAGTACTAAGTGTAGGCTACTACGTGTA
1 -TGTGTAGTACTAAGTGCAGGCTACTATGTGTA
13792 TCAGATGGAT
Statistics
Matches: 108, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
48 5 0.05
49 21 0.19
50 31 0.29
51 17 0.16
52 33 0.31
53 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGTTAATTCGATCAC
Done.